Starting phenix.real_space_refine on Fri Jan 19 15:31:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tac_25769/01_2024/7tac_25769_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tac_25769/01_2024/7tac_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tac_25769/01_2024/7tac_25769.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tac_25769/01_2024/7tac_25769.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tac_25769/01_2024/7tac_25769_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tac_25769/01_2024/7tac_25769_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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 Residue "A GLU 200": "OE1" <-> "OE2" Residue "B TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C ASP 267": "OD1" <-> "OD2" Residue "C GLU 300": "OE1" <-> "OE2" Residue "D PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 263": "OE1" <-> "OE2" Residue "E GLU 329": "OE1" <-> "OE2" Residue "F GLU 253": "OE1" <-> "OE2" Residue "F GLU 263": "OE1" <-> "OE2" Residue "F GLU 329": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/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, 'ASP:plan': 1, 'ARG:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP: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: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} 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: {'GLN:plan1': 1, 'ARG:plan': 2} 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: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 4, 'TRP:plan': 1, 'HIS:plan': 3} 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: 6.36, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 4.77 Conformation dependent library (CDL) restraints added in 2.3 seconds 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... running ksdssp... Secondary structure from input PDB file: 75 helices and 2 sheets defined 75.5% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 43 through 58 Processing helix chain 'A' and resid 60 through 63 Processing helix chain 'A' and resid 81 through 87 Processing helix chain 'A' and resid 89 through 98 Processing helix chain 'A' and resid 114 through 117 No H-bonds generated for 'chain 'A' and resid 114 through 117' Processing helix chain 'A' and resid 125 through 137 Processing helix chain 'A' and resid 161 through 177 Processing helix chain 'A' and resid 180 through 193 Processing helix chain 'A' and resid 199 through 211 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 229 removed outlier: 3.739A pdb=" N CYS A 216 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET A 217 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LYS A 218 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 219 " --> pdb=" O CYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 240 Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 265 through 275 Processing helix chain 'A' and resid 279 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 293 through 296 No H-bonds generated for 'chain 'A' and resid 293 through 296' Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 308 through 317 removed outlier: 3.783A pdb=" N LEU A 317 " --> pdb=" O ASP A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 339 Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 375 through 378 Processing helix chain 'A' and resid 390 through 403 Processing helix chain 'B' and resid 43 through 63 Proline residue: B 60 - end of helix removed outlier: 3.582A pdb=" N PHE B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 87 Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 114 through 117 No H-bonds generated for 'chain 'B' and resid 114 through 117' Processing helix chain 'B' and resid 125 through 137 Processing helix chain 'B' and resid 161 through 176 Processing helix chain 'B' and resid 180 through 196 removed outlier: 4.757A pdb=" N ASP B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LYS B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 211 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 229 removed outlier: 3.815A pdb=" N CYS B 216 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET B 217 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LYS B 218 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 240 Processing helix chain 'B' and resid 243 through 255 Processing helix chain 'B' and resid 265 through 275 Processing helix chain 'B' and resid 281 through 287 Processing helix chain 'B' and resid 293 through 296 No H-bonds generated for 'chain 'B' and resid 293 through 296' Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 308 through 316 Processing helix chain 'B' and resid 332 through 339 Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 375 through 378 Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'C' and resid 165 through 193 removed outlier: 3.524A pdb=" N THR C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 225 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 227 through 232 Processing helix chain 'C' and resid 239 through 243 Processing helix chain 'C' and resid 251 through 262 Proline residue: C 260 - end of helix Processing helix chain 'C' and resid 267 through 307 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 349 Processing helix chain 'C' and resid 352 through 377 removed outlier: 3.742A pdb=" N ALA C 377 " --> pdb=" O SER C 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 193 Processing helix chain 'D' and resid 198 through 225 Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 240 through 243 Processing helix chain 'D' and resid 251 through 262 Proline residue: D 260 - end of helix Processing helix chain 'D' and resid 267 through 306 Processing helix chain 'D' and resid 317 through 349 Processing helix chain 'D' and resid 352 through 377 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 193 Processing helix chain 'E' and resid 198 through 223 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 227 through 232 Processing helix chain 'E' and resid 239 through 242 Processing helix chain 'E' and resid 251 through 262 Proline residue: E 260 - end of helix Processing helix chain 'E' and resid 267 through 307 Processing helix chain 'E' and resid 317 through 349 Processing helix chain 'E' and resid 352 through 377 Processing helix chain 'F' and resid 165 through 194 removed outlier: 3.945A pdb=" N GLN F 193 " --> pdb=" O ARG F 189 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA F 194 " --> pdb=" O THR F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 225 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 228 through 232 Processing helix chain 'F' and resid 238 through 243 removed outlier: 3.928A pdb=" N PHE F 243 " --> pdb=" O THR F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 262 Proline residue: F 260 - end of helix Processing helix chain 'F' and resid 267 through 306 Processing helix chain 'F' and resid 317 through 349 Processing helix chain 'F' and resid 352 through 376 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= A, first strand: chain 'A' and resid 76 through 79 Processing sheet with id= B, first strand: chain 'B' and resid 76 through 79 823 hydrogen bonds defined for protein. 2379 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: 3.51 Time building geometry restraints manager: 5.12 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: 98.84 - 105.88: 162 105.88 - 112.91: 6634 112.91 - 119.95: 4321 119.95 - 126.98: 5006 126.98 - 134.02: 100 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: 247 2.70 - 3.25: 12703 3.25 - 3.80: 19486 3.80 - 4.35: 23684 4.35 - 4.90: 38672 Nonbonded interactions: 94792 Sorted by model distance: nonbonded pdb=" O MET C 172 " pdb=" OG1 THR C 175 " model vdw 2.149 2.440 nonbonded pdb=" OD1 ASP B 277 " pdb=" OG1 THR B 310 " model vdw 2.167 2.440 nonbonded pdb=" OG SER E 252 " pdb=" OE1 GLU E 253 " model vdw 2.191 2.440 nonbonded pdb=" ND2 ASN B 323 " pdb=" OG SER B 354 " model vdw 2.228 2.520 nonbonded pdb=" O ASP F 206 " pdb=" ND2 ASN F 210 " model vdw 2.234 2.520 ... (remaining 94787 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 378 or resid 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: 2.830 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: 12.420 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 36.300 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 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 12013 Z= 0.270 Angle : 0.856 10.374 16223 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (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 TRP 0.036 0.003 TRP F 177 HIS 0.011 0.001 HIS E 337 PHE 0.025 0.002 PHE F 242 TYR 0.030 0.003 TYR A 186 ARG 0.010 0.001 ARG E 339 *********************** 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 fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.375 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: 0.5880 (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: 0.2220 time to fit residues: 72.6988 Evaluate side-chains 185 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 75 optimal weight: 0.5980 chunk 59 optimal weight: 0.0980 chunk 116 optimal weight: 0.9980 chunk 44 optimal weight: 0.0050 chunk 70 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS B 269 ASN B 307 ASN C 176 HIS C 282 GLN C 324 ASN ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 GLN E 324 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12013 Z= 0.170 Angle : 0.576 12.090 16223 Z= 0.280 Chirality : 0.036 0.170 1906 Planarity : 0.004 0.046 2069 Dihedral : 5.162 58.952 1673 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.95 % Allowed : 7.47 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.22), residues: 1498 helix: 2.25 (0.15), residues: 1162 sheet: 0.65 (0.96), residues: 32 loop : -0.48 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP F 177 HIS 0.009 0.001 HIS C 176 PHE 0.022 0.002 PHE B 90 TYR 0.023 0.002 TYR A 186 ARG 0.004 0.000 ARG B 339 *********************** 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 237 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 213 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7436 (mtpt) cc_final: 0.6606 (mmtm) REVERT: B 318 ASP cc_start: 0.7791 (t0) cc_final: 0.7445 (t0) REVERT: C 333 ASN cc_start: 0.5854 (t0) cc_final: 0.5023 (t0) REVERT: C 337 HIS cc_start: 0.4771 (m170) cc_final: 0.4256 (m90) REVERT: C 348 LYS cc_start: 0.7241 (mptt) cc_final: 0.6227 (pttt) REVERT: E 318 MET cc_start: 0.4965 (mmt) cc_final: 0.4160 (mmt) REVERT: E 322 MET cc_start: 0.8091 (tmm) cc_final: 0.7556 (tmm) REVERT: F 187 GLU cc_start: 0.4310 (OUTLIER) cc_final: 0.3686 (pt0) REVERT: F 203 MET cc_start: 0.6333 (ppp) cc_final: 0.5778 (ppp) REVERT: F 245 TRP cc_start: 0.5541 (t60) cc_final: 0.5328 (t60) outliers start: 24 outliers final: 12 residues processed: 225 average time/residue: 0.2309 time to fit residues: 74.9408 Evaluate side-chains 203 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 190 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 364 THR 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 175 THR 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 74 optimal weight: 0.3980 chunk 41 optimal weight: 0.3980 chunk 111 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 134 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN E 211 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12013 Z= 0.191 Angle : 0.553 11.996 16223 Z= 0.267 Chirality : 0.036 0.236 1906 Planarity : 0.004 0.043 2069 Dihedral : 5.031 57.284 1673 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.95 % Allowed : 10.96 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.22), residues: 1498 helix: 2.42 (0.15), residues: 1166 sheet: 1.12 (0.97), residues: 32 loop : -0.27 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP F 177 HIS 0.006 0.001 HIS E 337 PHE 0.017 0.002 PHE A 90 TYR 0.023 0.002 TYR A 186 ARG 0.005 0.000 ARG C 339 *********************** 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 225 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 201 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7496 (mtpt) cc_final: 0.6796 (mmtm) REVERT: B 211 ILE cc_start: 0.9132 (tt) cc_final: 0.8930 (tt) REVERT: B 318 ASP cc_start: 0.7775 (t0) cc_final: 0.7392 (t0) REVERT: C 333 ASN cc_start: 0.6014 (t0) cc_final: 0.5103 (t0) REVERT: C 337 HIS cc_start: 0.4715 (m170) cc_final: 0.4059 (m90) REVERT: D 334 GLN cc_start: 0.6581 (mm-40) cc_final: 0.6231 (mp10) REVERT: E 267 ASP cc_start: 0.6719 (t0) cc_final: 0.6510 (m-30) REVERT: E 318 MET cc_start: 0.4691 (mmt) cc_final: 0.3990 (mmt) REVERT: E 322 MET cc_start: 0.8106 (tmm) cc_final: 0.7572 (tmm) REVERT: F 322 MET cc_start: 0.5382 (mtm) cc_final: 0.4766 (mtm) REVERT: F 326 GLN cc_start: 0.7303 (tp40) cc_final: 0.6998 (mp10) outliers start: 24 outliers final: 18 residues processed: 213 average time/residue: 0.2276 time to fit residues: 69.8413 Evaluate side-chains 202 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 184 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 364 THR 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 364 THR Chi-restraints excluded: chain C residue 192 LEU 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 273 VAL Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 175 THR 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 133 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 90 optimal weight: 0.3980 chunk 135 optimal weight: 0.0370 chunk 143 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 128 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 ASN D 367 HIS E 210 ASN E 211 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12013 Z= 0.182 Angle : 0.534 9.829 16223 Z= 0.260 Chirality : 0.035 0.152 1906 Planarity : 0.004 0.045 2069 Dihedral : 5.120 59.824 1673 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.35 % Allowed : 11.85 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.22), residues: 1498 helix: 2.49 (0.15), residues: 1164 sheet: 1.24 (0.96), residues: 32 loop : -0.03 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 245 HIS 0.006 0.001 HIS D 367 PHE 0.013 0.001 PHE A 91 TYR 0.022 0.002 TYR A 186 ARG 0.006 0.000 ARG E 339 *********************** 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 227 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 198 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7513 (mtpt) cc_final: 0.6695 (mmtm) REVERT: B 211 ILE cc_start: 0.9047 (tt) cc_final: 0.8816 (tt) REVERT: B 318 ASP cc_start: 0.7776 (t0) cc_final: 0.7383 (t0) REVERT: C 333 ASN cc_start: 0.6053 (t0) cc_final: 0.5070 (t0) REVERT: C 337 HIS cc_start: 0.4731 (m170) cc_final: 0.4341 (m90) REVERT: D 364 GLU cc_start: 0.6857 (pp20) cc_final: 0.6599 (tt0) REVERT: E 212 TYR cc_start: 0.7760 (m-80) cc_final: 0.7444 (m-80) REVERT: E 267 ASP cc_start: 0.6701 (t0) cc_final: 0.6490 (m-30) REVERT: E 318 MET cc_start: 0.4773 (mmt) cc_final: 0.4195 (mmt) REVERT: E 322 MET cc_start: 0.8040 (tmm) cc_final: 0.7496 (tmm) REVERT: F 188 ILE cc_start: 0.3689 (OUTLIER) cc_final: 0.3421 (mm) outliers start: 29 outliers final: 18 residues processed: 215 average time/residue: 0.2248 time to fit residues: 70.6600 Evaluate side-chains 205 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 186 time to evaluate : 1.433 ------------------------------------------------------------------------------- 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 A residue 364 THR 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 364 THR 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 273 VAL Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain F residue 175 THR 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 119 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 122 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 HIS E 210 ASN E 211 HIS E 305 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12013 Z= 0.294 Angle : 0.617 10.882 16223 Z= 0.304 Chirality : 0.038 0.221 1906 Planarity : 0.004 0.052 2069 Dihedral : 5.934 58.416 1673 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.68 % Allowed : 12.91 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.22), residues: 1498 helix: 2.29 (0.15), residues: 1148 sheet: 0.76 (1.01), residues: 32 loop : 0.07 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP F 177 HIS 0.007 0.001 HIS C 211 PHE 0.015 0.002 PHE B 63 TYR 0.023 0.002 TYR A 186 ARG 0.006 0.001 ARG C 339 *********************** 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 228 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 195 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 SER cc_start: 0.8850 (m) cc_final: 0.8636 (m) REVERT: A 340 LYS cc_start: 0.7499 (mtpt) cc_final: 0.6743 (mmtm) REVERT: B 318 ASP cc_start: 0.7788 (t0) cc_final: 0.7336 (t0) REVERT: C 231 MET cc_start: 0.6777 (OUTLIER) cc_final: 0.6557 (mtm) REVERT: C 333 ASN cc_start: 0.5997 (t0) cc_final: 0.4796 (t0) REVERT: C 337 HIS cc_start: 0.4867 (m170) cc_final: 0.4417 (m90) REVERT: E 318 MET cc_start: 0.4977 (mmt) cc_final: 0.4473 (mmt) REVERT: E 322 MET cc_start: 0.8079 (tmm) cc_final: 0.7601 (tmm) outliers start: 33 outliers final: 23 residues processed: 214 average time/residue: 0.2359 time to fit residues: 73.6441 Evaluate side-chains 208 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 184 time to evaluate : 1.381 ------------------------------------------------------------------------------- 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 147 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 364 THR 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 270 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 275 ASN 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 175 THR Chi-restraints excluded: chain F residue 208 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.0870 chunk 128 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 ASN C 324 ASN C 337 HIS D 367 HIS E 211 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12013 Z= 0.183 Angle : 0.554 10.820 16223 Z= 0.267 Chirality : 0.036 0.287 1906 Planarity : 0.004 0.052 2069 Dihedral : 5.489 55.330 1673 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.70 % Allowed : 15.83 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.22), residues: 1498 helix: 2.45 (0.15), residues: 1152 sheet: -0.08 (1.11), residues: 20 loop : 0.15 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 245 HIS 0.006 0.001 HIS D 367 PHE 0.018 0.001 PHE F 216 TYR 0.022 0.002 TYR A 186 ARG 0.005 0.000 ARG C 236 *********************** 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 212 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 191 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 SER cc_start: 0.8767 (m) cc_final: 0.8561 (m) REVERT: A 287 LYS cc_start: 0.7691 (ptmt) cc_final: 0.7431 (ptmt) REVERT: A 340 LYS cc_start: 0.7457 (mtpt) cc_final: 0.6749 (mmtm) REVERT: C 333 ASN cc_start: 0.6094 (t0) cc_final: 0.4701 (t0) REVERT: C 337 HIS cc_start: 0.4726 (m-70) cc_final: 0.4451 (m-70) REVERT: C 339 ARG cc_start: 0.6857 (mtt-85) cc_final: 0.6649 (mtt180) REVERT: E 263 GLU cc_start: 0.7330 (pt0) cc_final: 0.6955 (mt-10) REVERT: E 267 ASP cc_start: 0.6824 (t70) cc_final: 0.6561 (m-30) REVERT: E 318 MET cc_start: 0.4941 (mmt) cc_final: 0.4625 (mmt) REVERT: E 322 MET cc_start: 0.8053 (tmm) cc_final: 0.7557 (tmm) REVERT: F 259 MET cc_start: -0.0391 (mmt) cc_final: -0.0705 (mmt) REVERT: F 318 MET cc_start: 0.2273 (mmm) cc_final: 0.1804 (mmm) REVERT: F 339 ARG cc_start: 0.6976 (tmm-80) cc_final: 0.6204 (tmm-80) outliers start: 21 outliers final: 17 residues processed: 200 average time/residue: 0.2201 time to fit residues: 65.3117 Evaluate side-chains 200 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 183 time to evaluate : 1.528 ------------------------------------------------------------------------------- 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 299 LEU Chi-restraints excluded: chain A residue 364 THR 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 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 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 138 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12013 Z= 0.291 Angle : 0.640 12.921 16223 Z= 0.311 Chirality : 0.039 0.310 1906 Planarity : 0.004 0.058 2069 Dihedral : 5.845 53.431 1673 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.44 % Allowed : 15.58 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.22), residues: 1498 helix: 2.17 (0.15), residues: 1150 sheet: -1.23 (0.97), residues: 24 loop : 0.08 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP F 177 HIS 0.006 0.001 HIS A 300 PHE 0.021 0.002 PHE C 331 TYR 0.022 0.002 TYR A 186 ARG 0.005 0.001 ARG D 236 *********************** 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 221 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 191 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7546 (mtpt) cc_final: 0.6862 (mmtm) REVERT: B 211 ILE cc_start: 0.8901 (tt) cc_final: 0.8519 (tp) REVERT: C 192 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8198 (tt) REVERT: E 263 GLU cc_start: 0.7360 (pt0) cc_final: 0.6835 (mt-10) REVERT: E 318 MET cc_start: 0.4379 (mmt) cc_final: 0.4089 (mmt) REVERT: E 322 MET cc_start: 0.8077 (tmm) cc_final: 0.7610 (tmm) REVERT: F 246 ILE cc_start: 0.7374 (mt) cc_final: 0.6939 (mt) REVERT: F 339 ARG cc_start: 0.6972 (tmm-80) cc_final: 0.6244 (tmm-80) outliers start: 30 outliers final: 27 residues processed: 207 average time/residue: 0.2212 time to fit residues: 66.6901 Evaluate side-chains 211 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 183 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 164 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 364 THR 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 364 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 275 ASN 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 175 THR Chi-restraints excluded: chain F residue 203 MET 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 56 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 42 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 129 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 ASN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 ASN F 305 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12013 Z= 0.199 Angle : 0.584 11.588 16223 Z= 0.281 Chirality : 0.037 0.351 1906 Planarity : 0.004 0.057 2069 Dihedral : 5.447 51.255 1673 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.19 % Allowed : 16.88 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.22), residues: 1498 helix: 2.35 (0.15), residues: 1150 sheet: -0.68 (1.11), residues: 20 loop : 0.12 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 245 HIS 0.006 0.001 HIS E 211 PHE 0.019 0.001 PHE C 331 TYR 0.021 0.002 TYR A 186 ARG 0.004 0.000 ARG D 370 *********************** 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 fitting. rotamer outliers: 27 poor density : 192 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7473 (mtpt) cc_final: 0.6711 (mmtm) REVERT: B 211 ILE cc_start: 0.8735 (tt) cc_final: 0.8354 (tp) REVERT: C 192 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8107 (tt) REVERT: C 250 ARG cc_start: 0.7860 (mmm160) cc_final: 0.7408 (mmm160) REVERT: D 306 ILE cc_start: 0.5151 (mm) cc_final: 0.4889 (tp) REVERT: D 364 GLU cc_start: 0.6909 (pp20) cc_final: 0.6472 (tt0) REVERT: E 263 GLU cc_start: 0.7260 (pt0) cc_final: 0.6911 (mt-10) REVERT: E 265 LEU cc_start: 0.7978 (mt) cc_final: 0.7650 (mp) REVERT: E 318 MET cc_start: 0.4431 (mmt) cc_final: 0.4168 (mmt) REVERT: E 322 MET cc_start: 0.8040 (tmm) cc_final: 0.7569 (tmm) outliers start: 27 outliers final: 23 residues processed: 206 average time/residue: 0.2211 time to fit residues: 66.5268 Evaluate side-chains 209 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 185 time to evaluate : 1.334 ------------------------------------------------------------------------------- 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 164 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 364 THR 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 364 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 215 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 203 MET Chi-restraints excluded: chain F residue 208 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 57 optimal weight: 0.1980 chunk 104 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 ASN C 337 HIS ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 ASN E 211 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12013 Z= 0.227 Angle : 0.611 11.906 16223 Z= 0.297 Chirality : 0.038 0.334 1906 Planarity : 0.004 0.058 2069 Dihedral : 5.600 50.401 1673 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.35 % Allowed : 17.29 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.22), residues: 1498 helix: 2.27 (0.15), residues: 1148 sheet: -0.79 (1.10), residues: 20 loop : 0.02 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP F 177 HIS 0.007 0.001 HIS C 337 PHE 0.020 0.001 PHE C 331 TYR 0.022 0.002 TYR A 186 ARG 0.010 0.001 ARG C 339 *********************** 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 215 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 186 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7525 (mtpt) cc_final: 0.6717 (mmtm) REVERT: B 211 ILE cc_start: 0.8817 (tt) cc_final: 0.8400 (tp) REVERT: B 318 ASP cc_start: 0.7740 (t0) cc_final: 0.7337 (t0) REVERT: B 397 ILE cc_start: 0.8200 (tp) cc_final: 0.7966 (tp) REVERT: C 192 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8133 (tt) REVERT: C 348 LYS cc_start: 0.7603 (mptt) cc_final: 0.6633 (pttp) REVERT: D 306 ILE cc_start: 0.5188 (mm) cc_final: 0.4926 (tp) REVERT: D 364 GLU cc_start: 0.6954 (pp20) cc_final: 0.6513 (tt0) REVERT: E 263 GLU cc_start: 0.7284 (pt0) cc_final: 0.6942 (mt-10) REVERT: E 265 LEU cc_start: 0.7978 (mt) cc_final: 0.7683 (mp) REVERT: E 318 MET cc_start: 0.4432 (mmt) cc_final: 0.4180 (mmt) REVERT: E 322 MET cc_start: 0.8099 (tmm) cc_final: 0.7611 (tmm) REVERT: F 339 ARG cc_start: 0.6466 (tmm-80) cc_final: 0.6068 (tmm-80) outliers start: 29 outliers final: 25 residues processed: 202 average time/residue: 0.2379 time to fit residues: 69.7572 Evaluate side-chains 209 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 183 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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 147 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 364 THR 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 364 THR Chi-restraints excluded: chain C residue 192 LEU 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 246 ILE 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 203 MET 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 85 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 135 optimal weight: 0.2980 chunk 117 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12013 Z= 0.206 Angle : 0.604 11.894 16223 Z= 0.294 Chirality : 0.037 0.303 1906 Planarity : 0.004 0.058 2069 Dihedral : 5.584 54.690 1673 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.95 % Allowed : 17.86 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.22), residues: 1498 helix: 2.30 (0.15), residues: 1148 sheet: -0.81 (1.08), residues: 20 loop : -0.10 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 245 HIS 0.012 0.001 HIS C 337 PHE 0.019 0.001 PHE C 331 TYR 0.021 0.002 TYR A 186 ARG 0.008 0.000 ARG C 339 ********************** 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 214 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 190 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7479 (mtpt) cc_final: 0.6684 (mmtm) REVERT: B 211 ILE cc_start: 0.8753 (tt) cc_final: 0.8336 (tp) REVERT: B 318 ASP cc_start: 0.7697 (t0) cc_final: 0.7295 (t0) REVERT: B 397 ILE cc_start: 0.8128 (tp) cc_final: 0.7872 (tp) REVERT: C 192 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8149 (tt) REVERT: D 306 ILE cc_start: 0.5201 (mm) cc_final: 0.4957 (tp) REVERT: D 364 GLU cc_start: 0.6944 (pp20) cc_final: 0.6504 (tt0) REVERT: E 263 GLU cc_start: 0.7335 (pt0) cc_final: 0.6953 (mt-10) REVERT: E 265 LEU cc_start: 0.7951 (mt) cc_final: 0.7656 (mp) REVERT: E 318 MET cc_start: 0.4395 (mmt) cc_final: 0.4169 (mmt) REVERT: E 322 MET cc_start: 0.8100 (tmm) cc_final: 0.7634 (tmm) REVERT: F 177 TRP cc_start: 0.3917 (t60) cc_final: 0.3626 (t60) outliers start: 24 outliers final: 23 residues processed: 203 average time/residue: 0.2200 time to fit residues: 65.1212 Evaluate side-chains 208 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 184 time to evaluate : 1.367 ------------------------------------------------------------------------------- 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 164 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 364 THR 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 364 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 206 ASP 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 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 203 MET 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 35 optimal weight: 0.0970 chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 6 optimal weight: 0.0570 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.221157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.186618 restraints weight = 20179.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.184257 restraints weight = 15086.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.186443 restraints weight = 12697.207| |-----------------------------------------------------------------------------| r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12013 Z= 0.165 Angle : 0.580 12.176 16223 Z= 0.280 Chirality : 0.036 0.311 1906 Planarity : 0.004 0.058 2069 Dihedral : 5.332 56.608 1673 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.03 % Allowed : 18.02 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.22), residues: 1498 helix: 2.45 (0.16), residues: 1148 sheet: -0.42 (1.14), residues: 20 loop : -0.14 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 245 HIS 0.012 0.001 HIS C 337 PHE 0.020 0.001 PHE F 216 TYR 0.020 0.001 TYR A 186 ARG 0.011 0.000 ARG F 339 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2448.61 seconds wall clock time: 46 minutes 9.69 seconds (2769.69 seconds total)