Starting phenix.real_space_refine on Thu Nov 14 18:59:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr2_16802/11_2024/8cr2_16802.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr2_16802/11_2024/8cr2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr2_16802/11_2024/8cr2_16802.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr2_16802/11_2024/8cr2_16802.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr2_16802/11_2024/8cr2_16802.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr2_16802/11_2024/8cr2_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 4.60, 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: 1.99 Conformation dependent library (CDL) restraints added in 1.1 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: 0.76 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: 1.79 Time building geometry restraints manager: 2.23 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: 0.010 Assert all atoms have isotropic ADPs: 0.030 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: 21.080 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.280 ------------------------------------------------------------------------------- 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 6975 Z= 0.281 Angle : 1.068 15.462 9413 Z= 0.593 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 *********************** 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 : 0.811 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: 0.2571 time to fit residues: 69.1133 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 : 0.806 ------------------------------------------------------------------------------- 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: 6.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4805 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 6975 Z= 0.278 Angle : 0.836 11.792 9413 Z= 0.435 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 *********************** 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 : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.5355 (tp-100) cc_final: 0.4985 (tp-100) REVERT: B 326 ARG cc_start: 0.4368 (tpt90) cc_final: 0.2062 (tpp-160) REVERT: C 1116 MET cc_start: 0.4218 (ttt) cc_final: 0.3979 (ttp) REVERT: D 217 PHE cc_start: 0.6231 (m-80) cc_final: 0.5905 (m-80) REVERT: D 224 TYR cc_start: 0.4991 (t80) cc_final: 0.4565 (t80) REVERT: D 259 ARG cc_start: 0.3943 (mtt180) cc_final: 0.3522 (ttm170) REVERT: D 261 MET cc_start: 0.4583 (ptt) cc_final: 0.3610 (tmm) REVERT: D 270 VAL cc_start: 0.5285 (m) cc_final: 0.4942 (p) REVERT: D 290 TYR cc_start: 0.2811 (t80) cc_final: 0.0822 (t80) REVERT: D 1079 ILE cc_start: 0.8265 (pt) cc_final: 0.8030 (pt) outliers start: 6 outliers final: 0 residues processed: 178 average time/residue: 0.2011 time to fit residues: 47.0274 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 : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 75 optimal weight: 0.0040 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- 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 ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 moved from start: 0.8404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6975 Z= 0.290 Angle : 0.817 10.324 9413 Z= 0.431 Chirality : 0.048 0.180 1081 Planarity : 0.007 0.149 1172 Dihedral : 4.952 18.133 908 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.52 % Allowed : 5.11 % Favored : 94.36 % 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 (0.28), residues: 833 helix: 0.45 (0.21), residues: 545 sheet: -2.77 (0.49), residues: 90 loop : -1.26 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP D1011 HIS 0.009 0.002 HIS B 314 PHE 0.037 0.002 PHE A 165 TYR 0.027 0.002 TYR D 230 ARG 0.019 0.001 ARG D1050 *********************** 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 174 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 170 time to evaluate : 0.914 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: 0.7695 (m-10) cc_final: 0.7347 (m-10) REVERT: B 326 ARG cc_start: 0.4091 (tpt90) cc_final: 0.2103 (tpp-160) REVERT: B 338 LEU cc_start: 0.3277 (mt) cc_final: 0.2829 (mt) REVERT: C 1116 MET cc_start: 0.4756 (ttt) cc_final: 0.4308 (ttt) REVERT: D 221 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8327 (mm-40) REVERT: D 259 ARG cc_start: 0.4423 (mtt180) cc_final: 0.2298 (mtt180) REVERT: D 261 MET cc_start: 0.4649 (ptt) cc_final: 0.3547 (tmm) REVERT: D 265 SER cc_start: 0.5334 (t) cc_final: 0.5109 (p) REVERT: D 1022 ASN cc_start: 0.8350 (m-40) cc_final: 0.8138 (m110) REVERT: D 1079 ILE cc_start: 0.8496 (pt) cc_final: 0.7962 (pt) REVERT: D 1082 MET cc_start: 0.7931 (tpt) cc_final: 0.7381 (mmt) outliers start: 4 outliers final: 1 residues processed: 174 average time/residue: 0.2120 time to fit residues: 47.9487 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 : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 39 optimal weight: 0.0060 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 0.0010 chunk 80 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 overall best weight: 0.9606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS B 305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.9818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6975 Z= 0.250 Angle : 0.740 11.748 9413 Z= 0.387 Chirality : 0.046 0.201 1081 Planarity : 0.005 0.053 1172 Dihedral : 4.442 17.197 908 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.39 % Allowed : 3.80 % Favored : 95.81 % 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: 0.03 (0.29), residues: 833 helix: 0.92 (0.21), residues: 541 sheet: -2.63 (0.49), residues: 91 loop : -0.88 (0.47), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP D1011 HIS 0.005 0.001 HIS D1008 PHE 0.021 0.002 PHE D1108 TYR 0.017 0.002 TYR D 224 ARG 0.009 0.001 ARG D1050 *********************** 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 148 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 145 time to evaluate : 0.825 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: 0.7678 (tpp) cc_final: 0.7308 (tpp) REVERT: A 174 LEU cc_start: 0.7127 (tt) cc_final: 0.6364 (tt) REVERT: A 240 GLU cc_start: 0.6226 (pp20) cc_final: 0.5911 (pp20) REVERT: A 264 GLU cc_start: 0.6781 (pt0) cc_final: 0.6553 (pt0) REVERT: A 272 THR cc_start: 0.8344 (t) cc_final: 0.8076 (m) REVERT: B 230 ARG cc_start: 0.8050 (tpp80) cc_final: 0.7776 (tpm170) REVERT: C 1116 MET cc_start: 0.4875 (ttt) cc_final: 0.4390 (ttt) REVERT: D 261 MET cc_start: 0.4425 (ptt) cc_final: 0.3434 (tmm) REVERT: D 267 MET cc_start: 0.1937 (mmm) cc_final: 0.1050 (mpp) REVERT: D 1048 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6011 (pp30) REVERT: D 1049 MET cc_start: 0.6951 (ptp) cc_final: 0.6511 (ptt) REVERT: D 1079 ILE cc_start: 0.8643 (pt) cc_final: 0.8396 (pt) outliers start: 3 outliers final: 0 residues processed: 148 average time/residue: 0.1980 time to fit residues: 38.8725 Evaluate side-chains 111 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS B 172 HIS B 235 GLN B 305 GLN D1022 ASN ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 1.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 6975 Z= 0.316 Angle : 0.789 9.642 9413 Z= 0.415 Chirality : 0.048 0.192 1081 Planarity : 0.005 0.052 1172 Dihedral : 4.683 16.841 908 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.39 % Allowed : 3.93 % 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: -0.05 (0.29), residues: 833 helix: 0.90 (0.22), residues: 531 sheet: -2.72 (0.46), residues: 96 loop : -0.88 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP D1011 HIS 0.006 0.002 HIS D1008 PHE 0.027 0.002 PHE A 41 TYR 0.025 0.002 TYR D 230 ARG 0.006 0.001 ARG D1050 *********************** 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 158 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 155 time to evaluate : 0.876 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: 0.7306 (tt) cc_final: 0.6781 (tt) REVERT: A 240 GLU cc_start: 0.6235 (pp20) cc_final: 0.5456 (tm-30) REVERT: B 37 LEU cc_start: 0.8318 (mm) cc_final: 0.8116 (mm) REVERT: B 230 ARG cc_start: 0.7718 (tpp80) cc_final: 0.7367 (tpm170) REVERT: B 291 MET cc_start: 0.8328 (ppp) cc_final: 0.8009 (ppp) REVERT: B 332 ASN cc_start: 0.7508 (m110) cc_final: 0.7302 (m110) REVERT: D 261 MET cc_start: 0.4952 (ptt) cc_final: 0.3909 (tmm) REVERT: D 1082 MET cc_start: 0.8010 (mmm) cc_final: 0.7525 (mmt) REVERT: D 1096 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6585 (tp-100) outliers start: 3 outliers final: 1 residues processed: 157 average time/residue: 0.1938 time to fit residues: 40.2324 Evaluate side-chains 120 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 chunk 80 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.0570 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 1.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6975 Z= 0.222 Angle : 0.721 12.121 9413 Z= 0.371 Chirality : 0.045 0.189 1081 Planarity : 0.004 0.055 1172 Dihedral : 4.335 17.827 908 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % 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: 0.18 (0.29), residues: 833 helix: 1.09 (0.22), residues: 531 sheet: -2.19 (0.50), residues: 93 loop : -1.08 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.004 TRP D1158 HIS 0.004 0.001 HIS B 314 PHE 0.020 0.002 PHE D1108 TYR 0.022 0.002 TYR D 224 ARG 0.005 0.001 ARG B 295 *********************** 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 152 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.7024 (tp) cc_final: 0.6674 (tp) REVERT: A 240 GLU cc_start: 0.6059 (pp20) cc_final: 0.5340 (pt0) REVERT: B 37 LEU cc_start: 0.8324 (mm) cc_final: 0.8048 (mm) REVERT: B 158 MET cc_start: 0.7528 (mtm) cc_final: 0.7274 (mtp) REVERT: B 332 ASN cc_start: 0.7716 (m110) cc_final: 0.7426 (m110) REVERT: C 1116 MET cc_start: 0.4768 (ttt) cc_final: 0.4524 (ttt) REVERT: D 261 MET cc_start: 0.5432 (ptt) cc_final: 0.4085 (tmm) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2082 time to fit residues: 41.8239 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 : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 48 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 0.0060 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 1.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6975 Z= 0.217 Angle : 0.724 8.578 9413 Z= 0.379 Chirality : 0.045 0.155 1081 Planarity : 0.005 0.055 1172 Dihedral : 4.344 17.913 908 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: 0.28 (0.29), residues: 833 helix: 1.09 (0.22), residues: 545 sheet: -2.00 (0.51), residues: 96 loop : -1.00 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.004 TRP D1158 HIS 0.003 0.001 HIS A 314 PHE 0.018 0.002 PHE D 279 TYR 0.029 0.002 TYR D 224 ARG 0.008 0.001 ARG D1050 *********************** 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 155 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.7224 (tp) cc_final: 0.6757 (tp) REVERT: A 70 ILE cc_start: 0.9038 (tt) cc_final: 0.8664 (mt) REVERT: A 174 LEU cc_start: 0.7121 (tp) cc_final: 0.6748 (tp) REVERT: A 240 GLU cc_start: 0.5966 (pp20) cc_final: 0.5554 (pt0) REVERT: B 37 LEU cc_start: 0.8384 (mm) cc_final: 0.8132 (mm) REVERT: B 306 MET cc_start: 0.8140 (mtp) cc_final: 0.7819 (ttp) REVERT: B 332 ASN cc_start: 0.7821 (m110) cc_final: 0.7553 (m110) REVERT: C 1065 MET cc_start: 0.8449 (mmp) cc_final: 0.8200 (mmp) REVERT: C 1116 MET cc_start: 0.5109 (ttt) cc_final: 0.4780 (ttt) REVERT: D 261 MET cc_start: 0.5547 (ptt) cc_final: 0.4332 (tmm) REVERT: D 267 MET cc_start: 0.3063 (mmm) cc_final: 0.2170 (mpp) REVERT: D 1065 MET cc_start: 0.8597 (tpp) cc_final: 0.8087 (mmm) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1771 time to fit residues: 37.3550 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 : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS B 305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 1.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 6975 Z= 0.455 Angle : 0.932 15.551 9413 Z= 0.491 Chirality : 0.052 0.222 1081 Planarity : 0.006 0.054 1172 Dihedral : 5.584 28.757 908 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % 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: -0.43 (0.29), residues: 833 helix: 0.59 (0.21), residues: 542 sheet: -2.84 (0.51), residues: 93 loop : -1.10 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.005 TRP D1158 HIS 0.009 0.002 HIS A 314 PHE 0.039 0.003 PHE D1019 TYR 0.035 0.003 TYR B 302 ARG 0.025 0.001 ARG D1050 *********************** 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 163 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 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 61 LEU cc_start: 0.8013 (tp) cc_final: 0.7753 (tp) REVERT: A 230 ARG cc_start: 0.8892 (ptm160) cc_final: 0.8588 (ptm-80) REVERT: A 240 GLU cc_start: 0.5992 (pp20) cc_final: 0.5304 (pt0) REVERT: A 279 GLN cc_start: 0.8689 (mp10) cc_final: 0.7995 (mp10) REVERT: B 95 LYS cc_start: 0.8050 (tptm) cc_final: 0.7843 (tppt) REVERT: B 306 MET cc_start: 0.8621 (mtp) cc_final: 0.8412 (mtm) REVERT: B 332 ASN cc_start: 0.8362 (m110) cc_final: 0.8073 (m110) REVERT: C 1045 GLN cc_start: 0.8336 (mm110) cc_final: 0.7771 (mm110) REVERT: C 1054 GLN cc_start: 0.8424 (mp10) cc_final: 0.8221 (mp10) REVERT: C 1080 ASN cc_start: 0.9007 (m-40) cc_final: 0.8766 (m-40) REVERT: D 261 MET cc_start: 0.5646 (ptt) cc_final: 0.4555 (tmm) REVERT: D 265 SER cc_start: 0.5546 (p) cc_final: 0.5317 (p) REVERT: D 1049 MET cc_start: 0.7128 (ptp) cc_final: 0.6782 (ptp) REVERT: D 1052 GLU cc_start: 0.9023 (pm20) cc_final: 0.8779 (pm20) REVERT: D 1059 GLU cc_start: 0.6471 (mm-30) cc_final: 0.6267 (tp30) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1826 time to fit residues: 40.3028 Evaluate side-chains 121 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 44 optimal weight: 0.0050 chunk 32 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN B 235 GLN ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 1.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6975 Z= 0.226 Angle : 0.779 8.509 9413 Z= 0.407 Chirality : 0.047 0.236 1081 Planarity : 0.005 0.056 1172 Dihedral : 4.779 30.179 908 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.05 (0.22), residues: 538 sheet: -2.39 (0.58), residues: 84 loop : -1.23 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.098 0.004 TRP D1158 HIS 0.006 0.001 HIS B 273 PHE 0.018 0.002 PHE D1031 TYR 0.029 0.002 TYR D 228 ARG 0.009 0.001 ARG D1050 *********************** 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 151 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.840 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: 0.8060 (tp) cc_final: 0.7175 (tp) REVERT: A 240 GLU cc_start: 0.5591 (pp20) cc_final: 0.5259 (tp30) REVERT: B 37 LEU cc_start: 0.8506 (mm) cc_final: 0.8301 (mm) REVERT: B 95 LYS cc_start: 0.7982 (tptm) cc_final: 0.7771 (tppt) REVERT: B 306 MET cc_start: 0.8401 (mtp) cc_final: 0.8131 (mtm) REVERT: B 332 ASN cc_start: 0.8283 (m110) cc_final: 0.8048 (m110) REVERT: C 1065 MET cc_start: 0.8450 (mmp) cc_final: 0.7856 (mmp) REVERT: C 1072 TYR cc_start: 0.8171 (t80) cc_final: 0.7752 (t80) REVERT: C 1086 LEU cc_start: 0.7660 (tp) cc_final: 0.7056 (tp) REVERT: D 261 MET cc_start: 0.5295 (ptt) cc_final: 0.4231 (tmm) REVERT: D 267 MET cc_start: 0.3130 (mmm) cc_final: 0.2585 (mpp) REVERT: D 1059 GLU cc_start: 0.6458 (mm-30) cc_final: 0.6248 (tp30) REVERT: D 1068 GLU cc_start: 0.6426 (mm-30) cc_final: 0.6065 (mm-30) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1891 time to fit residues: 38.0473 Evaluate side-chains 128 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 0.5980 chunk 82 optimal weight: 0.2980 chunk 76 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 HIS C1080 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 1.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6975 Z= 0.228 Angle : 0.793 8.286 9413 Z= 0.418 Chirality : 0.048 0.255 1081 Planarity : 0.005 0.056 1172 Dihedral : 4.711 24.990 908 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: 0.18 (0.29), residues: 833 helix: 1.02 (0.22), residues: 545 sheet: -2.36 (0.57), residues: 87 loop : -0.97 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.003 TRP D1158 HIS 0.004 0.001 HIS B 323 PHE 0.015 0.002 PHE D1108 TYR 0.018 0.002 TYR B 148 ARG 0.018 0.001 ARG A 65 ********************** 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 153 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.7901 (tp) cc_final: 0.7578 (tp) REVERT: A 240 GLU cc_start: 0.5612 (pp20) cc_final: 0.5327 (tp30) REVERT: B 37 LEU cc_start: 0.8549 (mm) cc_final: 0.8297 (mm) REVERT: B 95 LYS cc_start: 0.7968 (tptm) cc_final: 0.7762 (tppt) REVERT: B 306 MET cc_start: 0.8464 (mtp) cc_final: 0.8151 (mtm) REVERT: C 1065 MET cc_start: 0.8534 (mmp) cc_final: 0.7906 (mmp) REVERT: C 1072 TYR cc_start: 0.8222 (t80) cc_final: 0.7621 (t80) REVERT: C 1076 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7693 (mm-30) REVERT: C 1116 MET cc_start: 0.5403 (ttt) cc_final: 0.5174 (ttt) REVERT: D 221 GLN cc_start: 0.8665 (mp10) cc_final: 0.8065 (mp10) REVERT: D 261 MET cc_start: 0.5351 (ptt) cc_final: 0.4350 (tmm) REVERT: D 267 MET cc_start: 0.3204 (mmm) cc_final: 0.2692 (mpp) REVERT: D 1068 GLU cc_start: 0.6462 (mm-30) cc_final: 0.6133 (mm-30) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1849 time to fit residues: 38.0348 Evaluate side-chains 131 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 8 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN B 323 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.199880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.175476 restraints weight = 9478.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.165104 restraints weight = 10569.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.162857 restraints weight = 11215.092| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 1.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6975 Z= 0.216 Angle : 0.797 8.169 9413 Z= 0.420 Chirality : 0.047 0.222 1081 Planarity : 0.005 0.056 1172 Dihedral : 4.546 22.314 908 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: 0.33 (0.30), residues: 833 helix: 1.10 (0.22), residues: 544 sheet: -2.23 (0.59), residues: 87 loop : -0.83 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.005 TRP D1158 HIS 0.005 0.001 HIS B 323 PHE 0.016 0.001 PHE D 279 TYR 0.018 0.002 TYR B 148 ARG 0.014 0.001 ARG A 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1713.86 seconds wall clock time: 32 minutes 5.02 seconds (1925.02 seconds total)