Starting phenix.real_space_refine on Wed Feb 14 05:48:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id6_35358/02_2024/8id6_35358_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id6_35358/02_2024/8id6_35358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id6_35358/02_2024/8id6_35358.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id6_35358/02_2024/8id6_35358.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id6_35358/02_2024/8id6_35358_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id6_35358/02_2024/8id6_35358_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5596 2.51 5 N 1478 2.21 5 O 1597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8727 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2206 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 12, 'TRANS': 277} Chain breaks: 3 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 67 Chain: "A" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1769 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2569 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 28 Chain: "Y" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 409 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "S" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1754 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'OLA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.11, per 1000 atoms: 0.59 Number of scatterers: 8727 At special positions: 0 Unit cell: (106.47, 128.778, 115.596, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1597 8.00 N 1478 7.00 C 5596 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 160 " - pdb=" SG CYS S 230 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.49 Conformation dependent library (CDL) restraints added in 1.8 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 13 sheets defined 32.0% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'R' and resid 38 through 68 removed outlier: 3.983A pdb=" N THR R 45 " --> pdb=" O ALA R 41 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU R 47 " --> pdb=" O GLU R 43 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL R 48 " --> pdb=" O THR R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 89 Processing helix chain 'R' and resid 92 through 100 Processing helix chain 'R' and resid 110 through 113 No H-bonds generated for 'chain 'R' and resid 110 through 113' Processing helix chain 'R' and resid 116 through 142 removed outlier: 3.656A pdb=" N LEU R 120 " --> pdb=" O TYR R 116 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 168 removed outlier: 3.738A pdb=" N ALA R 160 " --> pdb=" O ALA R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 175 removed outlier: 3.873A pdb=" N VAL R 175 " --> pdb=" O PRO R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 215 Processing helix chain 'R' and resid 217 through 243 Processing helix chain 'R' and resid 249 through 289 removed outlier: 4.428A pdb=" N ILE R 253 " --> pdb=" O GLU R 249 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG R 254 " --> pdb=" O SER R 250 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE R 273 " --> pdb=" O LEU R 269 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE R 274 " --> pdb=" O MET R 270 " (cutoff:3.500A) Proline residue: R 279 - end of helix Processing helix chain 'R' and resid 302 through 315 removed outlier: 3.624A pdb=" N ASN R 313 " --> pdb=" O PHE R 309 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 320 No H-bonds generated for 'chain 'R' and resid 317 through 320' Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.863A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 309 removed outlier: 3.684A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.574A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'Y' and resid 8 through 23 Processing helix chain 'Y' and resid 30 through 43 Processing helix chain 'Y' and resid 45 through 47 No H-bonds generated for 'chain 'Y' and resid 45 through 47' Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 222 through 224 No H-bonds generated for 'chain 'S' and resid 222 through 224' Processing sheet with id= A, first strand: chain 'R' and resid 177 through 181 Processing sheet with id= B, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.871A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.824A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.786A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 152 removed outlier: 6.782A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.637A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.779A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.604A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.715A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.169A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 147 through 149 removed outlier: 6.675A pdb=" N LYS S 245 " --> pdb=" O VAL S 148 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY S 226 " --> pdb=" O LEU S 246 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU S 179 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LEU S 188 " --> pdb=" O LEU S 179 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 156 through 161 393 hydrogen bonds defined for protein. 1122 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: 2.33 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1480 1.32 - 1.45: 2392 1.45 - 1.57: 4952 1.57 - 1.70: 0 1.70 - 1.82: 81 Bond restraints: 8905 Sorted by residual: bond pdb=" C GLY R 151 " pdb=" N ARG R 152 " ideal model delta sigma weight residual 1.335 1.227 0.107 1.25e-02 6.40e+03 7.37e+01 bond pdb=" C ARG R 264 " pdb=" O ARG R 264 " ideal model delta sigma weight residual 1.237 1.198 0.038 1.16e-02 7.43e+03 1.09e+01 bond pdb=" N ARG R 152 " pdb=" CA ARG R 152 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.20e-02 6.94e+03 6.64e+00 bond pdb=" C ARG A 21 " pdb=" O ARG A 21 " ideal model delta sigma weight residual 1.237 1.208 0.029 1.17e-02 7.31e+03 5.95e+00 bond pdb=" CA ARG R 264 " pdb=" C ARG R 264 " ideal model delta sigma weight residual 1.524 1.496 0.027 1.26e-02 6.30e+03 4.73e+00 ... (remaining 8900 not shown) Histogram of bond angle deviations from ideal: 99.60 - 106.48: 195 106.48 - 113.36: 4914 113.36 - 120.24: 3133 120.24 - 127.12: 3752 127.12 - 134.01: 93 Bond angle restraints: 12087 Sorted by residual: angle pdb=" N SER S 194 " pdb=" CA SER S 194 " pdb=" C SER S 194 " ideal model delta sigma weight residual 112.88 118.50 -5.62 1.29e+00 6.01e-01 1.89e+01 angle pdb=" N ASN S 195 " pdb=" CA ASN S 195 " pdb=" C ASN S 195 " ideal model delta sigma weight residual 108.52 115.14 -6.62 1.63e+00 3.76e-01 1.65e+01 angle pdb=" N MET S 193 " pdb=" CA MET S 193 " pdb=" C MET S 193 " ideal model delta sigma weight residual 110.80 119.06 -8.26 2.13e+00 2.20e-01 1.50e+01 angle pdb=" CA TYR R 247 " pdb=" CB TYR R 247 " pdb=" CG TYR R 247 " ideal model delta sigma weight residual 113.90 120.14 -6.24 1.80e+00 3.09e-01 1.20e+01 angle pdb=" N ILE R 92 " pdb=" CA ILE R 92 " pdb=" C ILE R 92 " ideal model delta sigma weight residual 108.88 115.75 -6.87 2.16e+00 2.14e-01 1.01e+01 ... (remaining 12082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 4958 17.24 - 34.48: 236 34.48 - 51.72: 44 51.72 - 68.96: 15 68.96 - 86.21: 6 Dihedral angle restraints: 5259 sinusoidal: 1958 harmonic: 3301 Sorted by residual: dihedral pdb=" N MET S 193 " pdb=" C MET S 193 " pdb=" CA MET S 193 " pdb=" CB MET S 193 " ideal model delta harmonic sigma weight residual 122.80 132.18 -9.38 0 2.50e+00 1.60e-01 1.41e+01 dihedral pdb=" C MET S 193 " pdb=" N MET S 193 " pdb=" CA MET S 193 " pdb=" CB MET S 193 " ideal model delta harmonic sigma weight residual -122.60 -131.70 9.10 0 2.50e+00 1.60e-01 1.32e+01 dihedral pdb=" CA PHE S 32 " pdb=" C PHE S 32 " pdb=" N GLY S 33 " pdb=" CA GLY S 33 " ideal model delta harmonic sigma weight residual 180.00 162.64 17.36 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 5256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1308 0.087 - 0.174: 99 0.174 - 0.261: 5 0.261 - 0.348: 1 0.348 - 0.435: 1 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CA MET S 193 " pdb=" N MET S 193 " pdb=" C MET S 193 " pdb=" CB MET S 193 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.44 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CA ARG S 192 " pdb=" N ARG S 192 " pdb=" C ARG S 192 " pdb=" CB ARG S 192 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA SER S 194 " pdb=" N SER S 194 " pdb=" C SER S 194 " pdb=" CB SER S 194 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1411 not shown) Planarity restraints: 1515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR Y 52 " -0.067 5.00e-02 4.00e+02 9.92e-02 1.58e+01 pdb=" N PRO Y 53 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO Y 53 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO Y 53 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 151 " -0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C GLY R 151 " 0.066 2.00e-02 2.50e+03 pdb=" O GLY R 151 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG R 152 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER S 106 " 0.043 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO S 107 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO S 107 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO S 107 " 0.036 5.00e-02 4.00e+02 ... (remaining 1512 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 324 2.72 - 3.27: 8520 3.27 - 3.81: 13973 3.81 - 4.36: 17842 4.36 - 4.90: 30361 Nonbonded interactions: 71020 Sorted by model distance: nonbonded pdb=" NH1 ARG R 238 " pdb=" OD1 ASP R 259 " model vdw 2.180 2.520 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.234 2.440 nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.236 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.255 2.440 nonbonded pdb=" OE1 GLN A 52 " pdb=" ND2 ASN A 331 " model vdw 2.286 2.520 ... (remaining 71015 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 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: 1.960 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 26.320 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 0.107 8905 Z= 0.241 Angle : 0.668 8.258 12087 Z= 0.370 Chirality : 0.048 0.435 1414 Planarity : 0.006 0.099 1515 Dihedral : 11.398 86.206 3118 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.86 (0.25), residues: 1119 helix: 1.10 (0.27), residues: 383 sheet: 1.33 (0.29), residues: 283 loop : -0.32 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 82 HIS 0.006 0.001 HIS A 188 PHE 0.021 0.002 PHE A 189 TYR 0.017 0.002 TYR S 191 ARG 0.005 0.001 ARG S 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: Y 21 MET cc_start: 0.6695 (mpp) cc_final: 0.6441 (ttp) outliers start: 0 outliers final: 1 residues processed: 137 average time/residue: 1.4201 time to fit residues: 205.5412 Evaluate side-chains 94 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 87 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 80 ASN R 322 ASN A 195 HIS A 255 ASN B 44 GLN B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 187 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8905 Z= 0.376 Angle : 0.650 7.408 12087 Z= 0.340 Chirality : 0.047 0.182 1414 Planarity : 0.005 0.082 1515 Dihedral : 5.486 55.617 1235 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.61 % Allowed : 7.93 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.24), residues: 1119 helix: 1.35 (0.27), residues: 376 sheet: 0.99 (0.29), residues: 291 loop : -0.59 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.009 0.002 HIS B 62 PHE 0.021 0.002 PHE B 151 TYR 0.028 0.002 TYR B 105 ARG 0.006 0.001 ARG S 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 0.927 Fit side-chains REVERT: B 118 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7332 (p0) REVERT: B 188 MET cc_start: 0.8917 (mmm) cc_final: 0.8579 (mmp) REVERT: B 197 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.7242 (mmp-170) REVERT: Y 21 MET cc_start: 0.6862 (mpp) cc_final: 0.6542 (ttt) REVERT: S 113 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8214 (tp-100) outliers start: 24 outliers final: 9 residues processed: 102 average time/residue: 1.4921 time to fit residues: 161.2657 Evaluate side-chains 94 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain Y residue 52 THR Chi-restraints excluded: chain S residue 156 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 0.0870 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 90 optimal weight: 0.1980 chunk 34 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 322 ASN A 195 HIS B 44 GLN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8905 Z= 0.214 Angle : 0.533 7.323 12087 Z= 0.281 Chirality : 0.043 0.155 1414 Planarity : 0.004 0.070 1515 Dihedral : 5.194 52.327 1235 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.83 % Allowed : 8.26 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.89 (0.25), residues: 1119 helix: 1.62 (0.28), residues: 386 sheet: 1.06 (0.29), residues: 285 loop : -0.62 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 PHE 0.014 0.002 PHE B 278 TYR 0.013 0.001 TYR S 191 ARG 0.004 0.000 ARG R 238 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 90 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: R 214 LEU cc_start: 0.8240 (mp) cc_final: 0.7618 (tt) REVERT: B 118 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7324 (p0) REVERT: B 188 MET cc_start: 0.8886 (mmm) cc_final: 0.8582 (mmp) REVERT: B 220 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8604 (mt0) REVERT: Y 21 MET cc_start: 0.7152 (mpp) cc_final: 0.6651 (ttt) outliers start: 26 outliers final: 14 residues processed: 105 average time/residue: 1.4695 time to fit residues: 163.1673 Evaluate side-chains 104 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 276 MET Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 156 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 29 optimal weight: 0.0070 chunk 90 optimal weight: 0.0000 overall best weight: 0.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 144 GLN A 195 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8905 Z= 0.125 Angle : 0.474 6.802 12087 Z= 0.248 Chirality : 0.040 0.141 1414 Planarity : 0.004 0.059 1515 Dihedral : 4.922 49.168 1235 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.17 % Allowed : 9.57 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.12 (0.25), residues: 1119 helix: 1.96 (0.28), residues: 382 sheet: 1.13 (0.29), residues: 285 loop : -0.57 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE A 189 TYR 0.011 0.001 TYR S 191 ARG 0.002 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: R 214 LEU cc_start: 0.8281 (mp) cc_final: 0.7651 (tt) REVERT: B 118 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7215 (p0) REVERT: B 188 MET cc_start: 0.8890 (mmm) cc_final: 0.8570 (mmp) REVERT: B 220 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8573 (mt0) REVERT: Y 21 MET cc_start: 0.7298 (mpp) cc_final: 0.6684 (ttt) outliers start: 20 outliers final: 10 residues processed: 104 average time/residue: 1.3279 time to fit residues: 146.8796 Evaluate side-chains 97 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 276 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 322 ASN B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8905 Z= 0.304 Angle : 0.569 6.961 12087 Z= 0.299 Chirality : 0.044 0.169 1414 Planarity : 0.005 0.073 1515 Dihedral : 5.161 50.755 1235 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.72 % Allowed : 10.87 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.84 (0.24), residues: 1119 helix: 1.68 (0.27), residues: 389 sheet: 0.95 (0.29), residues: 286 loop : -0.72 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.007 0.001 HIS B 62 PHE 0.017 0.002 PHE B 278 TYR 0.014 0.002 TYR S 191 ARG 0.004 0.000 ARG S 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 89 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 214 LEU cc_start: 0.8417 (mp) cc_final: 0.7766 (tt) REVERT: A 53 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6289 (mtt) REVERT: B 118 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7344 (p0) REVERT: B 188 MET cc_start: 0.8858 (mmm) cc_final: 0.8585 (mmp) REVERT: B 220 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8547 (mt0) REVERT: Y 21 MET cc_start: 0.7343 (mpp) cc_final: 0.6687 (ttt) outliers start: 25 outliers final: 17 residues processed: 103 average time/residue: 1.4100 time to fit residues: 153.8459 Evaluate side-chains 106 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 276 MET Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 205 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 26 optimal weight: 0.0020 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 322 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8905 Z= 0.135 Angle : 0.475 6.882 12087 Z= 0.248 Chirality : 0.040 0.140 1414 Planarity : 0.004 0.061 1515 Dihedral : 4.900 50.671 1235 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.83 % Allowed : 11.41 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.12 (0.25), residues: 1119 helix: 2.10 (0.28), residues: 382 sheet: 1.01 (0.29), residues: 286 loop : -0.62 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE B 151 TYR 0.012 0.001 TYR S 191 ARG 0.002 0.000 ARG R 238 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 89 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: R 214 LEU cc_start: 0.8369 (mp) cc_final: 0.7730 (tt) REVERT: A 53 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.6413 (mtt) REVERT: B 118 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7221 (p0) REVERT: B 188 MET cc_start: 0.8855 (mmm) cc_final: 0.8582 (mmp) REVERT: B 220 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8563 (mt0) REVERT: Y 21 MET cc_start: 0.7296 (mpp) cc_final: 0.6698 (ttt) REVERT: S 76 LYS cc_start: 0.7618 (mtpp) cc_final: 0.7345 (pttt) outliers start: 26 outliers final: 14 residues processed: 103 average time/residue: 1.4024 time to fit residues: 153.1122 Evaluate side-chains 102 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 276 MET Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 156 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 0.0980 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 322 ASN A 22 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8905 Z= 0.161 Angle : 0.499 10.598 12087 Z= 0.257 Chirality : 0.041 0.146 1414 Planarity : 0.004 0.062 1515 Dihedral : 4.831 51.483 1235 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.50 % Allowed : 11.74 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.15 (0.25), residues: 1119 helix: 2.08 (0.28), residues: 388 sheet: 0.96 (0.29), residues: 293 loop : -0.58 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE B 151 TYR 0.011 0.001 TYR S 191 ARG 0.005 0.000 ARG R 238 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 214 LEU cc_start: 0.8382 (mp) cc_final: 0.7741 (tt) REVERT: B 118 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7226 (p0) REVERT: B 188 MET cc_start: 0.8871 (mmm) cc_final: 0.8583 (mmp) REVERT: B 220 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8585 (mt0) REVERT: Y 21 MET cc_start: 0.7277 (mpp) cc_final: 0.6666 (ttt) outliers start: 23 outliers final: 14 residues processed: 101 average time/residue: 1.3761 time to fit residues: 147.7979 Evaluate side-chains 101 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 156 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 10 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 322 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8905 Z= 0.188 Angle : 0.509 7.994 12087 Z= 0.264 Chirality : 0.041 0.151 1414 Planarity : 0.004 0.065 1515 Dihedral : 4.882 52.703 1235 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.28 % Allowed : 11.96 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.12 (0.25), residues: 1119 helix: 2.10 (0.28), residues: 387 sheet: 0.93 (0.29), residues: 287 loop : -0.61 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE B 151 TYR 0.012 0.001 TYR S 191 ARG 0.006 0.000 ARG R 238 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 214 LEU cc_start: 0.8452 (mp) cc_final: 0.7764 (tt) REVERT: A 53 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6575 (mtm) REVERT: B 118 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7245 (p0) REVERT: B 188 MET cc_start: 0.8863 (mmm) cc_final: 0.8552 (mmp) REVERT: B 220 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8596 (mt0) REVERT: Y 21 MET cc_start: 0.7122 (mpp) cc_final: 0.6473 (ttt) outliers start: 21 outliers final: 13 residues processed: 99 average time/residue: 1.4227 time to fit residues: 149.6797 Evaluate side-chains 100 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 205 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 95 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 322 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8905 Z= 0.197 Angle : 0.525 10.630 12087 Z= 0.270 Chirality : 0.041 0.151 1414 Planarity : 0.004 0.067 1515 Dihedral : 4.874 53.447 1235 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.17 % Allowed : 12.17 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.15 (0.25), residues: 1119 helix: 2.14 (0.28), residues: 388 sheet: 0.97 (0.29), residues: 285 loop : -0.62 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE B 278 TYR 0.012 0.001 TYR S 191 ARG 0.005 0.000 ARG R 238 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 113 LEU cc_start: 0.6313 (OUTLIER) cc_final: 0.6035 (tp) REVERT: R 214 LEU cc_start: 0.8414 (mp) cc_final: 0.7788 (tt) REVERT: A 53 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6694 (mtm) REVERT: B 118 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7233 (p0) REVERT: B 188 MET cc_start: 0.8870 (mmm) cc_final: 0.8584 (mmp) REVERT: B 220 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8561 (mt0) REVERT: Y 21 MET cc_start: 0.7105 (mpp) cc_final: 0.6420 (ttt) outliers start: 20 outliers final: 14 residues processed: 99 average time/residue: 1.3695 time to fit residues: 143.9914 Evaluate side-chains 104 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 205 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 88 optimal weight: 0.0030 chunk 9 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 54 optimal weight: 0.0470 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.5888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 322 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8905 Z= 0.132 Angle : 0.476 7.391 12087 Z= 0.247 Chirality : 0.040 0.138 1414 Planarity : 0.004 0.060 1515 Dihedral : 4.717 57.014 1235 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.96 % Allowed : 12.61 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.27 (0.25), residues: 1119 helix: 2.29 (0.28), residues: 389 sheet: 1.04 (0.29), residues: 284 loop : -0.61 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE A 189 TYR 0.010 0.001 TYR B 59 ARG 0.005 0.000 ARG R 238 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 214 LEU cc_start: 0.8401 (mp) cc_final: 0.7785 (tt) REVERT: B 118 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7244 (p0) REVERT: B 188 MET cc_start: 0.8854 (mmm) cc_final: 0.8575 (mmp) REVERT: B 220 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8617 (mt0) REVERT: Y 21 MET cc_start: 0.7056 (mpp) cc_final: 0.6405 (ttt) outliers start: 18 outliers final: 11 residues processed: 100 average time/residue: 1.3914 time to fit residues: 147.7012 Evaluate side-chains 102 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 205 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 chunk 91 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 322 ASN A 255 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN S 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.192390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.127353 restraints weight = 9268.795| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.44 r_work: 0.2883 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8905 Z= 0.339 Angle : 0.595 9.327 12087 Z= 0.309 Chirality : 0.045 0.166 1414 Planarity : 0.005 0.073 1515 Dihedral : 5.031 51.012 1235 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.17 % Allowed : 12.83 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.98 (0.25), residues: 1119 helix: 1.98 (0.27), residues: 389 sheet: 0.94 (0.29), residues: 290 loop : -0.78 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.006 0.001 HIS S 35 PHE 0.016 0.002 PHE B 278 TYR 0.014 0.002 TYR S 191 ARG 0.005 0.000 ARG R 238 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3462.93 seconds wall clock time: 62 minutes 20.44 seconds (3740.44 seconds total)