Starting phenix.real_space_refine on Fri Jul 19 05:09:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uny_42421/07_2024/8uny_42421.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uny_42421/07_2024/8uny_42421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uny_42421/07_2024/8uny_42421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uny_42421/07_2024/8uny_42421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uny_42421/07_2024/8uny_42421.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uny_42421/07_2024/8uny_42421.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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 36 5.16 5 C 4217 2.51 5 N 1131 2.21 5 O 1159 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 219": "NH1" <-> "NH2" Residue "R GLU 306": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6546 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1687 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 237, 1675 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 12, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 211 Conformer: "B" Number of residues, atoms: 237, 1675 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 12, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 211 bond proxies already assigned to first conformer: 1693 Chain: "B" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2386 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 6, 'ARG:plan': 9, 'ASN:plan1': 5, 'ASP:plan': 15} Unresolved non-hydrogen planarities: 149 Chain: "G" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 316 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "R" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2110 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 128 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: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 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: 5.68, per 1000 atoms: 0.87 Number of scatterers: 6546 At special positions: 0 Unit cell: (85.0346, 137.097, 99.7855, 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 36 16.00 P 3 15.00 O 1159 8.00 N 1131 7.00 C 4217 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " 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: 2.60 Conformation dependent library (CDL) restraints added in 1.6 seconds 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1730 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 48.6% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 10 through 40 removed outlier: 3.564A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 65 removed outlier: 3.580A pdb=" N LYS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 4.055A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.870A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.901A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 317' Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.663A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 5 through 26 removed outlier: 3.780A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 13 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.648A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 61 removed outlier: 3.527A pdb=" N VAL R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE R 47 " --> pdb=" O ILE R 43 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 Processing helix chain 'R' and resid 68 through 86 removed outlier: 3.847A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 97 Processing helix chain 'R' and resid 102 through 137 removed outlier: 4.057A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 166 removed outlier: 3.948A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.617A pdb=" N ALA R 200 " --> pdb=" O ASN R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 238 removed outlier: 3.980A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 287 removed outlier: 4.038A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 299 removed outlier: 4.541A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.611A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 320 No H-bonds generated for 'chain 'R' and resid 318 through 320' Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 4.022A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 219 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 214 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.581A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.236A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, 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: 4.543A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.169A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.100A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.995A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 277 removed outlier: 3.548A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 296 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 1059 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: 1.89 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1019 1.32 - 1.44: 1908 1.44 - 1.57: 3709 1.57 - 1.69: 6 1.69 - 1.82: 47 Bond restraints: 6689 Sorted by residual: bond pdb=" C SER R 74 " pdb=" N LEU R 75 " ideal model delta sigma weight residual 1.335 1.398 -0.063 1.30e-02 5.92e+03 2.35e+01 bond pdb=" C LYS A 17 " pdb=" O LYS A 17 " ideal model delta sigma weight residual 1.237 1.291 -0.054 1.17e-02 7.31e+03 2.17e+01 bond pdb=" C GLU A 21 " pdb=" O GLU A 21 " ideal model delta sigma weight residual 1.237 1.289 -0.053 1.17e-02 7.31e+03 2.01e+01 bond pdb=" C PRO R 168 " pdb=" O PRO R 168 " ideal model delta sigma weight residual 1.237 1.191 0.046 1.20e-02 6.94e+03 1.50e+01 bond pdb=" N ILE R 43 " pdb=" CA ILE R 43 " ideal model delta sigma weight residual 1.458 1.504 -0.047 1.41e-02 5.03e+03 1.09e+01 ... (remaining 6684 not shown) Histogram of bond angle deviations from ideal: 100.02 - 106.86: 161 106.86 - 113.70: 3766 113.70 - 120.53: 2719 120.53 - 127.37: 2449 127.37 - 134.21: 78 Bond angle restraints: 9173 Sorted by residual: angle pdb=" N ASN A 23 " pdb=" CA ASN A 23 " pdb=" C ASN A 23 " ideal model delta sigma weight residual 111.28 103.32 7.96 1.09e+00 8.42e-01 5.34e+01 angle pdb=" C LYS A 24 " pdb=" N LYS A 25 " pdb=" CA LYS A 25 " ideal model delta sigma weight residual 120.44 111.59 8.85 1.36e+00 5.41e-01 4.24e+01 angle pdb=" N SER R 165 " pdb=" CA SER R 165 " pdb=" C SER R 165 " ideal model delta sigma weight residual 111.14 118.08 -6.94 1.08e+00 8.57e-01 4.13e+01 angle pdb=" C TYR A 37 " pdb=" N ARG A 38 " pdb=" CA ARG A 38 " ideal model delta sigma weight residual 121.14 111.68 9.46 1.75e+00 3.27e-01 2.92e+01 angle pdb=" N ARG A 13 " pdb=" CA ARG A 13 " pdb=" C ARG A 13 " ideal model delta sigma weight residual 111.28 105.49 5.79 1.09e+00 8.42e-01 2.82e+01 ... (remaining 9168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.95: 3760 31.95 - 63.89: 76 63.89 - 95.84: 5 95.84 - 127.79: 3 127.79 - 159.73: 3 Dihedral angle restraints: 3847 sinusoidal: 1182 harmonic: 2665 Sorted by residual: dihedral pdb=" CB CYS R 184 " pdb=" SG CYS R 184 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual 93.00 168.43 -75.43 1 1.00e+01 1.00e-02 7.18e+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 260.87 101.14 159.73 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -44.75 149.34 1 2.00e+01 2.50e-03 4.46e+01 ... (remaining 3844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 775 0.047 - 0.093: 214 0.093 - 0.140: 84 0.140 - 0.187: 36 0.187 - 0.233: 6 Chirality restraints: 1115 Sorted by residual: chirality pdb=" CA GLN A 12 " pdb=" N GLN A 12 " pdb=" C GLN A 12 " pdb=" CB GLN A 12 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA VAL B 133 " pdb=" N VAL B 133 " pdb=" C VAL B 133 " pdb=" CB VAL B 133 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA MET R 171 " pdb=" N MET R 171 " pdb=" C MET R 171 " pdb=" CB MET R 171 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1112 not shown) Planarity restraints: 1145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 215 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.29e+00 pdb=" C GLU B 215 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU B 215 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY B 216 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 173 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.02e+00 pdb=" C THR B 173 " 0.049 2.00e-02 2.50e+03 pdb=" O THR B 173 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY B 174 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 11 " -0.013 2.00e-02 2.50e+03 2.71e-02 7.33e+00 pdb=" C ASP A 11 " 0.047 2.00e-02 2.50e+03 pdb=" O ASP A 11 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN A 12 " -0.016 2.00e-02 2.50e+03 ... (remaining 1142 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1459 2.78 - 3.31: 6203 3.31 - 3.84: 10050 3.84 - 4.37: 10841 4.37 - 4.90: 19726 Nonbonded interactions: 48279 Sorted by model distance: nonbonded pdb=" SG CYS B 271 " pdb=" OD1 ASP B 291 " model vdw 2.255 3.400 nonbonded pdb=" N GLU R 306 " pdb=" OE1 GLU R 306 " model vdw 2.262 2.520 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.276 2.440 nonbonded pdb=" OE1 GLU R 107 " pdb=" OH TYR R 174 " model vdw 2.331 2.440 nonbonded pdb=" O HIS A 64 " pdb=" C VAL A 65 " model vdw 2.354 3.270 ... (remaining 48274 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.230 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 0.063 6689 Z= 0.405 Angle : 0.966 9.998 9173 Z= 0.668 Chirality : 0.057 0.233 1115 Planarity : 0.006 0.092 1145 Dihedral : 14.644 159.734 2111 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: 1.32 (0.29), residues: 899 helix: 2.35 (0.27), residues: 386 sheet: 0.70 (0.44), residues: 168 loop : -0.76 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 105 HIS 0.009 0.001 HIS R 296 PHE 0.010 0.001 PHE B 234 TYR 0.043 0.001 TYR R 185 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.767 Fit side-chains REVERT: A 51 SER cc_start: 0.9275 (p) cc_final: 0.9043 (p) REVERT: A 311 TYR cc_start: 0.9266 (m-80) cc_final: 0.8978 (m-80) REVERT: B 89 LYS cc_start: 0.8742 (mttp) cc_final: 0.8375 (mtmt) REVERT: B 111 TYR cc_start: 0.8649 (m-80) cc_final: 0.8411 (m-80) REVERT: B 254 ASP cc_start: 0.8490 (t70) cc_final: 0.8235 (t0) REVERT: R 232 LYS cc_start: 0.8145 (tppp) cc_final: 0.7942 (ttmm) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1657 time to fit residues: 23.3286 Evaluate side-chains 70 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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: 10.0000 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 45 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 278 ASN R 296 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6689 Z= 0.178 Angle : 0.530 6.273 9173 Z= 0.283 Chirality : 0.041 0.152 1115 Planarity : 0.004 0.040 1145 Dihedral : 9.488 153.006 998 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.52 % Allowed : 9.93 % Favored : 89.55 % 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: 1.29 (0.29), residues: 899 helix: 2.21 (0.27), residues: 395 sheet: 0.71 (0.41), residues: 180 loop : -0.79 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 158 HIS 0.008 0.001 HIS A 220 PHE 0.010 0.001 PHE A 363 TYR 0.033 0.002 TYR R 185 ARG 0.005 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.738 Fit side-chains REVERT: A 51 SER cc_start: 0.9216 (p) cc_final: 0.8957 (p) REVERT: B 89 LYS cc_start: 0.8798 (mttp) cc_final: 0.8375 (mtpt) REVERT: B 254 ASP cc_start: 0.8498 (t70) cc_final: 0.8271 (t0) REVERT: R 175 ARG cc_start: 0.8234 (mtp180) cc_final: 0.7883 (mmm160) outliers start: 3 outliers final: 2 residues processed: 91 average time/residue: 0.1765 time to fit residues: 21.9505 Evaluate side-chains 80 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain R residue 56 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 79 optimal weight: 0.0770 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS R 296 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6689 Z= 0.200 Angle : 0.504 6.527 9173 Z= 0.272 Chirality : 0.040 0.149 1115 Planarity : 0.003 0.040 1145 Dihedral : 8.039 142.273 998 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.92 % Allowed : 10.63 % Favored : 87.46 % 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: 1.38 (0.29), residues: 899 helix: 2.33 (0.27), residues: 400 sheet: 0.56 (0.42), residues: 180 loop : -0.72 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 313 HIS 0.006 0.001 HIS A 220 PHE 0.012 0.001 PHE B 241 TYR 0.047 0.002 TYR R 185 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 0.735 Fit side-chains REVERT: A 51 SER cc_start: 0.9134 (p) cc_final: 0.8869 (p) REVERT: B 89 LYS cc_start: 0.8864 (mttp) cc_final: 0.8336 (mtpt) REVERT: B 254 ASP cc_start: 0.8499 (t70) cc_final: 0.8268 (t0) outliers start: 11 outliers final: 8 residues processed: 88 average time/residue: 0.1695 time to fit residues: 20.5922 Evaluate side-chains 82 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 4.9990 chunk 42 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 0.0980 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 183 HIS G 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6689 Z= 0.211 Angle : 0.494 6.019 9173 Z= 0.266 Chirality : 0.040 0.145 1115 Planarity : 0.003 0.037 1145 Dihedral : 7.316 135.223 998 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.92 % Allowed : 12.54 % Favored : 85.54 % 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: 1.43 (0.30), residues: 899 helix: 2.53 (0.27), residues: 393 sheet: 0.43 (0.41), residues: 180 loop : -0.76 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 313 HIS 0.006 0.001 HIS A 362 PHE 0.012 0.001 PHE B 241 TYR 0.032 0.002 TYR R 185 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.735 Fit side-chains REVERT: A 51 SER cc_start: 0.9059 (p) cc_final: 0.8804 (p) REVERT: B 89 LYS cc_start: 0.8864 (mttp) cc_final: 0.8332 (mtpt) REVERT: B 254 ASP cc_start: 0.8488 (t70) cc_final: 0.8277 (t0) outliers start: 11 outliers final: 9 residues processed: 89 average time/residue: 0.1656 time to fit residues: 20.3537 Evaluate side-chains 84 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 59 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6689 Z= 0.159 Angle : 0.461 6.045 9173 Z= 0.248 Chirality : 0.040 0.141 1115 Planarity : 0.003 0.035 1145 Dihedral : 6.932 132.183 998 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.79 % Allowed : 13.24 % Favored : 83.97 % 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: 1.51 (0.30), residues: 899 helix: 2.66 (0.27), residues: 389 sheet: 0.40 (0.41), residues: 180 loop : -0.70 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.007 0.001 HIS R 296 PHE 0.009 0.001 PHE B 241 TYR 0.028 0.001 TYR R 185 ARG 0.002 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 0.741 Fit side-chains REVERT: A 51 SER cc_start: 0.9135 (p) cc_final: 0.8894 (p) REVERT: B 89 LYS cc_start: 0.8868 (mttp) cc_final: 0.8338 (mtpt) REVERT: B 228 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7070 (m-30) REVERT: B 254 ASP cc_start: 0.8332 (t70) cc_final: 0.8101 (t0) outliers start: 16 outliers final: 13 residues processed: 95 average time/residue: 0.1630 time to fit residues: 21.4242 Evaluate side-chains 91 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.0570 chunk 21 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6689 Z= 0.148 Angle : 0.460 6.401 9173 Z= 0.245 Chirality : 0.039 0.140 1115 Planarity : 0.003 0.035 1145 Dihedral : 6.650 129.525 998 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.61 % Allowed : 15.16 % Favored : 82.23 % 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: 1.55 (0.30), residues: 899 helix: 2.84 (0.27), residues: 383 sheet: 0.25 (0.40), residues: 185 loop : -0.71 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 339 HIS 0.007 0.001 HIS R 296 PHE 0.009 0.001 PHE B 241 TYR 0.025 0.001 TYR R 185 ARG 0.005 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.756 Fit side-chains REVERT: A 51 SER cc_start: 0.9134 (p) cc_final: 0.8897 (p) REVERT: B 89 LYS cc_start: 0.8865 (mttp) cc_final: 0.8345 (mtpt) REVERT: B 228 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7079 (m-30) REVERT: B 254 ASP cc_start: 0.8307 (t70) cc_final: 0.8085 (t0) REVERT: R 111 SER cc_start: 0.8668 (m) cc_final: 0.7969 (t) outliers start: 15 outliers final: 13 residues processed: 96 average time/residue: 0.1621 time to fit residues: 22.0279 Evaluate side-chains 96 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 0.2980 chunk 85 optimal weight: 0.0050 chunk 53 optimal weight: 0.0870 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 overall best weight: 0.4574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 267 GLN A 271 ASN G 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6689 Z= 0.136 Angle : 0.465 9.826 9173 Z= 0.244 Chirality : 0.039 0.172 1115 Planarity : 0.003 0.031 1145 Dihedral : 6.480 127.873 998 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.48 % Allowed : 14.81 % Favored : 81.71 % 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: 1.62 (0.30), residues: 899 helix: 2.90 (0.27), residues: 383 sheet: 0.30 (0.40), residues: 184 loop : -0.68 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 339 HIS 0.007 0.001 HIS R 296 PHE 0.007 0.001 PHE B 241 TYR 0.046 0.001 TYR R 185 ARG 0.003 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 0.724 Fit side-chains REVERT: A 51 SER cc_start: 0.9140 (p) cc_final: 0.8911 (p) REVERT: B 89 LYS cc_start: 0.8847 (mttp) cc_final: 0.8345 (mtpt) REVERT: B 228 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7058 (m-30) REVERT: B 254 ASP cc_start: 0.8154 (t70) cc_final: 0.7923 (t0) REVERT: R 111 SER cc_start: 0.8658 (m) cc_final: 0.7964 (t) outliers start: 20 outliers final: 14 residues processed: 102 average time/residue: 0.1544 time to fit residues: 21.9975 Evaluate side-chains 100 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 271 ASN G 18 GLN ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6689 Z= 0.191 Angle : 0.495 7.960 9173 Z= 0.262 Chirality : 0.040 0.175 1115 Planarity : 0.003 0.032 1145 Dihedral : 6.486 127.584 998 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.96 % Allowed : 15.51 % Favored : 81.53 % 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: 1.60 (0.29), residues: 899 helix: 2.89 (0.27), residues: 387 sheet: 0.28 (0.41), residues: 180 loop : -0.74 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 339 HIS 0.006 0.001 HIS R 296 PHE 0.011 0.001 PHE B 241 TYR 0.041 0.002 TYR R 185 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 0.824 Fit side-chains REVERT: A 51 SER cc_start: 0.9095 (p) cc_final: 0.8861 (p) REVERT: B 89 LYS cc_start: 0.8873 (mttp) cc_final: 0.8327 (mtpt) REVERT: B 228 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7138 (m-30) REVERT: B 254 ASP cc_start: 0.8211 (t70) cc_final: 0.7988 (t0) REVERT: R 111 SER cc_start: 0.8724 (m) cc_final: 0.8042 (t) outliers start: 17 outliers final: 15 residues processed: 91 average time/residue: 0.1807 time to fit residues: 22.5173 Evaluate side-chains 97 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 52 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS G 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6689 Z= 0.152 Angle : 0.470 8.707 9173 Z= 0.248 Chirality : 0.039 0.163 1115 Planarity : 0.003 0.030 1145 Dihedral : 6.410 127.203 998 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.79 % Allowed : 15.33 % Favored : 81.88 % 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: 1.62 (0.30), residues: 899 helix: 2.95 (0.27), residues: 383 sheet: 0.23 (0.41), residues: 180 loop : -0.70 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 339 HIS 0.007 0.001 HIS R 296 PHE 0.009 0.001 PHE B 241 TYR 0.040 0.001 TYR R 185 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.777 Fit side-chains REVERT: B 89 LYS cc_start: 0.8847 (mttp) cc_final: 0.8323 (mtpt) REVERT: B 228 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.6976 (m-30) REVERT: B 254 ASP cc_start: 0.8279 (t70) cc_final: 0.8045 (t0) REVERT: R 111 SER cc_start: 0.8710 (m) cc_final: 0.8014 (t) outliers start: 16 outliers final: 15 residues processed: 94 average time/residue: 0.1611 time to fit residues: 21.0428 Evaluate side-chains 97 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS G 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6689 Z= 0.211 Angle : 0.508 8.460 9173 Z= 0.271 Chirality : 0.040 0.163 1115 Planarity : 0.003 0.030 1145 Dihedral : 6.481 127.546 998 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.14 % Allowed : 15.16 % Favored : 81.71 % 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: 1.57 (0.30), residues: 899 helix: 2.91 (0.27), residues: 387 sheet: 0.23 (0.42), residues: 175 loop : -0.78 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 339 HIS 0.007 0.001 HIS A 220 PHE 0.012 0.001 PHE B 241 TYR 0.041 0.002 TYR R 185 ARG 0.004 0.000 ARG R 228 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 0.746 Fit side-chains REVERT: A 51 SER cc_start: 0.9042 (p) cc_final: 0.8809 (p) REVERT: B 89 LYS cc_start: 0.8862 (mttp) cc_final: 0.8316 (mtpt) REVERT: B 228 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7018 (m-30) REVERT: B 254 ASP cc_start: 0.8287 (t70) cc_final: 0.8052 (t0) REVERT: R 111 SER cc_start: 0.8755 (m) cc_final: 0.8083 (t) REVERT: R 161 SER cc_start: 0.8707 (t) cc_final: 0.8236 (p) outliers start: 18 outliers final: 16 residues processed: 91 average time/residue: 0.1785 time to fit residues: 22.5296 Evaluate side-chains 98 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 0.2980 chunk 29 optimal weight: 0.1980 chunk 72 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.122370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.096934 restraints weight = 50280.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.101647 restraints weight = 15043.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.104926 restraints weight = 7119.090| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6689 Z= 0.137 Angle : 0.470 9.135 9173 Z= 0.247 Chirality : 0.039 0.155 1115 Planarity : 0.003 0.029 1145 Dihedral : 6.313 126.662 998 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.61 % Allowed : 16.03 % Favored : 81.36 % 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: 1.64 (0.30), residues: 899 helix: 2.98 (0.27), residues: 383 sheet: 0.32 (0.43), residues: 169 loop : -0.72 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.007 0.001 HIS R 296 PHE 0.008 0.001 PHE B 241 TYR 0.038 0.001 TYR R 185 ARG 0.005 0.000 ARG R 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1615.13 seconds wall clock time: 29 minutes 43.31 seconds (1783.31 seconds total)