Starting phenix.real_space_refine on Fri Sep 11 22:07:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tac_25769/09_2026/7tac_25769.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tac_25769/09_2026/7tac_25769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tac_25769/09_2026/7tac_25769.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tac_25769/09_2026/7tac_25769.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tac_25769/09_2026/7tac_25769.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tac_25769/09_2026/7tac_25769.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tac_25769/09_2026/7tac_25769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tac_25769/09_2026/7tac_25769.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 1.122 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 72 5.16 5 C 7534 2.51 5 N 2035 2.21 5 O 2199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11842 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2639 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 336} Chain breaks: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 2633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2633 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 10, 'TRANS': 336} Chain breaks: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1636 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1636 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1652 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1572 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 4, 'GLN:plan1': 5, 'HIS:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 76 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 771 SG CYS A 150 43.231 83.744 17.623 1.00 46.79 S ATOM 807 SG CYS A 155 43.958 85.238 14.260 1.00 53.57 S ATOM 841 SG CYS A 160 45.852 86.489 17.320 1.00 34.61 S ATOM 3408 SG CYS B 150 114.440 101.749 17.362 1.00 48.62 S ATOM 3444 SG CYS B 155 113.698 100.211 14.040 1.00 60.84 S ATOM 3478 SG CYS B 160 111.868 98.966 17.163 1.00 35.04 S Time building chain proxies: 2.63, per 1000 atoms: 0.22 Number of scatterers: 11842 At special positions: 0 Unit cell: (159.9, 186.55, 104.468, 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 2 29.99 S 72 16.00 O 2199 8.00 N 2035 7.00 C 7534 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 499.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" ND1 HIS A 157 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 150 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 155 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 160 " pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" ND1 HIS B 157 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 150 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 155 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 160 " Number of angles added : 6 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2944 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 4 sheets defined 83.4% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 42 through 59 Processing helix chain 'A' and resid 60 through 64 removed outlier: 3.953A pdb=" N TYR A 64 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 88 removed outlier: 3.584A pdb=" N LEU A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 99 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 124 through 138 removed outlier: 3.918A pdb=" N VAL A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 178 Processing helix chain 'A' and resid 179 through 194 Processing helix chain 'A' and resid 198 through 212 removed outlier: 3.832A pdb=" N VAL A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 230 Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 264 through 276 Processing helix chain 'A' and resid 278 through 288 removed outlier: 3.609A pdb=" N GLU A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 331 through 340 Processing helix chain 'A' and resid 341 through 350 Processing helix chain 'A' and resid 364 through 373 removed outlier: 3.552A pdb=" N THR A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.919A pdb=" N ASN A 379 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 404 Processing helix chain 'B' and resid 43 through 59 Processing helix chain 'B' and resid 60 through 64 removed outlier: 3.837A pdb=" N TYR B 64 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 88 removed outlier: 3.626A pdb=" N LEU B 84 " --> pdb=" O HIS B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 99 Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 124 through 138 removed outlier: 3.894A pdb=" N VAL B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 178 Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 198 through 212 removed outlier: 3.930A pdb=" N VAL B 204 " --> pdb=" O GLU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 216 through 230 Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 242 through 256 Processing helix chain 'B' and resid 264 through 276 Processing helix chain 'B' and resid 280 through 288 removed outlier: 3.754A pdb=" N LEU B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 307 through 317 Processing helix chain 'B' and resid 331 through 340 Processing helix chain 'B' and resid 341 through 352 Processing helix chain 'B' and resid 364 through 372 Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.585A pdb=" N ASN B 379 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 403 Processing helix chain 'C' and resid 165 through 194 removed outlier: 3.524A pdb=" N THR C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 226 removed outlier: 3.666A pdb=" N MET C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 204 " --> pdb=" O GLU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 233 removed outlier: 3.558A pdb=" N GLY C 233 " --> pdb=" O PHE C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 244 Processing helix chain 'C' and resid 250 through 263 Proline residue: C 260 - end of helix Processing helix chain 'C' and resid 266 through 308 removed outlier: 3.589A pdb=" N GLN C 305 " --> pdb=" O SER C 301 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE C 306 " --> pdb=" O ILE C 302 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS C 307 " --> pdb=" O ALA C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 350 Processing helix chain 'C' and resid 351 through 376 Processing helix chain 'D' and resid 165 through 194 Processing helix chain 'D' and resid 197 through 226 Processing helix chain 'D' and resid 226 through 233 removed outlier: 3.763A pdb=" N GLY D 233 " --> pdb=" O PHE D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 244 Processing helix chain 'D' and resid 250 through 259 Processing helix chain 'D' and resid 266 through 307 Processing helix chain 'D' and resid 317 through 350 Processing helix chain 'D' and resid 351 through 378 removed outlier: 3.571A pdb=" N LEU D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TRP D 376 " --> pdb=" O LEU D 372 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA D 377 " --> pdb=" O SER D 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 194 Processing helix chain 'E' and resid 197 through 224 removed outlier: 3.813A pdb=" N MET E 203 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU E 204 " --> pdb=" O GLU E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 233 Processing helix chain 'E' and resid 238 through 242 Processing helix chain 'E' and resid 250 through 263 Proline residue: E 260 - end of helix removed outlier: 3.534A pdb=" N GLU E 263 " --> pdb=" O MET E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 308 Processing helix chain 'E' and resid 317 through 350 Processing helix chain 'E' and resid 351 through 376 Processing helix chain 'F' and resid 165 through 192 Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 198 through 226 removed outlier: 3.673A pdb=" N MET F 203 " --> pdb=" O ILE F 199 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU F 204 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL F 205 " --> pdb=" O LEU F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 233 Processing helix chain 'F' and resid 237 through 242 Processing helix chain 'F' and resid 250 through 263 Proline residue: F 260 - end of helix Processing helix chain 'F' and resid 266 through 307 Processing helix chain 'F' and resid 317 through 350 Processing helix chain 'F' and resid 351 through 377 removed outlier: 3.558A pdb=" N ALA F 356 " --> pdb=" O THR F 352 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ARG F 357 " --> pdb=" O ARG F 353 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 Processing sheet with id=AA2, first strand: chain 'B' and resid 76 through 79 removed outlier: 6.553A pdb=" N LYS B 68 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 244 through 245 Processing sheet with id=AA4, first strand: chain 'F' and resid 244 through 245 937 hydrogen bonds defined for protein. 2754 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: 1.68 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3934 1.34 - 1.46: 2336 1.46 - 1.58: 5627 1.58 - 1.70: 0 1.70 - 1.82: 116 Bond restraints: 12013 Sorted by residual: bond pdb=" CG1 ILE C 246 " pdb=" CD1 ILE C 246 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.35e+00 bond pdb=" CB PRO C 264 " pdb=" CG PRO C 264 " ideal model delta sigma weight residual 1.506 1.458 0.048 3.90e-02 6.57e+02 1.52e+00 bond pdb=" CG1 ILE F 188 " pdb=" CD1 ILE F 188 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.39e+00 bond pdb=" CG PRO C 264 " pdb=" CD PRO C 264 " ideal model delta sigma weight residual 1.512 1.481 0.031 2.70e-02 1.37e+03 1.34e+00 bond pdb=" CB ILE C 196 " pdb=" CG2 ILE C 196 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.33e+00 ... (remaining 12008 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 15673 2.07 - 4.15: 445 4.15 - 6.22: 75 6.22 - 8.30: 21 8.30 - 10.37: 9 Bond angle restraints: 16223 Sorted by residual: angle pdb=" N LYS B 272 " pdb=" CA LYS B 272 " pdb=" CB LYS B 272 " ideal model delta sigma weight residual 110.28 115.99 -5.71 1.55e+00 4.16e-01 1.36e+01 angle pdb=" CA TRP C 245 " pdb=" CB TRP C 245 " pdb=" CG TRP C 245 " ideal model delta sigma weight residual 113.60 120.34 -6.74 1.90e+00 2.77e-01 1.26e+01 angle pdb=" N SER E 238 " pdb=" CA SER E 238 " pdb=" C SER E 238 " ideal model delta sigma weight residual 111.28 115.15 -3.87 1.09e+00 8.42e-01 1.26e+01 angle pdb=" N THR E 239 " pdb=" CA THR E 239 " pdb=" C THR E 239 " ideal model delta sigma weight residual 111.36 115.01 -3.65 1.09e+00 8.42e-01 1.12e+01 angle pdb=" CB LYS B 272 " pdb=" CG LYS B 272 " pdb=" CD LYS B 272 " ideal model delta sigma weight residual 111.30 118.99 -7.69 2.30e+00 1.89e-01 1.12e+01 ... (remaining 16218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6611 17.98 - 35.96: 601 35.96 - 53.94: 112 53.94 - 71.92: 18 71.92 - 89.90: 17 Dihedral angle restraints: 7359 sinusoidal: 2871 harmonic: 4488 Sorted by residual: dihedral pdb=" CB GLU F 284 " pdb=" CG GLU F 284 " pdb=" CD GLU F 284 " pdb=" OE1 GLU F 284 " ideal model delta sinusoidal sigma weight residual 0.00 89.66 -89.66 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG D 236 " pdb=" CD ARG D 236 " pdb=" NE ARG D 236 " pdb=" CZ ARG D 236 " ideal model delta sinusoidal sigma weight residual -90.00 -134.58 44.58 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CA ASN C 333 " pdb=" CB ASN C 333 " pdb=" CG ASN C 333 " pdb=" OD1 ASN C 333 " ideal model delta sinusoidal sigma weight residual -90.00 -158.26 68.26 2 2.00e+01 2.50e-03 1.04e+01 ... (remaining 7356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1320 0.040 - 0.080: 418 0.080 - 0.120: 126 0.120 - 0.160: 34 0.160 - 0.201: 8 Chirality restraints: 1906 Sorted by residual: chirality pdb=" CA LYS E 348 " pdb=" N LYS E 348 " pdb=" C LYS E 348 " pdb=" CB LYS E 348 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA GLU E 240 " pdb=" N GLU E 240 " pdb=" C GLU E 240 " pdb=" CB GLU E 240 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.77e-01 chirality pdb=" CG LEU F 369 " pdb=" CB LEU F 369 " pdb=" CD1 LEU F 369 " pdb=" CD2 LEU F 369 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 9.13e-01 ... (remaining 1903 not shown) Planarity restraints: 2069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 206 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C ASP F 206 " -0.056 2.00e-02 2.50e+03 pdb=" O ASP F 206 " 0.021 2.00e-02 2.50e+03 pdb=" N SER F 207 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU F 263 " 0.049 5.00e-02 4.00e+02 7.45e-02 8.88e+00 pdb=" N PRO F 264 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO F 264 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 264 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 202 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.63e+00 pdb=" C LYS F 202 " -0.051 2.00e-02 2.50e+03 pdb=" O LYS F 202 " 0.019 2.00e-02 2.50e+03 pdb=" N MET F 203 " 0.017 2.00e-02 2.50e+03 ... (remaining 2066 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 241 2.70 - 3.25: 12604 3.25 - 3.80: 19389 3.80 - 4.35: 23473 4.35 - 4.90: 38629 Nonbonded interactions: 94336 Sorted by model distance: nonbonded pdb=" O MET C 172 " pdb=" OG1 THR C 175 " model vdw 2.149 3.040 nonbonded pdb=" OD1 ASP B 277 " pdb=" OG1 THR B 310 " model vdw 2.167 3.040 nonbonded pdb=" OG SER E 252 " pdb=" OE1 GLU E 253 " model vdw 2.191 3.040 nonbonded pdb=" ND2 ASN B 323 " pdb=" OG SER B 354 " model vdw 2.228 3.120 nonbonded pdb=" O ASP F 206 " pdb=" ND2 ASN F 210 " model vdw 2.234 3.120 ... (remaining 94331 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 42 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 115 or (resid 116 and (name N or n \ ame CA or name C or name O or name CB )) or resid 117 through 232 or (resid 233 \ and (name N or name CA or name C or name O or name CB )) or resid 234 through 25 \ 9 or (resid 260 and (name N or name CA or name C or name O or name CB )) or resi \ d 261 or (resid 262 through 263 and (name N or name CA or name C or name O or na \ me CB )) or resid 264 through 366 or (resid 367 and (name N or name CA or name C \ or name O or name CB )) or resid 368 through 376 or (resid 377 and (name N or n \ ame CA or name C or name O or name CB )) or resid 378 through 379 or (resid 388 \ and (name N or name CA or name C or name O or name CB )) or resid 389 through 39 \ 5 or (resid 396 and (name N or name CA or name C or name O or name CB )) or resi \ d 397 through 399 or (resid 400 through 404 and (name N or name CA or name C or \ name O or name CB )) or resid 701)) selection = (chain 'B' and (resid 42 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 84 or (resid 85 through 86 and (na \ me N or name CA or name C or name O or name CB )) or resid 87 through 110 or (re \ sid 111 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name CE )) or resid 112 through 228 or (resid 229 and (name N or name CA \ or name C or name O or name CB or name CG or name CD )) or resid 230 through 258 \ or (resid 259 through 260 and (name N or name CA or name C or name O or name CB \ )) or resid 261 through 262 or (resid 263 and (name N or name CA or name C or n \ ame O or name CB )) or resid 264 through 356 or (resid 357 through 358 and (name \ N or name CA or name C or name O or name CB )) or resid 359 through 391 or (res \ id 392 and (name N or name CA or name C or name O or name CB )) or resid 393 thr \ ough 401 or (resid 402 through 404 and (name N or name CA or name C or name O or \ name CB )) or resid 701)) } ncs_group { reference = (chain 'C' and (resid 164 through 178 or (resid 179 through 180 and (name N or n \ ame CA or name C or name O or name CB )) or resid 181 through 194 or (resid 195 \ and (name N or name CA or name C or name O or name CB )) or resid 196 through 19 \ 9 or (resid 200 and (name N or name CA or name C or name O or name CB )) or resi \ d 201 through 233 or (resid 234 and (name N or name CA or name C or name O or na \ me CB )) or resid 235 or (resid 236 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name NE )) or resid 237 or (resid 238 and (na \ me N or name CA or name C or name O or name CB )) or resid 239 through 240 or (r \ esid 241 and (name N or name CA or name C or name O or name CB )) or resid 242 t \ hrough 243 or (resid 244 and (name N or name CA or name C or name O or name CB ) \ ) or resid 245 through 258 or (resid 259 and (name N or name CA or name C or nam \ e O or name CB )) or resid 260 through 295 or (resid 296 and (name N or name CA \ or name C or name O or name CB )) or resid 297 through 305 or (resid 306 through \ 307 and (name N or name CA or name C or name O or name CB )) or resid 316 throu \ gh 336 or (resid 337 and (name N or name CA or name C or name O or name CB )) or \ resid 338 through 339 or (resid 340 and (name N or name CA or name C or name O \ or name CB )) or resid 341 through 343 or (resid 344 and (name N or name CA or n \ ame C or name O or name CB )) or resid 345 through 356 or (resid 357 and (name N \ or name CA or name C or name O or name CB )) or resid 358 through 366 or (resid \ 367 and (name N or name CA or name C or name O or name CB )) or resid 368 throu \ gh 375 or (resid 376 through 378 and (name N or name CA or name C or name O or n \ ame CB )) or resid 501)) selection = (chain 'D' and (resid 164 through 178 or (resid 179 through 180 and (name N or n \ ame CA or name C or name O or name CB )) or resid 181 through 192 or (resid 193 \ through 195 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 6 through 199 or (resid 200 and (name N or name CA or name C or name O or name C \ B )) or resid 201 through 213 or (resid 214 and (name N or name CA or name C or \ name O or name CB )) or resid 215 through 226 or (resid 227 and (name N or name \ CA or name C or name O or name CB )) or resid 228 through 233 or (resid 234 and \ (name N or name CA or name C or name O or name CB )) or resid 235 or (resid 236 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or n \ ame NE )) or resid 237 or (resid 238 and (name N or name CA or name C or name O \ or name CB )) or resid 239 or (resid 240 through 241 and (name N or name CA or n \ ame C or name O or name CB )) or resid 242 through 243 or (resid 244 and (name N \ or name CA or name C or name O or name CB )) or resid 245 through 292 or (resid \ 293 and (name N or name CA or name C or name O or name CB or name CG or name CD \ )) or resid 294 through 295 or (resid 296 and (name N or name CA or name C or n \ ame O or name CB )) or resid 297 through 305 or (resid 306 through 316 and (name \ N or name CA or name C or name O or name CB )) or resid 317 through 321 or (res \ id 322 and (name N or name CA or name C or name O or name CB or name CG )) or re \ sid 323 through 328 or (resid 329 and (name N or name CA or name C or name O or \ name CB )) or resid 330 through 336 or (resid 337 and (name N or name CA or name \ C or name O or name CB )) or resid 338 through 339 or (resid 340 and (name N or \ name CA or name C or name O or name CB )) or resid 341 through 343 or (resid 34 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 345 through \ 356 or (resid 357 and (name N or name CA or name C or name O or name CB )) or re \ sid 358 through 366 or (resid 367 and (name N or name CA or name C or name O or \ name CB )) or resid 368 through 375 or (resid 376 through 378 and (name N or nam \ e CA or name C or name O or name CB )) or resid 501)) selection = (chain 'E' and (resid 164 through 178 or (resid 179 through 180 and (name N or n \ ame CA or name C or name O or name CB )) or resid 181 through 192 or (resid 193 \ through 195 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 6 through 199 or (resid 200 and (name N or name CA or name C or name O or name C \ B )) or resid 201 through 213 or (resid 214 and (name N or name CA or name C or \ name O or name CB )) or resid 215 through 226 or (resid 227 and (name N or name \ CA or name C or name O or name CB )) or resid 228 through 235 or (resid 236 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ NE )) or resid 237 or (resid 238 and (name N or name CA or name C or name O or n \ ame CB )) or resid 239 or (resid 240 through 241 and (name N or name CA or name \ C or name O or name CB )) or resid 242 through 243 or (resid 244 and (name N or \ name CA or name C or name O or name CB )) or resid 245 through 258 or (resid 259 \ and (name N or name CA or name C or name O or name CB )) or resid 260 through 2 \ 95 or (resid 296 and (name N or name CA or name C or name O or name CB )) or res \ id 297 through 307 or resid 316 through 321 or (resid 322 and (name N or name CA \ or name C or name O or name CB or name CG )) or resid 323 through 328 or (resid \ 329 and (name N or name CA or name C or name O or name CB )) or resid 330 throu \ gh 336 or (resid 337 and (name N or name CA or name C or name O or name CB )) or \ resid 338 through 339 or (resid 340 and (name N or name CA or name C or name O \ or name CB )) or resid 341 through 343 or (resid 344 and (name N or name CA or n \ ame C or name O or name CB )) or resid 345 through 356 or (resid 357 and (name N \ or name CA or name C or name O or name CB )) or resid 358 through 366 or (resid \ 367 and (name N or name CA or name C or name O or name CB )) or resid 368 throu \ gh 375 or (resid 376 through 378 and (name N or name CA or name C or name O or n \ ame CB )) or resid 501)) selection = (chain 'F' and (resid 164 through 213 or (resid 214 and (name N or name CA or na \ me C or name O or name CB )) or resid 215 through 226 or (resid 227 and (name N \ or name CA or name C or name O or name CB )) or resid 228 through 233 or (resid \ 234 and (name N or name CA or name C or name O or name CB )) or resid 235 throug \ h 258 or (resid 259 and (name N or name CA or name C or name O or name CB )) or \ resid 260 through 292 or (resid 293 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD )) or resid 294 through 305 or (resid 306 throug \ h 316 and (name N or name CA or name C or name O or name CB )) or resid 317 thro \ ugh 321 or (resid 322 and (name N or name CA or name C or name O or name CB or n \ ame CG )) or resid 323 through 328 or (resid 329 and (name N or name CA or name \ C or name O or name CB )) or resid 330 through 501)) } 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: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.050 Find NCS groups from input model: 0.290 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 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 0.060 12021 Z= 0.186 Angle : 0.858 10.374 16229 Z= 0.442 Chirality : 0.046 0.201 1906 Planarity : 0.005 0.075 2069 Dihedral : 14.711 89.902 4415 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.21), residues: 1498 helix: 1.17 (0.14), residues: 1160 sheet: -0.47 (1.06), residues: 24 loop : -1.20 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 339 TYR 0.030 0.003 TYR A 186 PHE 0.025 0.002 PHE F 242 TRP 0.036 0.003 TRP F 177 HIS 0.011 0.001 HIS E 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (12013) covalent geometry : angle 0.85591 / 0.44 (16223) hydrogen bonds : bond 0.12905 / 8.98 ( 937) hydrogen bonds : angle 4.55537 / 3.30 ( 2754) metal coordination : bond 0.01406 / 0.73 ( 8) metal coordination : angle 2.98535 / 1.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 318 ASP cc_start: 0.7774 (t0) cc_final: 0.7543 (t0) REVERT: C 333 ASN cc_start: 0.5881 (t0) cc_final: 0.3910 (t0) REVERT: C 348 LYS cc_start: 0.6990 (mptt) cc_final: 0.6112 (pttp) REVERT: D 181 GLN cc_start: 0.7132 (tm-30) cc_final: 0.6929 (tm-30) REVERT: E 318 MET cc_start: 0.4882 (mmt) cc_final: 0.3731 (mmt) REVERT: E 322 MET cc_start: 0.7955 (tmm) cc_final: 0.7633 (tmm) REVERT: F 259 MET cc_start: -0.0646 (mmp) cc_final: -0.1220 (mmp) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1028 time to fit residues: 34.6509 Evaluate side-chains 185 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 HIS B 269 ASN C 176 HIS C 333 ASN C 341 GLN E 324 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.225671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.189751 restraints weight = 20440.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.186938 restraints weight = 15346.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.187809 restraints weight = 11553.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.189114 restraints weight = 9263.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.189372 restraints weight = 8142.635| |-----------------------------------------------------------------------------| r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12021 Z= 0.152 Angle : 0.626 12.066 16229 Z= 0.309 Chirality : 0.038 0.179 1906 Planarity : 0.004 0.043 2069 Dihedral : 5.355 59.777 1673 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.79 % Allowed : 8.20 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.21), residues: 1498 helix: 2.19 (0.15), residues: 1190 sheet: 0.27 (1.09), residues: 20 loop : -0.44 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 339 TYR 0.024 0.002 TYR A 186 PHE 0.020 0.002 PHE B 90 TRP 0.050 0.002 TRP F 177 HIS 0.011 0.001 HIS C 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (12013) covalent geometry : angle 0.62521 / 0.31 (16223) hydrogen bonds : bond 0.04319 / 2.91 ( 937) hydrogen bonds : angle 3.78227 / 2.73 ( 2754) metal coordination : bond 0.01085 / 0.59 ( 8) metal coordination : angle 1.81500 / 0.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7623 (mtpt) cc_final: 0.6843 (mtpp) REVERT: B 318 ASP cc_start: 0.8248 (t0) cc_final: 0.7939 (t0) REVERT: B 346 LEU cc_start: 0.7459 (pp) cc_final: 0.7259 (pp) REVERT: C 333 ASN cc_start: 0.6233 (t0) cc_final: 0.5416 (t0) REVERT: C 337 HIS cc_start: 0.4837 (m170) cc_final: 0.4188 (m90) REVERT: C 348 LYS cc_start: 0.7246 (mptt) cc_final: 0.6229 (pttp) REVERT: D 193 GLN cc_start: 0.7298 (pp30) cc_final: 0.6975 (pt0) REVERT: E 318 MET cc_start: 0.5172 (mmt) cc_final: 0.4314 (mmt) REVERT: E 322 MET cc_start: 0.8384 (tmm) cc_final: 0.7761 (tmm) REVERT: F 187 GLU cc_start: 0.4667 (OUTLIER) cc_final: 0.4321 (pt0) REVERT: F 203 MET cc_start: 0.6747 (ppp) cc_final: 0.6377 (ppp) REVERT: F 231 MET cc_start: 0.4475 (mtm) cc_final: 0.4238 (mtt) outliers start: 22 outliers final: 13 residues processed: 215 average time/residue: 0.1077 time to fit residues: 33.8999 Evaluate side-chains 195 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 208 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 129 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 HIS E 210 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.223277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.187675 restraints weight = 20531.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.185447 restraints weight = 15380.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.187138 restraints weight = 11616.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.187725 restraints weight = 9011.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.187942 restraints weight = 8312.240| |-----------------------------------------------------------------------------| r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12021 Z= 0.151 Angle : 0.589 10.820 16229 Z= 0.289 Chirality : 0.038 0.264 1906 Planarity : 0.004 0.043 2069 Dihedral : 5.329 59.094 1673 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.11 % Allowed : 11.28 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.22), residues: 1498 helix: 2.44 (0.15), residues: 1192 sheet: 0.08 (1.08), residues: 20 loop : -0.19 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 339 TYR 0.024 0.002 TYR A 186 PHE 0.015 0.002 PHE A 91 TRP 0.042 0.003 TRP F 177 HIS 0.006 0.001 HIS D 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (12013) covalent geometry : angle 0.58767 / 0.29 (16223) hydrogen bonds : bond 0.04089 / 2.75 ( 937) hydrogen bonds : angle 3.69137 / 2.65 ( 2754) metal coordination : bond 0.00757 / 0.45 ( 8) metal coordination : angle 1.92363 / 1.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 240 SER cc_start: 0.8898 (m) cc_final: 0.8694 (m) REVERT: B 318 ASP cc_start: 0.8270 (t0) cc_final: 0.7928 (t0) REVERT: C 235 TRP cc_start: 0.6892 (p-90) cc_final: 0.6390 (p-90) REVERT: C 333 ASN cc_start: 0.6281 (t0) cc_final: 0.5339 (t0) REVERT: C 337 HIS cc_start: 0.4953 (m170) cc_final: 0.4185 (m90) REVERT: C 348 LYS cc_start: 0.7364 (mptt) cc_final: 0.6310 (pttp) REVERT: D 203 MET cc_start: 0.3076 (mpp) cc_final: 0.2848 (mpp) REVERT: D 364 GLU cc_start: 0.7445 (pt0) cc_final: 0.7115 (pp20) REVERT: E 250 ARG cc_start: 0.6692 (ptm160) cc_final: 0.6491 (ptm160) REVERT: E 318 MET cc_start: 0.4903 (mmt) cc_final: 0.4160 (mmt) REVERT: E 322 MET cc_start: 0.8288 (tmm) cc_final: 0.7684 (tmm) REVERT: E 329 GLU cc_start: 0.7554 (tp30) cc_final: 0.7227 (tt0) REVERT: F 322 MET cc_start: 0.5473 (mtm) cc_final: 0.4736 (mtm) REVERT: F 326 GLN cc_start: 0.7489 (tp40) cc_final: 0.6986 (mp10) outliers start: 26 outliers final: 17 residues processed: 210 average time/residue: 0.1086 time to fit residues: 33.4957 Evaluate side-chains 199 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain F residue 208 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 41 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN D 367 HIS E 210 ASN E 211 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.222993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.186736 restraints weight = 20354.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.185194 restraints weight = 14331.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.186403 restraints weight = 11828.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.187135 restraints weight = 8897.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.187534 restraints weight = 7699.853| |-----------------------------------------------------------------------------| r_work (final): 0.4353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12021 Z= 0.142 Angle : 0.581 10.085 16229 Z= 0.284 Chirality : 0.037 0.168 1906 Planarity : 0.004 0.048 2069 Dihedral : 5.367 57.808 1673 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.11 % Allowed : 13.15 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.07 (0.22), residues: 1498 helix: 2.50 (0.15), residues: 1192 sheet: 0.75 (0.94), residues: 32 loop : 0.10 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 339 TYR 0.023 0.002 TYR A 186 PHE 0.012 0.001 PHE B 90 TRP 0.028 0.002 TRP F 245 HIS 0.005 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (12013) covalent geometry : angle 0.57971 / 0.28 (16223) hydrogen bonds : bond 0.03869 / 2.59 ( 937) hydrogen bonds : angle 3.62679 / 2.60 ( 2754) metal coordination : bond 0.00695 / 0.42 ( 8) metal coordination : angle 1.97511 / 1.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 SER cc_start: 0.8947 (m) cc_final: 0.8737 (m) REVERT: B 211 ILE cc_start: 0.9119 (tt) cc_final: 0.8757 (tt) REVERT: B 318 ASP cc_start: 0.8236 (t0) cc_final: 0.7872 (t0) REVERT: C 186 SER cc_start: 0.7757 (t) cc_final: 0.7552 (p) REVERT: C 235 TRP cc_start: 0.6960 (p-90) cc_final: 0.6422 (p-90) REVERT: C 333 ASN cc_start: 0.6298 (t0) cc_final: 0.5269 (t0) REVERT: C 337 HIS cc_start: 0.4897 (m170) cc_final: 0.4371 (m90) REVERT: D 364 GLU cc_start: 0.7475 (pt0) cc_final: 0.7216 (pp20) REVERT: E 318 MET cc_start: 0.5002 (mmt) cc_final: 0.4450 (mmt) REVERT: E 322 MET cc_start: 0.8378 (tmm) cc_final: 0.7770 (tmm) REVERT: F 188 ILE cc_start: 0.3831 (OUTLIER) cc_final: 0.3626 (mm) REVERT: F 326 GLN cc_start: 0.7399 (tp40) cc_final: 0.6917 (mp10) outliers start: 26 outliers final: 17 residues processed: 220 average time/residue: 0.0963 time to fit residues: 31.6173 Evaluate side-chains 203 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 208 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 4 optimal weight: 0.0870 chunk 138 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 8 optimal weight: 0.2980 chunk 111 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 HIS E 210 ASN E 211 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.222985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.186800 restraints weight = 20344.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.185623 restraints weight = 13277.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.186309 restraints weight = 10372.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.187223 restraints weight = 8838.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.189207 restraints weight = 8232.974| |-----------------------------------------------------------------------------| r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12021 Z= 0.130 Angle : 0.568 10.472 16229 Z= 0.275 Chirality : 0.037 0.284 1906 Planarity : 0.004 0.050 2069 Dihedral : 5.249 58.804 1673 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.95 % Allowed : 14.29 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.22), residues: 1498 helix: 2.61 (0.15), residues: 1188 sheet: 0.71 (0.97), residues: 32 loop : 0.14 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 222 TYR 0.022 0.002 TYR A 186 PHE 0.010 0.001 PHE B 90 TRP 0.032 0.002 TRP F 177 HIS 0.005 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (12013) covalent geometry : angle 0.56693 / 0.27 (16223) hydrogen bonds : bond 0.03691 / 2.47 ( 937) hydrogen bonds : angle 3.56056 / 2.54 ( 2754) metal coordination : bond 0.00658 / 0.39 ( 8) metal coordination : angle 1.96487 / 1.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 SER cc_start: 0.8937 (m) cc_final: 0.8725 (m) REVERT: B 211 ILE cc_start: 0.9120 (tt) cc_final: 0.8735 (tt) REVERT: B 283 LYS cc_start: 0.8626 (mttt) cc_final: 0.8397 (mttt) REVERT: B 318 ASP cc_start: 0.8200 (t0) cc_final: 0.7941 (t0) REVERT: C 192 LEU cc_start: 0.7891 (tt) cc_final: 0.7572 (tt) REVERT: C 333 ASN cc_start: 0.6341 (t0) cc_final: 0.5233 (t0) REVERT: C 337 HIS cc_start: 0.4873 (m170) cc_final: 0.4271 (m90) REVERT: D 203 MET cc_start: 0.2988 (OUTLIER) cc_final: 0.2757 (mpp) REVERT: D 364 GLU cc_start: 0.7415 (pt0) cc_final: 0.7152 (pp20) REVERT: E 263 GLU cc_start: 0.7810 (pt0) cc_final: 0.7433 (mt-10) REVERT: E 267 ASP cc_start: 0.6988 (t70) cc_final: 0.6558 (m-30) REVERT: E 318 MET cc_start: 0.5043 (mmt) cc_final: 0.4572 (mmt) REVERT: E 322 MET cc_start: 0.8387 (tmm) cc_final: 0.7778 (tmm) outliers start: 24 outliers final: 20 residues processed: 216 average time/residue: 0.1023 time to fit residues: 32.6775 Evaluate side-chains 205 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain F residue 208 CYS Chi-restraints excluded: chain F residue 362 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 144 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 chunk 142 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 17 optimal weight: 0.0980 chunk 50 optimal weight: 0.0980 chunk 110 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 HIS E 211 HIS E 305 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.223287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.187352 restraints weight = 20415.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.186522 restraints weight = 12924.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.187281 restraints weight = 10227.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.188152 restraints weight = 8491.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.188344 restraints weight = 7937.789| |-----------------------------------------------------------------------------| r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12021 Z= 0.121 Angle : 0.576 14.134 16229 Z= 0.276 Chirality : 0.037 0.243 1906 Planarity : 0.004 0.050 2069 Dihedral : 5.181 57.962 1673 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.03 % Allowed : 15.83 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.25 (0.22), residues: 1498 helix: 2.61 (0.15), residues: 1196 sheet: 0.77 (0.99), residues: 32 loop : 0.21 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 339 TYR 0.021 0.002 TYR A 186 PHE 0.017 0.001 PHE F 216 TRP 0.025 0.002 TRP F 177 HIS 0.007 0.001 HIS C 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (12013) covalent geometry : angle 0.57473 / 0.28 (16223) hydrogen bonds : bond 0.03588 / 2.39 ( 937) hydrogen bonds : angle 3.57641 / 2.55 ( 2754) metal coordination : bond 0.00616 / 0.35 ( 8) metal coordination : angle 1.95914 / 1.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 SER cc_start: 0.8939 (m) cc_final: 0.8734 (m) REVERT: A 287 LYS cc_start: 0.7701 (ptmt) cc_final: 0.7498 (ptmt) REVERT: B 211 ILE cc_start: 0.9100 (tt) cc_final: 0.8721 (tt) REVERT: B 283 LYS cc_start: 0.8594 (mttt) cc_final: 0.8329 (mttt) REVERT: B 318 ASP cc_start: 0.8282 (t0) cc_final: 0.8008 (t0) REVERT: C 192 LEU cc_start: 0.8023 (tt) cc_final: 0.7671 (tt) REVERT: C 333 ASN cc_start: 0.6384 (t0) cc_final: 0.5188 (t0) REVERT: C 337 HIS cc_start: 0.4964 (m170) cc_final: 0.4428 (m90) REVERT: C 346 MET cc_start: 0.7547 (tpt) cc_final: 0.6932 (tpt) REVERT: D 203 MET cc_start: 0.3048 (OUTLIER) cc_final: 0.2846 (mpp) REVERT: D 364 GLU cc_start: 0.7379 (pt0) cc_final: 0.7137 (pp20) REVERT: E 263 GLU cc_start: 0.7731 (pt0) cc_final: 0.7327 (mt-10) REVERT: E 267 ASP cc_start: 0.7030 (t70) cc_final: 0.6612 (m-30) REVERT: E 318 MET cc_start: 0.5045 (mmt) cc_final: 0.4745 (mmt) REVERT: E 322 MET cc_start: 0.8354 (tmm) cc_final: 0.7767 (tmm) outliers start: 25 outliers final: 19 residues processed: 215 average time/residue: 0.0983 time to fit residues: 31.8776 Evaluate side-chains 212 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain F residue 208 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 76 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 55 optimal weight: 0.0040 chunk 77 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 HIS ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.222391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.186240 restraints weight = 20197.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.185251 restraints weight = 13605.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.186500 restraints weight = 10084.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.186975 restraints weight = 8030.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.187398 restraints weight = 6975.532| |-----------------------------------------------------------------------------| r_work (final): 0.4355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12021 Z= 0.132 Angle : 0.615 13.769 16229 Z= 0.291 Chirality : 0.038 0.297 1906 Planarity : 0.004 0.051 2069 Dihedral : 5.189 53.362 1673 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.35 % Allowed : 16.31 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.22), residues: 1498 helix: 2.63 (0.15), residues: 1194 sheet: -0.93 (0.95), residues: 24 loop : 0.19 (0.41), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 339 TYR 0.020 0.002 TYR A 186 PHE 0.019 0.001 PHE C 331 TRP 0.043 0.002 TRP F 177 HIS 0.007 0.001 HIS C 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (12013) covalent geometry : angle 0.61432 / 0.29 (16223) hydrogen bonds : bond 0.03693 / 2.45 ( 937) hydrogen bonds : angle 3.66129 / 2.60 ( 2754) metal coordination : bond 0.00600 / 0.36 ( 8) metal coordination : angle 2.06832 / 1.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 SER cc_start: 0.8949 (m) cc_final: 0.8736 (m) REVERT: A 287 LYS cc_start: 0.7730 (ptmt) cc_final: 0.7503 (ptmt) REVERT: B 211 ILE cc_start: 0.9126 (tt) cc_final: 0.8765 (tt) REVERT: B 283 LYS cc_start: 0.8602 (mttt) cc_final: 0.8364 (mttt) REVERT: B 318 ASP cc_start: 0.8334 (t0) cc_final: 0.8051 (t0) REVERT: B 397 ILE cc_start: 0.7974 (tp) cc_final: 0.7763 (tp) REVERT: C 235 TRP cc_start: 0.6640 (p-90) cc_final: 0.5874 (p-90) REVERT: C 346 MET cc_start: 0.7586 (tpt) cc_final: 0.7014 (tpt) REVERT: D 364 GLU cc_start: 0.7470 (pt0) cc_final: 0.7200 (pp20) REVERT: E 200 GLU cc_start: 0.7878 (pm20) cc_final: 0.7591 (pm20) REVERT: E 263 GLU cc_start: 0.7733 (pt0) cc_final: 0.7328 (mt-10) REVERT: E 267 ASP cc_start: 0.6994 (t70) cc_final: 0.6626 (m-30) REVERT: E 318 MET cc_start: 0.4859 (mmt) cc_final: 0.4560 (mmt) REVERT: E 322 MET cc_start: 0.8369 (tmm) cc_final: 0.7842 (tmm) outliers start: 29 outliers final: 20 residues processed: 212 average time/residue: 0.0967 time to fit residues: 30.9069 Evaluate side-chains 207 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain F residue 208 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 6 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 HIS E 211 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.218404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.182226 restraints weight = 20400.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.180480 restraints weight = 13111.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.182071 restraints weight = 12754.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.182531 restraints weight = 8965.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.182811 restraints weight = 8637.141| |-----------------------------------------------------------------------------| r_work (final): 0.4304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12021 Z= 0.192 Angle : 0.688 13.144 16229 Z= 0.332 Chirality : 0.041 0.347 1906 Planarity : 0.004 0.054 2069 Dihedral : 5.875 54.757 1673 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.03 % Allowed : 17.53 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.22), residues: 1498 helix: 2.38 (0.15), residues: 1194 sheet: -1.57 (0.87), residues: 24 loop : 0.12 (0.40), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 339 TYR 0.022 0.002 TYR A 186 PHE 0.020 0.001 PHE C 331 TRP 0.083 0.003 TRP F 177 HIS 0.009 0.002 HIS F 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (12013) covalent geometry : angle 0.68671 / 0.33 (16223) hydrogen bonds : bond 0.04258 / 2.82 ( 937) hydrogen bonds : angle 3.94417 / 2.80 ( 2754) metal coordination : bond 0.00992 / 0.61 ( 8) metal coordination : angle 2.37321 / 1.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 LYS cc_start: 0.7862 (ptmt) cc_final: 0.7629 (ptmt) REVERT: B 283 LYS cc_start: 0.8617 (mttt) cc_final: 0.8402 (mttt) REVERT: B 318 ASP cc_start: 0.8303 (t0) cc_final: 0.7987 (t0) REVERT: B 397 ILE cc_start: 0.8101 (tp) cc_final: 0.7885 (tp) REVERT: C 235 TRP cc_start: 0.6788 (p-90) cc_final: 0.5942 (p-90) REVERT: C 250 ARG cc_start: 0.8078 (mmm-85) cc_final: 0.7732 (mmm160) REVERT: C 337 HIS cc_start: 0.4867 (m-70) cc_final: 0.4597 (m-70) REVERT: C 339 ARG cc_start: 0.7115 (mtt-85) cc_final: 0.6727 (mtt-85) REVERT: C 345 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7180 (mp10) REVERT: D 364 GLU cc_start: 0.7526 (pt0) cc_final: 0.6987 (tt0) REVERT: E 200 GLU cc_start: 0.7896 (pm20) cc_final: 0.7559 (pm20) REVERT: E 263 GLU cc_start: 0.7728 (pt0) cc_final: 0.7215 (mt-10) REVERT: E 318 MET cc_start: 0.4710 (mmt) cc_final: 0.4396 (mmt) REVERT: E 322 MET cc_start: 0.8266 (tmm) cc_final: 0.7769 (tmm) outliers start: 25 outliers final: 23 residues processed: 208 average time/residue: 0.1087 time to fit residues: 33.1001 Evaluate side-chains 211 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain F residue 208 CYS Chi-restraints excluded: chain F residue 291 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 61 optimal weight: 0.6980 chunk 76 optimal weight: 0.2980 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 0.1980 chunk 69 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 114 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.9925 > 50:) chunk 54 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN D 333 ASN E 211 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.221346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.185342 restraints weight = 20191.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.184721 restraints weight = 13131.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.186200 restraints weight = 9598.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.186657 restraints weight = 7200.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.186963 restraints weight = 6449.988| |-----------------------------------------------------------------------------| r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12021 Z= 0.134 Angle : 0.641 12.325 16229 Z= 0.304 Chirality : 0.039 0.333 1906 Planarity : 0.004 0.054 2069 Dihedral : 5.540 58.249 1673 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.27 % Allowed : 17.61 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.22), residues: 1498 helix: 2.50 (0.15), residues: 1194 sheet: -1.13 (0.95), residues: 20 loop : -0.01 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 339 TYR 0.021 0.002 TYR A 186 PHE 0.018 0.001 PHE C 331 TRP 0.078 0.003 TRP F 177 HIS 0.007 0.001 HIS F 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (12013) covalent geometry : angle 0.63904 / 0.30 (16223) hydrogen bonds : bond 0.03762 / 2.50 ( 937) hydrogen bonds : angle 3.77060 / 2.68 ( 2754) metal coordination : bond 0.00651 / 0.40 ( 8) metal coordination : angle 2.33956 / 1.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: B 211 ILE cc_start: 0.9109 (tt) cc_final: 0.8744 (tt) REVERT: B 283 LYS cc_start: 0.8588 (mttt) cc_final: 0.8368 (mttt) REVERT: B 397 ILE cc_start: 0.7991 (tp) cc_final: 0.7743 (tp) REVERT: C 235 TRP cc_start: 0.6740 (p-90) cc_final: 0.5954 (p-90) REVERT: C 250 ARG cc_start: 0.7953 (mmm-85) cc_final: 0.7642 (mmm160) REVERT: C 345 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7097 (mp10) REVERT: D 364 GLU cc_start: 0.7479 (pt0) cc_final: 0.6947 (tt0) REVERT: E 263 GLU cc_start: 0.7775 (pt0) cc_final: 0.7461 (mt-10) REVERT: E 318 MET cc_start: 0.4769 (mmt) cc_final: 0.4550 (mmt) REVERT: E 322 MET cc_start: 0.8285 (tmm) cc_final: 0.7780 (tmm) REVERT: F 345 GLN cc_start: 0.7132 (tp-100) cc_final: 0.6877 (tp-100) outliers start: 28 outliers final: 22 residues processed: 209 average time/residue: 0.0961 time to fit residues: 30.2767 Evaluate side-chains 208 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain F residue 208 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 43 optimal weight: 0.6980 chunk 72 optimal weight: 0.2980 chunk 128 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 2 optimal weight: 0.0870 chunk 104 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.221199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.184803 restraints weight = 20346.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.183945 restraints weight = 12813.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.185244 restraints weight = 9476.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.185732 restraints weight = 7721.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.186293 restraints weight = 6579.865| |-----------------------------------------------------------------------------| r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12021 Z= 0.139 Angle : 0.669 14.064 16229 Z= 0.317 Chirality : 0.039 0.324 1906 Planarity : 0.004 0.054 2069 Dihedral : 5.334 54.192 1673 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.03 % Allowed : 18.51 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.99 (0.22), residues: 1498 helix: 2.49 (0.15), residues: 1194 sheet: -1.52 (0.86), residues: 24 loop : 0.01 (0.40), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 370 TYR 0.020 0.002 TYR A 186 PHE 0.017 0.001 PHE C 331 TRP 0.073 0.003 TRP F 177 HIS 0.008 0.001 HIS C 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (12013) covalent geometry : angle 0.66775 / 0.32 (16223) hydrogen bonds : bond 0.03796 / 2.52 ( 937) hydrogen bonds : angle 3.80703 / 2.71 ( 2754) metal coordination : bond 0.00635 / 0.39 ( 8) metal coordination : angle 2.16017 / 1.31 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: B 211 ILE cc_start: 0.9120 (tt) cc_final: 0.8763 (tt) REVERT: B 397 ILE cc_start: 0.7952 (tp) cc_final: 0.7729 (tp) REVERT: C 218 MET cc_start: 0.7769 (ptp) cc_final: 0.7557 (ptt) REVERT: C 235 TRP cc_start: 0.6695 (p-90) cc_final: 0.5963 (p-90) REVERT: C 345 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7203 (mp10) REVERT: D 364 GLU cc_start: 0.7527 (pt0) cc_final: 0.7000 (tt0) REVERT: E 263 GLU cc_start: 0.7797 (pt0) cc_final: 0.7478 (mt-10) REVERT: E 267 ASP cc_start: 0.7011 (t70) cc_final: 0.6583 (m-30) REVERT: E 322 MET cc_start: 0.8377 (tmm) cc_final: 0.7843 (tmm) outliers start: 25 outliers final: 22 residues processed: 201 average time/residue: 0.0919 time to fit residues: 27.9704 Evaluate side-chains 207 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain F residue 208 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 20 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 139 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 chunk 118 optimal weight: 0.0980 chunk 75 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 131 optimal weight: 0.3980 chunk 13 optimal weight: 0.4980 chunk 137 optimal weight: 0.0980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.223239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.187688 restraints weight = 20245.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.187075 restraints weight = 12659.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.188478 restraints weight = 9542.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.189048 restraints weight = 7487.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.190048 restraints weight = 7164.674| |-----------------------------------------------------------------------------| r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12021 Z= 0.123 Angle : 0.654 12.876 16229 Z= 0.310 Chirality : 0.038 0.331 1906 Planarity : 0.004 0.053 2069 Dihedral : 5.040 51.466 1673 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.03 % Allowed : 18.67 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.10 (0.22), residues: 1498 helix: 2.58 (0.15), residues: 1194 sheet: -0.76 (0.99), residues: 20 loop : -0.09 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 339 TYR 0.019 0.001 TYR A 186 PHE 0.016 0.001 PHE C 331 TRP 0.066 0.002 TRP F 177 HIS 0.018 0.001 HIS C 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (12013) covalent geometry : angle 0.65258 / 0.31 (16223) hydrogen bonds : bond 0.03560 / 2.38 ( 937) hydrogen bonds : angle 3.72068 / 2.65 ( 2754) metal coordination : bond 0.00633 / 0.36 ( 8) metal coordination : angle 2.12947 / 1.22 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2291.34 seconds wall clock time: 40 minutes 21.03 seconds (2421.03 seconds total)