Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 01:17:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id6_35358/04_2023/8id6_35358_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id6_35358/04_2023/8id6_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_35358/04_2023/8id6_35358.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id6_35358/04_2023/8id6_35358.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id6_35358/04_2023/8id6_35358_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id6_35358/04_2023/8id6_35358_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 5.21, per 1000 atoms: 0.60 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: 4.00 Conformation dependent library (CDL) restraints added in 1.5 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: 0.83 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: 2.60 Time building geometry restraints manager: 4.19 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: 0.300 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: 2.390 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.610 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.490 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.105 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 137 average time/residue: 1.4591 time to fit residues: 211.4372 Evaluate side-chains 94 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 1.014 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1418 time to fit residues: 1.6355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7957 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 8905 Z= 0.377 Angle : 0.660 7.579 12087 Z= 0.344 Chirality : 0.047 0.186 1414 Planarity : 0.006 0.083 1515 Dihedral : 5.425 56.468 1233 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 2.61 % 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: 0.68 (0.24), residues: 1119 helix: 1.25 (0.27), residues: 382 sheet: 0.99 (0.29), residues: 291 loop : -0.57 (0.27), residues: 446 *********************** 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 113 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 1.152 Fit side-chains outliers start: 24 outliers final: 10 residues processed: 101 average time/residue: 1.5177 time to fit residues: 162.4344 Evaluate side-chains 93 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 1.096 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 4 average time/residue: 0.4805 time to fit residues: 3.7385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 0.3980 chunk 110 optimal weight: 10.0000 chunk 90 optimal weight: 0.0770 chunk 34 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.6542 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 8905 Z= 0.140 Angle : 0.492 7.119 12087 Z= 0.258 Chirality : 0.041 0.140 1414 Planarity : 0.004 0.063 1515 Dihedral : 4.988 50.301 1233 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 2.61 % 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: 1.07 (0.25), residues: 1119 helix: 1.80 (0.28), residues: 385 sheet: 1.15 (0.29), residues: 285 loop : -0.54 (0.27), residues: 449 *********************** 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 118 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 1.106 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 106 average time/residue: 1.4276 time to fit residues: 160.6506 Evaluate side-chains 103 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 1.064 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 5 average time/residue: 0.3236 time to fit residues: 3.4211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 0.0870 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 144 GLN R 322 ASN A 22 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 8905 Z= 0.185 Angle : 0.510 6.962 12087 Z= 0.265 Chirality : 0.041 0.154 1414 Planarity : 0.004 0.065 1515 Dihedral : 4.911 51.320 1233 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 2.61 % 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: 1.02 (0.25), residues: 1119 helix: 1.86 (0.28), residues: 388 sheet: 1.03 (0.30), residues: 280 loop : -0.58 (0.27), residues: 451 *********************** 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 118 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 105 average time/residue: 1.3551 time to fit residues: 151.2329 Evaluate side-chains 101 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 1.022 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 6 average time/residue: 0.2918 time to fit residues: 3.5808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 8905 Z= 0.368 Angle : 0.609 7.321 12087 Z= 0.317 Chirality : 0.045 0.172 1414 Planarity : 0.005 0.078 1515 Dihedral : 5.215 52.285 1233 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 2.39 % 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: 0.67 (0.24), residues: 1119 helix: 1.56 (0.27), residues: 388 sheet: 0.86 (0.29), residues: 280 loop : -0.81 (0.26), residues: 451 *********************** 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 118 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 1.166 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 108 average time/residue: 1.4746 time to fit residues: 169.0521 Evaluate side-chains 103 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 5 average time/residue: 0.3168 time to fit residues: 3.3184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 0.0970 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 ** 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: 0.7903 moved from start: 0.2521 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= 0.138 Angle : 0.487 7.169 12087 Z= 0.251 Chirality : 0.040 0.138 1414 Planarity : 0.004 0.062 1515 Dihedral : 4.820 48.423 1233 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 2.83 % 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: 1.08 (0.25), residues: 1119 helix: 2.09 (0.28), residues: 385 sheet: 0.97 (0.29), residues: 290 loop : -0.69 (0.27), residues: 444 *********************** 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 120 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 94 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 17 residues processed: 108 average time/residue: 1.4401 time to fit residues: 164.9938 Evaluate side-chains 103 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.953 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 11 residues processed: 7 average time/residue: 0.2698 time to fit residues: 3.7077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 0.1980 chunk 107 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 0.0570 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 8905 Z= 0.120 Angle : 0.484 11.240 12087 Z= 0.245 Chirality : 0.040 0.135 1414 Planarity : 0.004 0.056 1515 Dihedral : 4.578 50.399 1233 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 2.28 % 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: 1.33 (0.25), residues: 1119 helix: 2.36 (0.27), residues: 387 sheet: 1.06 (0.29), residues: 290 loop : -0.60 (0.27), residues: 442 *********************** 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 120 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 111 average time/residue: 1.4761 time to fit residues: 174.2675 Evaluate side-chains 106 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 3 average time/residue: 0.5061 time to fit residues: 3.2278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 53 optimal weight: 0.0070 chunk 10 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- 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** S 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 8905 Z= 0.336 Angle : 0.604 9.789 12087 Z= 0.312 Chirality : 0.045 0.171 1414 Planarity : 0.005 0.073 1515 Dihedral : 5.012 47.162 1233 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 2.72 % 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: 0.96 (0.24), residues: 1119 helix: 2.00 (0.27), residues: 388 sheet: 0.83 (0.29), residues: 293 loop : -0.74 (0.26), residues: 438 *********************** 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 120 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 95 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 17 residues processed: 109 average time/residue: 1.4758 time to fit residues: 170.4342 Evaluate side-chains 109 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 1.072 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 6 average time/residue: 0.6424 time to fit residues: 5.5935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0060 chunk 100 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 8905 Z= 0.143 Angle : 0.535 13.460 12087 Z= 0.264 Chirality : 0.041 0.138 1414 Planarity : 0.004 0.062 1515 Dihedral : 4.689 48.656 1233 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 1.74 % 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: 1.19 (0.25), residues: 1119 helix: 2.28 (0.28), residues: 388 sheet: 0.90 (0.29), residues: 292 loop : -0.65 (0.27), residues: 439 *********************** 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 111 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 14 residues processed: 106 average time/residue: 1.4570 time to fit residues: 164.0423 Evaluate side-chains 106 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 1.114 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 4 average time/residue: 0.3828 time to fit residues: 3.2801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 88 optimal weight: 0.0870 chunk 9 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- 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: 0.7911 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 8905 Z= 0.163 Angle : 0.529 11.938 12087 Z= 0.267 Chirality : 0.041 0.147 1414 Planarity : 0.004 0.063 1515 Dihedral : 4.617 47.605 1233 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 1.63 % 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: 1.23 (0.25), residues: 1119 helix: 2.34 (0.27), residues: 389 sheet: 0.89 (0.28), residues: 292 loop : -0.64 (0.27), residues: 438 ********************** 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 106 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 102 average time/residue: 1.5506 time to fit residues: 167.4133 Evaluate side-chains 104 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.951 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 4 average time/residue: 0.3802 time to fit residues: 3.1140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 88 optimal weight: 0.0370 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 78 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.197297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.140787 restraints weight = 9261.997| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.10 r_work: 0.3013 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 8905 Z= 0.135 Angle : 0.521 11.952 12087 Z= 0.259 Chirality : 0.040 0.139 1414 Planarity : 0.004 0.059 1515 Dihedral : 4.500 48.802 1233 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 1.41 % 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: 1.31 (0.25), residues: 1119 helix: 2.46 (0.28), residues: 389 sheet: 0.90 (0.29), residues: 286 loop : -0.61 (0.27), residues: 444 =============================================================================== Job complete usr+sys time: 3550.14 seconds wall clock time: 63 minutes 44.52 seconds (3824.52 seconds total)