Starting phenix.real_space_refine on Tue May 7 02:58:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unp_42412/05_2024/8unp_42412_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unp_42412/05_2024/8unp_42412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unp_42412/05_2024/8unp_42412.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unp_42412/05_2024/8unp_42412.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unp_42412/05_2024/8unp_42412_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unp_42412/05_2024/8unp_42412_updated.pdb" } resolution = 3.3 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 43 5.16 5 C 4225 2.51 5 N 1130 2.21 5 O 1158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 6559 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1724 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 237, 1712 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 5, 'TRANS': 231} Chain breaks: 4 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 323 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 15, 'ARG:plan': 12, 'ASN:plan1': 3, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 191 Conformer: "B" Number of residues, atoms: 237, 1712 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 5, 'TRANS': 231} Chain breaks: 4 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 323 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 15, 'ARG:plan': 12, 'ASN:plan1': 3, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 191 bond proxies already assigned to first conformer: 1731 Chain: "B" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2357 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 7, 'ARG:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 144 Chain: "G" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 335 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "R" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2095 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 6, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 108 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 360 " occ=0.51 ... (22 atoms not shown) pdb=" OH BTYR A 360 " occ=0.49 Time building chain proxies: 5.32, per 1000 atoms: 0.81 Number of scatterers: 6559 At special positions: 0 Unit cell: (84.1669, 133.626, 96.3147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 43 16.00 P 3 15.00 O 1158 8.00 N 1130 7.00 C 4225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 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: 2.54 Conformation dependent library (CDL) restraints added in 1.8 seconds 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1720 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 8 sheets defined 42.6% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.927A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.576A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.572A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.693A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 7 through 25 removed outlier: 4.208A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 10 through 23 removed outlier: 3.683A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'R' and resid 32 through 60 removed outlier: 3.569A pdb=" N LEU R 45 " --> pdb=" O SER R 41 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE R 58 " --> pdb=" O VAL R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 96 removed outlier: 3.726A pdb=" N TYR R 70 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE R 71 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE R 72 " --> pdb=" O ASN R 69 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N VAL R 86 " --> pdb=" O GLY R 83 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N VAL R 87 " --> pdb=" O LEU R 84 " (cutoff:3.500A) Proline residue: R 88 - end of helix removed outlier: 3.760A pdb=" N THR R 96 " --> pdb=" O HIS R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 119 Processing helix chain 'R' and resid 122 through 136 Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 147 through 164 removed outlier: 3.829A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 170 No H-bonds generated for 'chain 'R' and resid 167 through 170' Processing helix chain 'R' and resid 179 through 186 Processing helix chain 'R' and resid 197 through 207 removed outlier: 3.703A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 237 removed outlier: 3.898A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 298 removed outlier: 3.854A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.376A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 326 removed outlier: 3.590A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 338 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.467A pdb=" N VAL A 287 " --> pdb=" O ATYR A 360 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.695A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 71 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.097A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.605A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.844A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 262 through 264 removed outlier: 3.790A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.513A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.735A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 885 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.98 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1303 1.33 - 1.45: 1701 1.45 - 1.57: 3635 1.57 - 1.69: 5 1.69 - 1.81: 59 Bond restraints: 6703 Sorted by residual: bond pdb=" CA GLN A 12 " pdb=" C GLN A 12 " ideal model delta sigma weight residual 1.523 1.452 0.071 1.41e-02 5.03e+03 2.53e+01 bond pdb=" CA ASP A 223 " pdb=" C ASP A 223 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.23e-02 6.61e+03 1.98e+01 bond pdb=" CA THR A 325 " pdb=" C THR A 325 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.24e-02 6.50e+03 1.98e+01 bond pdb=" C5 GTP A 401 " pdb=" C6 GTP A 401 " ideal model delta sigma weight residual 1.390 1.477 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C4 GTP A 401 " pdb=" C5 GTP A 401 " ideal model delta sigma weight residual 1.390 1.469 -0.079 2.00e-02 2.50e+03 1.54e+01 ... (remaining 6698 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.91: 162 106.91 - 114.20: 3912 114.20 - 121.48: 3517 121.48 - 128.77: 1525 128.77 - 136.06: 61 Bond angle restraints: 9177 Sorted by residual: angle pdb=" N GLN A 12 " pdb=" CA GLN A 12 " pdb=" C GLN A 12 " ideal model delta sigma weight residual 113.16 99.62 13.54 1.24e+00 6.50e-01 1.19e+02 angle pdb=" N ARG A 228 " pdb=" CA ARG A 228 " pdb=" C ARG A 228 " ideal model delta sigma weight residual 110.10 124.46 -14.36 1.49e+00 4.50e-01 9.28e+01 angle pdb=" N ILE R 58 " pdb=" CA ILE R 58 " pdb=" C ILE R 58 " ideal model delta sigma weight residual 110.62 101.44 9.18 1.02e+00 9.61e-01 8.09e+01 angle pdb=" N THR A 263 " pdb=" CA THR A 263 " pdb=" C THR A 263 " ideal model delta sigma weight residual 110.53 100.96 9.57 1.32e+00 5.74e-01 5.26e+01 angle pdb=" N ARG A 231 " pdb=" CA ARG A 231 " pdb=" C ARG A 231 " ideal model delta sigma weight residual 110.23 100.03 10.20 1.45e+00 4.76e-01 4.95e+01 ... (remaining 9172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.82: 3801 33.82 - 67.63: 48 67.63 - 101.45: 1 101.45 - 135.27: 2 135.27 - 169.08: 3 Dihedral angle restraints: 3855 sinusoidal: 1208 harmonic: 2647 Sorted by residual: dihedral pdb=" O5' GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PA GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sinusoidal sigma weight residual 274.12 105.04 169.08 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C4' GTP A 401 " pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual 260.87 100.64 160.23 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" O3B GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PB GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual 291.08 152.69 138.39 1 2.00e+01 2.50e-03 4.19e+01 ... (remaining 3852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 819 0.044 - 0.088: 206 0.088 - 0.132: 70 0.132 - 0.176: 7 0.176 - 0.219: 1 Chirality restraints: 1103 Sorted by residual: chirality pdb=" CA ARG A 228 " pdb=" N ARG A 228 " pdb=" C ARG A 228 " pdb=" CB ARG A 228 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA VAL R 44 " pdb=" N VAL R 44 " pdb=" C VAL R 44 " pdb=" CB VAL R 44 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ILE R 58 " pdb=" N ILE R 58 " pdb=" C ILE R 58 " pdb=" CB ILE R 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 1100 not shown) Planarity restraints: 1145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 320 " 0.053 5.00e-02 4.00e+02 8.08e-02 1.04e+01 pdb=" N PRO A 321 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 42 " 0.013 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" C LEU R 42 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU R 42 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE R 43 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 33 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.85e+00 pdb=" C VAL R 33 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL R 33 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL R 34 " -0.014 2.00e-02 2.50e+03 ... (remaining 1142 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 803 2.75 - 3.28: 6268 3.28 - 3.82: 10290 3.82 - 4.36: 11394 4.36 - 4.90: 20937 Nonbonded interactions: 49692 Sorted by model distance: nonbonded pdb=" OG1 THR A 55 " pdb=" O2A GTP A 401 " model vdw 2.207 2.440 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.233 2.440 nonbonded pdb=" N GLN A 12 " pdb=" N ARG A 13 " model vdw 2.246 2.560 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.249 2.440 nonbonded pdb=" OD1 ASN A 239 " pdb=" NZ LYS B 57 " model vdw 2.307 2.520 ... (remaining 49687 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=0.49 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: 3.600 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: 7.740 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.500 Find NCS groups from input model: 0.200 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 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 : 0.006 0.087 6703 Z= 0.368 Angle : 0.795 14.357 9177 Z= 0.502 Chirality : 0.044 0.219 1103 Planarity : 0.004 0.081 1145 Dihedral : 13.788 169.085 2132 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.82 (0.29), residues: 889 helix: 1.96 (0.27), residues: 400 sheet: 0.16 (0.40), residues: 171 loop : -1.06 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 313 HIS 0.010 0.001 HIS A 220 PHE 0.018 0.001 PHE A 222 TYR 0.019 0.001 TYR B 59 ARG 0.002 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.763 Fit side-chains REVERT: A 267 GLN cc_start: 0.8277 (tp-100) cc_final: 0.7739 (tp-100) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2366 time to fit residues: 29.0020 Evaluate side-chains 72 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 220 HIS A 254 ASN A 294 GLN R 241 HIS R 322 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6703 Z= 0.263 Angle : 0.527 7.741 9177 Z= 0.283 Chirality : 0.042 0.160 1103 Planarity : 0.004 0.040 1145 Dihedral : 10.710 178.068 990 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.37 % Allowed : 8.22 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 889 helix: 1.72 (0.26), residues: 413 sheet: 0.01 (0.38), residues: 185 loop : -1.01 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.006 0.001 HIS R 241 PHE 0.013 0.001 PHE A 212 TYR 0.016 0.001 TYR B 59 ARG 0.002 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.792 Fit side-chains REVERT: R 65 GLN cc_start: 0.6472 (mp10) cc_final: 0.6248 (mp10) outliers start: 8 outliers final: 6 residues processed: 76 average time/residue: 0.1944 time to fit residues: 19.8711 Evaluate side-chains 74 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 143 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 0.0070 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 79 optimal weight: 0.0980 overall best weight: 1.8204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6703 Z= 0.293 Angle : 0.527 7.086 9177 Z= 0.283 Chirality : 0.042 0.150 1103 Planarity : 0.004 0.043 1145 Dihedral : 10.562 179.551 990 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.37 % Allowed : 11.64 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.50 (0.28), residues: 889 helix: 1.55 (0.26), residues: 413 sheet: -0.10 (0.38), residues: 186 loop : -1.10 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.006 0.001 HIS R 241 PHE 0.014 0.001 PHE R 101 TYR 0.015 0.001 TYR B 59 ARG 0.004 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.810 Fit side-chains REVERT: A 294 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.7001 (mp10) REVERT: R 65 GLN cc_start: 0.6637 (mp10) cc_final: 0.6413 (mp10) outliers start: 8 outliers final: 7 residues processed: 80 average time/residue: 0.1879 time to fit residues: 20.4580 Evaluate side-chains 81 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 143 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN R 241 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6703 Z= 0.188 Angle : 0.460 7.463 9177 Z= 0.245 Chirality : 0.040 0.167 1103 Planarity : 0.003 0.042 1145 Dihedral : 10.338 179.251 990 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.54 % Allowed : 13.53 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.29), residues: 889 helix: 1.70 (0.27), residues: 411 sheet: 0.02 (0.38), residues: 185 loop : -1.03 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 297 HIS 0.006 0.001 HIS R 241 PHE 0.010 0.001 PHE A 212 TYR 0.014 0.001 TYR B 59 ARG 0.003 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.986 Fit side-chains REVERT: R 65 GLN cc_start: 0.6655 (mp10) cc_final: 0.6441 (mp10) outliers start: 9 outliers final: 7 residues processed: 86 average time/residue: 0.1778 time to fit residues: 20.9348 Evaluate side-chains 80 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 143 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 35 optimal weight: 0.0040 chunk 73 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 0.0000 chunk 77 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN R 241 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6703 Z= 0.111 Angle : 0.430 7.751 9177 Z= 0.225 Chirality : 0.039 0.166 1103 Planarity : 0.003 0.040 1145 Dihedral : 10.174 179.838 990 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.37 % Allowed : 14.04 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.95 (0.29), residues: 889 helix: 2.08 (0.27), residues: 396 sheet: 0.14 (0.39), residues: 174 loop : -0.95 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 297 HIS 0.006 0.001 HIS R 241 PHE 0.009 0.001 PHE B 241 TYR 0.005 0.001 TYR R 308 ARG 0.005 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.724 Fit side-chains REVERT: A 294 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8331 (mm-40) REVERT: R 65 GLN cc_start: 0.6673 (mp10) cc_final: 0.6448 (mp10) outliers start: 8 outliers final: 5 residues processed: 81 average time/residue: 0.1855 time to fit residues: 20.5042 Evaluate side-chains 78 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 143 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.0370 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 241 HIS R 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6703 Z= 0.140 Angle : 0.435 7.653 9177 Z= 0.229 Chirality : 0.039 0.171 1103 Planarity : 0.003 0.038 1145 Dihedral : 10.133 179.707 990 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.71 % Allowed : 14.73 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.29), residues: 889 helix: 2.13 (0.27), residues: 396 sheet: 0.14 (0.38), residues: 185 loop : -0.85 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 339 HIS 0.006 0.001 HIS R 241 PHE 0.009 0.001 PHE B 241 TYR 0.007 0.001 TYR B 59 ARG 0.003 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.940 Fit side-chains REVERT: R 65 GLN cc_start: 0.6625 (mp10) cc_final: 0.6411 (mp10) outliers start: 10 outliers final: 7 residues processed: 81 average time/residue: 0.2242 time to fit residues: 24.5655 Evaluate side-chains 80 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 143 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 85 optimal weight: 0.3980 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 39 optimal weight: 0.3980 chunk 34 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6703 Z= 0.161 Angle : 0.448 8.302 9177 Z= 0.236 Chirality : 0.040 0.182 1103 Planarity : 0.003 0.038 1145 Dihedral : 10.102 179.155 990 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.23 % Allowed : 14.04 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.29), residues: 889 helix: 2.08 (0.27), residues: 401 sheet: 0.11 (0.38), residues: 186 loop : -0.75 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 339 HIS 0.006 0.001 HIS R 241 PHE 0.009 0.001 PHE B 241 TYR 0.010 0.001 TYR B 59 ARG 0.003 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.996 Fit side-chains REVERT: R 65 GLN cc_start: 0.6583 (mp10) cc_final: 0.6365 (mp10) outliers start: 13 outliers final: 12 residues processed: 85 average time/residue: 0.2328 time to fit residues: 27.2355 Evaluate side-chains 86 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 292 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.7980 chunk 54 optimal weight: 0.0000 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6703 Z= 0.127 Angle : 0.426 7.555 9177 Z= 0.226 Chirality : 0.039 0.186 1103 Planarity : 0.003 0.038 1145 Dihedral : 10.033 178.407 990 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.05 % Allowed : 14.38 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.10 (0.29), residues: 889 helix: 2.15 (0.27), residues: 394 sheet: 0.19 (0.38), residues: 185 loop : -0.78 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.006 0.001 HIS R 241 PHE 0.009 0.001 PHE R 217 TYR 0.010 0.001 TYR R 219 ARG 0.003 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.814 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 80 average time/residue: 0.1827 time to fit residues: 20.1014 Evaluate side-chains 84 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 292 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 0.0020 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 84 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6703 Z= 0.127 Angle : 0.425 8.227 9177 Z= 0.224 Chirality : 0.039 0.188 1103 Planarity : 0.003 0.038 1145 Dihedral : 9.987 178.145 990 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.40 % Allowed : 13.70 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.29), residues: 889 helix: 2.19 (0.27), residues: 394 sheet: 0.25 (0.38), residues: 185 loop : -0.77 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.006 0.001 HIS R 241 PHE 0.009 0.001 PHE B 241 TYR 0.008 0.001 TYR B 59 ARG 0.002 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.651 Fit side-chains outliers start: 14 outliers final: 13 residues processed: 82 average time/residue: 0.1730 time to fit residues: 19.4428 Evaluate side-chains 86 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 7 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 10 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6703 Z= 0.122 Angle : 0.421 7.511 9177 Z= 0.222 Chirality : 0.039 0.191 1103 Planarity : 0.003 0.038 1145 Dihedral : 9.933 177.523 990 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.23 % Allowed : 14.04 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.16 (0.29), residues: 889 helix: 2.22 (0.27), residues: 394 sheet: 0.29 (0.39), residues: 180 loop : -0.81 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.006 0.001 HIS R 241 PHE 0.008 0.001 PHE B 241 TYR 0.007 0.001 TYR B 59 ARG 0.002 0.000 ARG R 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.738 Fit side-chains REVERT: B 156 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.8056 (mt0) outliers start: 13 outliers final: 10 residues processed: 86 average time/residue: 0.2046 time to fit residues: 23.4021 Evaluate side-chains 87 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 143 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.7980 chunk 70 optimal weight: 0.0870 chunk 29 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.125506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.098587 restraints weight = 42170.006| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 5.03 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6703 Z= 0.142 Angle : 0.428 8.345 9177 Z= 0.226 Chirality : 0.040 0.190 1103 Planarity : 0.003 0.037 1145 Dihedral : 9.920 177.266 990 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.23 % Allowed : 14.38 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.29), residues: 889 helix: 2.19 (0.27), residues: 394 sheet: 0.18 (0.38), residues: 186 loop : -0.75 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 211 HIS 0.006 0.001 HIS R 241 PHE 0.009 0.001 PHE B 241 TYR 0.009 0.001 TYR B 59 ARG 0.002 0.000 ARG R 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1817.17 seconds wall clock time: 34 minutes 3.14 seconds (2043.14 seconds total)