Starting phenix.real_space_refine on Tue Jun 10 18:38:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tac_25769/06_2025/7tac_25769.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tac_25769/06_2025/7tac_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/cci-nas-00/data/ceres_data/7tac_25769/06_2025/7tac_25769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tac_25769/06_2025/7tac_25769.map" model { file = "/net/cci-nas-00/data/ceres_data/7tac_25769/06_2025/7tac_25769.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tac_25769/06_2025/7tac_25769.cif" } 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. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.96, per 1000 atoms: 0.76 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: 3.51 Conformation dependent library (CDL) restraints added in 1.7 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... 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: 1.21 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: 3.46 Time building geometry restraints manager: 3.96 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 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: 3.350 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.810 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.360 ------------------------------------------------------------------------------- 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 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.12905 ( 937) hydrogen bonds : angle 4.55537 ( 2754) metal coordination : bond 0.01406 ( 8) metal coordination : angle 2.98535 ( 6) covalent geometry : bond 0.00421 (12013) covalent geometry : angle 0.85591 (16223) *********************** 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 : 1.443 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: 73.4175 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 : 1.476 ------------------------------------------------------------------------------- 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: 0.5980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 0.0980 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 134 optimal weight: 0.7980 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 B 269 ASN B 290 HIS C 176 HIS ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4721 r_free = 0.4721 target = 0.225936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.190018 restraints weight = 20288.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.187911 restraints weight = 14269.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.189571 restraints weight = 10842.001| |-----------------------------------------------------------------------------| r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12021 Z= 0.148 Angle : 0.624 12.105 16229 Z= 0.308 Chirality : 0.038 0.175 1906 Planarity : 0.004 0.044 2069 Dihedral : 5.303 59.744 1673 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.70 % Allowed : 8.28 % 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 (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 (0.21), residues: 1498 helix: 2.20 (0.15), residues: 1192 sheet: 0.32 (1.10), residues: 20 loop : -0.43 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP F 177 HIS 0.012 0.001 HIS C 176 PHE 0.019 0.002 PHE B 90 TYR 0.024 0.002 TYR A 186 ARG 0.005 0.001 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.04370 ( 937) hydrogen bonds : angle 3.77465 ( 2754) metal coordination : bond 0.01183 ( 8) metal coordination : angle 1.85597 ( 6) covalent geometry : bond 0.00329 (12013) covalent geometry : angle 0.62311 (16223) *********************** 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: 21 poor density : 205 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7599 (mtpt) cc_final: 0.6782 (mmtm) REVERT: B 318 ASP cc_start: 0.8238 (t0) cc_final: 0.7929 (t0) REVERT: C 333 ASN cc_start: 0.6288 (t0) cc_final: 0.5426 (t0) REVERT: C 337 HIS cc_start: 0.4866 (m170) cc_final: 0.4212 (m90) REVERT: C 348 LYS cc_start: 0.7216 (mptt) cc_final: 0.6220 (pttp) REVERT: D 193 GLN cc_start: 0.7324 (pp30) cc_final: 0.6961 (pt0) REVERT: E 318 MET cc_start: 0.5107 (mmt) cc_final: 0.4259 (mmt) REVERT: E 322 MET cc_start: 0.8408 (tmm) cc_final: 0.7844 (tmm) REVERT: F 203 MET cc_start: 0.6702 (ppp) cc_final: 0.6290 (ppp) REVERT: F 231 MET cc_start: 0.3941 (mtm) cc_final: 0.3670 (mtt) outliers start: 21 outliers final: 14 residues processed: 215 average time/residue: 0.2455 time to fit residues: 75.9369 Evaluate side-chains 196 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 1.443 ------------------------------------------------------------------------------- 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 E residue 328 LEU 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 2 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 43 optimal weight: 0.0050 chunk 128 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 147 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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** D 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.224365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.188136 restraints weight = 20588.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.186874 restraints weight = 13434.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.188078 restraints weight = 10339.055| |-----------------------------------------------------------------------------| r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12021 Z= 0.140 Angle : 0.575 11.063 16229 Z= 0.282 Chirality : 0.037 0.204 1906 Planarity : 0.004 0.042 2069 Dihedral : 5.166 56.408 1673 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.03 % Allowed : 11.28 % Favored : 86.69 % 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: 2.96 (0.22), residues: 1498 helix: 2.46 (0.15), residues: 1196 sheet: 0.16 (1.07), residues: 20 loop : -0.12 (0.38), residues: 282 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 0.015 0.001 PHE A 91 TYR 0.024 0.002 TYR A 186 ARG 0.003 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 937) hydrogen bonds : angle 3.64405 ( 2754) metal coordination : bond 0.00793 ( 8) metal coordination : angle 1.85039 ( 6) covalent geometry : bond 0.00319 (12013) covalent geometry : angle 0.57397 (16223) *********************** 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 223 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 318 ASP cc_start: 0.8276 (t0) cc_final: 0.7940 (t0) REVERT: C 203 MET cc_start: 0.6827 (mpp) cc_final: 0.6040 (mpp) REVERT: C 235 TRP cc_start: 0.6838 (p-90) cc_final: 0.6353 (p-90) REVERT: C 333 ASN cc_start: 0.6308 (t0) cc_final: 0.5297 (t0) REVERT: C 337 HIS cc_start: 0.4834 (m170) cc_final: 0.4063 (m90) REVERT: C 348 LYS cc_start: 0.7377 (mptt) cc_final: 0.6332 (pttp) REVERT: D 203 MET cc_start: 0.3078 (mpp) cc_final: 0.2848 (mpp) REVERT: E 250 ARG cc_start: 0.6711 (ptm160) cc_final: 0.6508 (ptm160) REVERT: E 318 MET cc_start: 0.4888 (mmt) cc_final: 0.4140 (mmt) REVERT: E 322 MET cc_start: 0.8366 (tmm) cc_final: 0.7712 (tmm) REVERT: E 329 GLU cc_start: 0.7565 (tp30) cc_final: 0.7270 (tt0) REVERT: F 322 MET cc_start: 0.5497 (mtm) cc_final: 0.4743 (mtm) REVERT: F 326 GLN cc_start: 0.7452 (tp40) cc_final: 0.6966 (mp10) outliers start: 25 outliers final: 16 residues processed: 210 average time/residue: 0.2258 time to fit residues: 68.3841 Evaluate side-chains 200 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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 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 142 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 334 GLN D 367 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.220876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.185051 restraints weight = 20338.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.182756 restraints weight = 13576.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.184595 restraints weight = 13178.266| |-----------------------------------------------------------------------------| r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12021 Z= 0.174 Angle : 0.620 10.003 16229 Z= 0.306 Chirality : 0.039 0.193 1906 Planarity : 0.004 0.048 2069 Dihedral : 5.768 55.495 1673 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.44 % Allowed : 12.66 % Favored : 84.90 % 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: 2.97 (0.22), residues: 1498 helix: 2.40 (0.15), residues: 1190 sheet: 0.60 (0.96), residues: 32 loop : 0.19 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 245 HIS 0.005 0.001 HIS B 266 PHE 0.014 0.002 PHE A 91 TYR 0.024 0.002 TYR A 186 ARG 0.010 0.001 ARG F 250 Details of bonding type rmsd hydrogen bonds : bond 0.04223 ( 937) hydrogen bonds : angle 3.75642 ( 2754) metal coordination : bond 0.00764 ( 8) metal coordination : angle 2.12730 ( 6) covalent geometry : bond 0.00405 (12013) covalent geometry : angle 0.61887 (16223) *********************** 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 229 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 318 ASP cc_start: 0.8256 (t0) cc_final: 0.8022 (t0) REVERT: C 235 TRP cc_start: 0.6925 (p-90) cc_final: 0.6386 (p-90) REVERT: C 333 ASN cc_start: 0.6346 (t0) cc_final: 0.5315 (t0) REVERT: C 337 HIS cc_start: 0.4827 (m170) cc_final: 0.4291 (m90) REVERT: E 211 HIS cc_start: 0.7191 (t70) cc_final: 0.6981 (t70) REVERT: E 250 ARG cc_start: 0.6780 (ptm160) cc_final: 0.6552 (ptm160) REVERT: E 318 MET cc_start: 0.4980 (mmt) cc_final: 0.4349 (mmt) REVERT: E 322 MET cc_start: 0.8297 (tmm) cc_final: 0.7704 (tmm) REVERT: F 216 PHE cc_start: 0.5224 (m-10) cc_final: 0.4993 (m-10) REVERT: F 326 GLN cc_start: 0.7420 (tp40) cc_final: 0.6921 (mp10) outliers start: 30 outliers final: 21 residues processed: 214 average time/residue: 0.2186 time to fit residues: 68.8118 Evaluate side-chains 204 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 1.330 ------------------------------------------------------------------------------- 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 270 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 262 VAL 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 275 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 33 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 48 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: ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 HIS E 305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.220790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.184481 restraints weight = 20181.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.182949 restraints weight = 14210.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.184353 restraints weight = 10558.261| |-----------------------------------------------------------------------------| r_work (final): 0.4321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12021 Z= 0.153 Angle : 0.598 10.598 16229 Z= 0.292 Chirality : 0.038 0.162 1906 Planarity : 0.004 0.053 2069 Dihedral : 5.709 58.667 1673 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.11 % Allowed : 14.61 % Favored : 83.28 % 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: 2.46 (0.15), residues: 1188 sheet: -1.12 (0.93), residues: 24 loop : 0.20 (0.40), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 177 HIS 0.005 0.001 HIS D 367 PHE 0.011 0.001 PHE C 331 TYR 0.023 0.002 TYR A 186 ARG 0.005 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.03929 ( 937) hydrogen bonds : angle 3.67565 ( 2754) metal coordination : bond 0.00895 ( 8) metal coordination : angle 2.35880 ( 6) covalent geometry : bond 0.00351 (12013) covalent geometry : angle 0.59688 (16223) *********************** 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 221 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 211 ILE cc_start: 0.9127 (tt) cc_final: 0.8746 (tt) REVERT: B 318 ASP cc_start: 0.8217 (t0) cc_final: 0.7950 (t0) REVERT: C 192 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7505 (tt) REVERT: C 235 TRP cc_start: 0.6941 (p-90) cc_final: 0.6522 (p-90) REVERT: C 333 ASN cc_start: 0.6409 (t0) cc_final: 0.5307 (t0) REVERT: C 337 HIS cc_start: 0.4872 (m170) cc_final: 0.4294 (m90) REVERT: D 203 MET cc_start: 0.3020 (OUTLIER) cc_final: 0.2808 (mpp) REVERT: D 364 GLU cc_start: 0.7552 (pt0) cc_final: 0.7283 (pp20) REVERT: E 211 HIS cc_start: 0.7259 (t70) cc_final: 0.6966 (t70) REVERT: E 263 GLU cc_start: 0.7866 (pt0) cc_final: 0.7428 (mt-10) REVERT: E 318 MET cc_start: 0.5094 (mmt) cc_final: 0.4721 (mmt) REVERT: E 322 MET cc_start: 0.8302 (tmm) cc_final: 0.8012 (ppp) REVERT: F 245 TRP cc_start: 0.5765 (t60) cc_final: 0.5508 (t60) outliers start: 26 outliers final: 19 residues processed: 210 average time/residue: 0.2240 time to fit residues: 68.4375 Evaluate side-chains 201 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 192 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 52 optimal weight: 0.0370 chunk 50 optimal weight: 0.9990 chunk 140 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.0370 chunk 7 optimal weight: 0.5980 chunk 118 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 HIS ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 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 = 0.222419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.186411 restraints weight = 20299.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.185726 restraints weight = 12829.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.186901 restraints weight = 9727.940| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.3096 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= 0.123 Angle : 0.573 10.546 16229 Z= 0.276 Chirality : 0.037 0.296 1906 Planarity : 0.004 0.051 2069 Dihedral : 5.287 59.799 1673 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.27 % Allowed : 15.91 % Favored : 81.82 % 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: 3.11 (0.22), residues: 1498 helix: 2.55 (0.15), residues: 1192 sheet: -1.02 (0.94), residues: 24 loop : 0.20 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 177 HIS 0.006 0.001 HIS D 367 PHE 0.019 0.001 PHE C 331 TYR 0.021 0.002 TYR A 186 ARG 0.006 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 937) hydrogen bonds : angle 3.58633 ( 2754) metal coordination : bond 0.00684 ( 8) metal coordination : angle 2.12599 ( 6) covalent geometry : bond 0.00271 (12013) covalent geometry : angle 0.57146 (16223) *********************** 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 230 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 LYS cc_start: 0.7814 (ptmt) cc_final: 0.7570 (ptmt) REVERT: B 211 ILE cc_start: 0.9103 (tt) cc_final: 0.8816 (tt) REVERT: B 283 LYS cc_start: 0.8627 (mttt) cc_final: 0.8350 (mttt) REVERT: B 318 ASP cc_start: 0.8284 (t0) cc_final: 0.8021 (t0) REVERT: C 186 SER cc_start: 0.7645 (t) cc_final: 0.7398 (p) REVERT: C 192 LEU cc_start: 0.7959 (tt) cc_final: 0.7472 (tt) REVERT: C 235 TRP cc_start: 0.6916 (p-90) cc_final: 0.6493 (p-90) REVERT: C 333 ASN cc_start: 0.6551 (t0) cc_final: 0.5198 (t0) REVERT: C 337 HIS cc_start: 0.4840 (m-70) cc_final: 0.4380 (m-70) REVERT: D 364 GLU cc_start: 0.7413 (pt0) cc_final: 0.7153 (pp20) REVERT: E 200 GLU cc_start: 0.7894 (pm20) cc_final: 0.7630 (pm20) REVERT: E 211 HIS cc_start: 0.7170 (t70) cc_final: 0.6896 (t70) REVERT: E 263 GLU cc_start: 0.7792 (pt0) cc_final: 0.7455 (mt-10) REVERT: E 267 ASP cc_start: 0.7045 (t70) cc_final: 0.6625 (m-30) REVERT: E 318 MET cc_start: 0.5006 (mmt) cc_final: 0.4614 (mmt) REVERT: E 322 MET cc_start: 0.8317 (tmm) cc_final: 0.7784 (tmm) outliers start: 28 outliers final: 19 residues processed: 215 average time/residue: 0.2109 time to fit residues: 67.1332 Evaluate side-chains 205 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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 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 17 optimal weight: 0.0980 chunk 138 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 56 optimal weight: 0.2980 chunk 116 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 HIS E 344 GLN 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 = 0.222473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.186237 restraints weight = 20394.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.185395 restraints weight = 13129.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.186196 restraints weight = 9827.571| |-----------------------------------------------------------------------------| r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12021 Z= 0.129 Angle : 0.588 10.597 16229 Z= 0.283 Chirality : 0.037 0.203 1906 Planarity : 0.004 0.051 2069 Dihedral : 5.176 57.023 1673 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.27 % Allowed : 16.96 % Favored : 80.76 % 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: 3.13 (0.22), residues: 1498 helix: 2.57 (0.15), residues: 1192 sheet: -1.09 (0.94), residues: 24 loop : 0.17 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 245 HIS 0.009 0.001 HIS C 211 PHE 0.017 0.001 PHE C 331 TYR 0.021 0.002 TYR A 186 ARG 0.007 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 937) hydrogen bonds : angle 3.62481 ( 2754) metal coordination : bond 0.00592 ( 8) metal coordination : angle 2.02647 ( 6) covalent geometry : bond 0.00292 (12013) covalent geometry : angle 0.58635 (16223) *********************** 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 223 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 LYS cc_start: 0.7771 (ptmt) cc_final: 0.7530 (ptmt) REVERT: B 211 ILE cc_start: 0.9116 (tt) cc_final: 0.8757 (tt) REVERT: B 283 LYS cc_start: 0.8606 (mttt) cc_final: 0.8353 (mttt) REVERT: B 318 ASP cc_start: 0.8292 (t0) cc_final: 0.8018 (t0) REVERT: B 397 ILE cc_start: 0.7974 (tp) cc_final: 0.7732 (tp) REVERT: C 192 LEU cc_start: 0.7985 (tt) cc_final: 0.7508 (tt) REVERT: C 235 TRP cc_start: 0.6942 (p-90) cc_final: 0.6490 (p-90) REVERT: C 345 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7308 (mp10) REVERT: D 364 GLU cc_start: 0.7443 (pt0) cc_final: 0.6932 (tt0) REVERT: E 200 GLU cc_start: 0.7912 (pm20) cc_final: 0.7630 (pm20) REVERT: E 211 HIS cc_start: 0.7179 (t70) cc_final: 0.6898 (t70) REVERT: E 263 GLU cc_start: 0.7801 (pt0) cc_final: 0.7462 (mt-10) REVERT: E 267 ASP cc_start: 0.7003 (t70) cc_final: 0.6625 (m-30) REVERT: E 318 MET cc_start: 0.4823 (mmt) cc_final: 0.4518 (mmt) REVERT: E 322 MET cc_start: 0.8322 (tmm) cc_final: 0.7788 (tmm) REVERT: F 246 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6594 (mt) REVERT: F 259 MET cc_start: -0.0576 (mmt) cc_final: -0.0879 (mmt) outliers start: 28 outliers final: 20 residues processed: 212 average time/residue: 0.2183 time to fit residues: 68.4620 Evaluate side-chains 209 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 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 246 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 6 optimal weight: 0.0050 chunk 32 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 136 optimal weight: 0.0980 chunk 132 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 50 optimal weight: 0.0870 chunk 90 optimal weight: 1.9990 overall best weight: 0.3372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4699 r_free = 0.4699 target = 0.223715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.188133 restraints weight = 20371.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.188071 restraints weight = 13171.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.189689 restraints weight = 9777.260| |-----------------------------------------------------------------------------| r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.3341 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= 0.117 Angle : 0.582 10.320 16229 Z= 0.278 Chirality : 0.037 0.249 1906 Planarity : 0.003 0.050 2069 Dihedral : 4.933 57.253 1673 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.22), residues: 1498 helix: 2.60 (0.15), residues: 1192 sheet: -0.85 (0.97), residues: 24 loop : 0.14 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 177 HIS 0.007 0.001 HIS C 211 PHE 0.016 0.001 PHE C 331 TYR 0.019 0.001 TYR A 186 ARG 0.006 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 937) hydrogen bonds : angle 3.58362 ( 2754) metal coordination : bond 0.00641 ( 8) metal coordination : angle 1.95781 ( 6) covalent geometry : bond 0.00256 (12013) covalent geometry : angle 0.58086 (16223) *********************** 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 225 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.7603 (tpt90) cc_final: 0.7344 (tpt170) REVERT: A 287 LYS cc_start: 0.7596 (ptmt) cc_final: 0.7394 (ptmt) REVERT: B 181 GLU cc_start: 0.7158 (mp0) cc_final: 0.6854 (mp0) REVERT: B 211 ILE cc_start: 0.9119 (tt) cc_final: 0.8853 (tt) REVERT: B 283 LYS cc_start: 0.8580 (mttt) cc_final: 0.8331 (mttt) REVERT: B 318 ASP cc_start: 0.8301 (t0) cc_final: 0.8023 (t0) REVERT: B 397 ILE cc_start: 0.7934 (tp) cc_final: 0.7705 (tp) REVERT: C 192 LEU cc_start: 0.7954 (tt) cc_final: 0.7471 (tt) REVERT: C 235 TRP cc_start: 0.6878 (p-90) cc_final: 0.6415 (p-90) REVERT: C 345 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7158 (mp10) REVERT: D 364 GLU cc_start: 0.7468 (pt0) cc_final: 0.6946 (tt0) REVERT: E 263 GLU cc_start: 0.7729 (pt0) cc_final: 0.7445 (mt-10) REVERT: E 267 ASP cc_start: 0.7026 (t70) cc_final: 0.6597 (m-30) REVERT: E 318 MET cc_start: 0.4593 (mmt) cc_final: 0.4256 (mmt) REVERT: E 322 MET cc_start: 0.8331 (tmm) cc_final: 0.7792 (tmm) REVERT: F 259 MET cc_start: -0.0526 (mmt) cc_final: -0.0802 (mmt) REVERT: F 318 MET cc_start: 0.1274 (mmm) cc_final: 0.0741 (mmm) outliers start: 25 outliers final: 20 residues processed: 214 average time/residue: 0.2217 time to fit residues: 68.9773 Evaluate side-chains 207 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 1.445 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 51 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 140 optimal weight: 5.9990 chunk 55 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 9 optimal weight: 0.1980 chunk 56 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.222939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.187406 restraints weight = 20343.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.186831 restraints weight = 12964.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.187403 restraints weight = 10053.395| |-----------------------------------------------------------------------------| r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 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 0.053 12021 Z= 0.128 Angle : 0.610 10.555 16229 Z= 0.296 Chirality : 0.038 0.307 1906 Planarity : 0.004 0.055 2069 Dihedral : 4.911 55.667 1673 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.87 % Allowed : 17.86 % Favored : 80.28 % 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: 3.15 (0.22), residues: 1498 helix: 2.60 (0.15), residues: 1192 sheet: -0.92 (0.96), residues: 24 loop : 0.07 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP F 177 HIS 0.007 0.001 HIS C 211 PHE 0.016 0.001 PHE C 331 TYR 0.020 0.002 TYR A 186 ARG 0.010 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 937) hydrogen bonds : angle 3.64385 ( 2754) metal coordination : bond 0.00568 ( 8) metal coordination : angle 1.96339 ( 6) covalent geometry : bond 0.00286 (12013) covalent geometry : angle 0.60915 (16223) *********************** 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 212 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: B 181 GLU cc_start: 0.7246 (mp0) cc_final: 0.7011 (mp0) REVERT: B 211 ILE cc_start: 0.9134 (tt) cc_final: 0.8862 (tt) REVERT: B 283 LYS cc_start: 0.8593 (mttt) cc_final: 0.8353 (mttt) REVERT: B 397 ILE cc_start: 0.7972 (tp) cc_final: 0.7717 (tp) REVERT: C 192 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7578 (tt) REVERT: C 235 TRP cc_start: 0.6977 (p-90) cc_final: 0.6467 (p-90) REVERT: C 345 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7256 (mp10) REVERT: D 364 GLU cc_start: 0.7452 (pt0) cc_final: 0.6929 (tt0) REVERT: E 263 GLU cc_start: 0.7824 (pt0) cc_final: 0.7493 (mt-10) REVERT: E 267 ASP cc_start: 0.6983 (t70) cc_final: 0.6597 (m-30) REVERT: E 318 MET cc_start: 0.4620 (mmt) cc_final: 0.4329 (mmt) REVERT: E 322 MET cc_start: 0.8314 (tmm) cc_final: 0.7782 (tmm) REVERT: F 259 MET cc_start: -0.0593 (mmt) cc_final: -0.0867 (mmt) outliers start: 23 outliers final: 21 residues processed: 201 average time/residue: 0.2166 time to fit residues: 64.5636 Evaluate side-chains 211 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 1.405 ------------------------------------------------------------------------------- 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 192 LEU 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 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 16 optimal weight: 0.9990 chunk 44 optimal weight: 0.0060 chunk 138 optimal weight: 0.0040 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 82 optimal weight: 0.0870 overall best weight: 0.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4712 r_free = 0.4712 target = 0.224981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.190191 restraints weight = 20139.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.188870 restraints weight = 12937.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.190359 restraints weight = 9827.580| |-----------------------------------------------------------------------------| r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.3507 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= 0.117 Angle : 0.619 10.963 16229 Z= 0.298 Chirality : 0.038 0.315 1906 Planarity : 0.004 0.074 2069 Dihedral : 4.686 51.791 1673 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.19 % Allowed : 18.02 % Favored : 79.79 % 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: 3.21 (0.22), residues: 1498 helix: 2.64 (0.15), residues: 1192 sheet: 0.02 (1.12), residues: 20 loop : 0.01 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 245 HIS 0.008 0.001 HIS D 337 PHE 0.014 0.001 PHE C 331 TYR 0.019 0.001 TYR A 186 ARG 0.011 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 937) hydrogen bonds : angle 3.63088 ( 2754) metal coordination : bond 0.00648 ( 8) metal coordination : angle 1.92869 ( 6) covalent geometry : bond 0.00251 (12013) covalent geometry : angle 0.61751 (16223) ********************** 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 227 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 181 GLU cc_start: 0.7109 (mp0) cc_final: 0.6843 (mp0) REVERT: B 211 ILE cc_start: 0.9116 (tt) cc_final: 0.8858 (tt) REVERT: B 283 LYS cc_start: 0.8567 (mttt) cc_final: 0.8338 (mttt) REVERT: B 397 ILE cc_start: 0.7764 (tp) cc_final: 0.7549 (tp) REVERT: C 192 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7403 (tt) REVERT: C 235 TRP cc_start: 0.6901 (p-90) cc_final: 0.6466 (p-90) REVERT: C 339 ARG cc_start: 0.6760 (mtt180) cc_final: 0.6408 (mtt-85) REVERT: C 345 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7069 (mp10) REVERT: D 364 GLU cc_start: 0.7455 (pt0) cc_final: 0.6935 (tt0) REVERT: E 263 GLU cc_start: 0.7734 (pt0) cc_final: 0.7456 (mt-10) REVERT: E 265 LEU cc_start: 0.7977 (mt) cc_final: 0.7648 (mp) REVERT: E 267 ASP cc_start: 0.6953 (t70) cc_final: 0.6584 (m-30) REVERT: E 322 MET cc_start: 0.8324 (tmm) cc_final: 0.7725 (tmm) outliers start: 27 outliers final: 22 residues processed: 215 average time/residue: 0.2114 time to fit residues: 66.8574 Evaluate side-chains 215 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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 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 198 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 192 LEU 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 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 349 ILE 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 100 optimal weight: 0.8980 chunk 76 optimal weight: 0.0980 chunk 129 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 132 optimal weight: 0.1980 chunk 133 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4694 r_free = 0.4694 target = 0.223095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.187923 restraints weight = 20257.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.186454 restraints weight = 13174.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.187793 restraints weight = 10116.148| |-----------------------------------------------------------------------------| r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12021 Z= 0.129 Angle : 0.624 10.912 16229 Z= 0.302 Chirality : 0.038 0.278 1906 Planarity : 0.004 0.067 2069 Dihedral : 4.764 47.881 1673 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.11 % Allowed : 18.10 % Favored : 79.79 % 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: 3.18 (0.22), residues: 1498 helix: 2.63 (0.15), residues: 1192 sheet: -0.74 (0.98), residues: 24 loop : 0.03 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP F 177 HIS 0.011 0.001 HIS D 337 PHE 0.015 0.001 PHE C 331 TYR 0.019 0.002 TYR A 186 ARG 0.008 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.03602 ( 937) hydrogen bonds : angle 3.66173 ( 2754) metal coordination : bond 0.00537 ( 8) metal coordination : angle 1.86945 ( 6) covalent geometry : bond 0.00288 (12013) covalent geometry : angle 0.62283 (16223) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4278.30 seconds wall clock time: 74 minutes 53.85 seconds (4493.85 seconds total)