Starting phenix.real_space_refine on Tue May 7 02:14:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uno_42411/05_2024/8uno_42411_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uno_42411/05_2024/8uno_42411.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/8uno_42411/05_2024/8uno_42411.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uno_42411/05_2024/8uno_42411.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uno_42411/05_2024/8uno_42411_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uno_42411/05_2024/8uno_42411_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= 0.023 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 37 5.16 5 C 4186 2.51 5 N 1117 2.21 5 O 1146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 226": "OE1" <-> "OE2" Residue "R GLU 107": "OE1" <-> "OE2" 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: 6489 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1669 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 223, 1657 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 5 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 142 Conformer: "B" Number of residues, atoms: 223, 1657 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 5 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 142 bond proxies already assigned to first conformer: 1674 Chain: "B" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2335 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 5, 'ARG:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 16} Unresolved non-hydrogen planarities: 154 Chain: "G" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 349 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "R" Number of atoms: 2089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2089 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 115 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: 4.80, per 1000 atoms: 0.74 Number of scatterers: 6489 At special positions: 0 Unit cell: (82.4315, 131.023, 95.447, 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 37 16.00 P 3 15.00 O 1146 8.00 N 1117 7.00 C 4186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 2.48 Conformation dependent library (CDL) restraints added in 1.6 seconds 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1700 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 8 sheets defined 44.0% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 15 through 39 removed outlier: 4.009A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 60 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 294 through 303 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 Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.688A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.845A 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: 3.873A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'G' and resid 10 through 23 removed outlier: 3.823A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 46 removed outlier: 5.199A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 60 removed outlier: 3.782A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 64 No H-bonds generated for 'chain 'R' and resid 62 through 64' Processing helix chain 'R' and resid 67 through 96 removed outlier: 4.402A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 103 through 136 removed outlier: 3.829A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) 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 163 removed outlier: 3.810A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (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: 4.050A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 237 removed outlier: 3.984A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 286 removed outlier: 3.715A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 298 removed outlier: 4.716A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 326 removed outlier: 3.728A pdb=" N GLY R 315 " --> pdb=" O LEU R 311 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR R 316 " --> pdb=" O ASN R 312 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (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 362 removed outlier: 7.497A pdb=" N VAL A 287 " --> pdb=" O ATYR A 360 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 208 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.713A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.964A 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: 7.049A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.102A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.960A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.347A 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: 3.711A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.906A 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: 6.584A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.907A 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: 6.830A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 930 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: 1.78 Time building geometry restraints manager: 2.66 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: 1617 1.33 - 1.45: 1351 1.45 - 1.57: 3607 1.57 - 1.69: 5 1.69 - 1.81: 51 Bond restraints: 6631 Sorted by residual: bond pdb=" C5 GTP A 401 " pdb=" C6 GTP A 401 " ideal model delta sigma weight residual 1.390 1.472 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" CA ASN A 254 " pdb=" C ASN A 254 " ideal model delta sigma weight residual 1.524 1.476 0.048 1.24e-02 6.50e+03 1.48e+01 bond pdb=" CA VAL R 39 " pdb=" C VAL R 39 " ideal model delta sigma weight residual 1.524 1.478 0.046 1.22e-02 6.72e+03 1.39e+01 bond pdb=" C4 GTP A 401 " pdb=" C5 GTP A 401 " ideal model delta sigma weight residual 1.390 1.459 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" CA GLU B 12 " pdb=" C GLU B 12 " ideal model delta sigma weight residual 1.522 1.477 0.045 1.41e-02 5.03e+03 1.03e+01 ... (remaining 6626 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.51: 210 107.51 - 114.61: 3897 114.61 - 121.71: 3529 121.71 - 128.81: 1387 128.81 - 135.91: 59 Bond angle restraints: 9082 Sorted by residual: angle pdb=" N GLU B 12 " pdb=" CA GLU B 12 " pdb=" C GLU B 12 " ideal model delta sigma weight residual 112.38 102.27 10.11 1.22e+00 6.72e-01 6.86e+01 angle pdb=" N LEU G 19 " pdb=" CA LEU G 19 " pdb=" C LEU G 19 " ideal model delta sigma weight residual 111.28 102.85 8.43 1.09e+00 8.42e-01 5.98e+01 angle pdb=" N ASN B 35 " pdb=" CA ASN B 35 " pdb=" C ASN B 35 " ideal model delta sigma weight residual 111.28 117.24 -5.96 1.09e+00 8.42e-01 2.99e+01 angle pdb=" N ASN B 36 " pdb=" CA ASN B 36 " pdb=" C ASN B 36 " ideal model delta sigma weight residual 111.28 116.68 -5.40 1.09e+00 8.42e-01 2.46e+01 angle pdb=" N GLN B 9 " pdb=" CA GLN B 9 " pdb=" C GLN B 9 " ideal model delta sigma weight residual 112.38 106.94 5.44 1.22e+00 6.72e-01 1.99e+01 ... (remaining 9077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.87: 3629 22.87 - 45.75: 163 45.75 - 68.62: 8 68.62 - 91.50: 7 91.50 - 114.37: 3 Dihedral angle restraints: 3810 sinusoidal: 1196 harmonic: 2614 Sorted by residual: dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual -56.21 -170.58 114.37 1 2.00e+01 2.50e-03 3.39e+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 2.67 101.92 1 2.00e+01 2.50e-03 2.90e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 165.10 -95.83 1 2.00e+01 2.50e-03 2.64e+01 ... (remaining 3807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 784 0.039 - 0.078: 219 0.078 - 0.118: 80 0.118 - 0.157: 10 0.157 - 0.196: 3 Chirality restraints: 1096 Sorted by residual: chirality pdb=" CA ALA B 11 " pdb=" N ALA B 11 " pdb=" C ALA B 11 " pdb=" CB ALA B 11 " both_signs ideal model delta sigma weight residual False 2.48 2.29 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CA ALA B 305 " pdb=" N ALA B 305 " pdb=" C ALA B 305 " pdb=" CB ALA B 305 " both_signs ideal model delta sigma weight residual False 2.48 2.32 0.17 2.00e-01 2.50e+01 6.99e-01 ... (remaining 1093 not shown) Planarity restraints: 1132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " -0.050 5.00e-02 4.00e+02 7.73e-02 9.57e+00 pdb=" N PRO B 39 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.048 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO G 49 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 253 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.89e+00 pdb=" C TYR A 253 " 0.045 2.00e-02 2.50e+03 pdb=" O TYR A 253 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN A 254 " -0.016 2.00e-02 2.50e+03 ... (remaining 1129 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1230 2.77 - 3.30: 6051 3.30 - 3.83: 9990 3.83 - 4.37: 11048 4.37 - 4.90: 20223 Nonbonded interactions: 48542 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.236 2.440 nonbonded pdb=" O SER R 111 " pdb=" OG SER R 165 " model vdw 2.333 2.440 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.347 2.440 nonbonded pdb=" N GLU A 50 " pdb=" O2G GTP A 401 " model vdw 2.368 2.520 nonbonded pdb=" N CYS A 365 " pdb=" OD2 ASP A 368 " model vdw 2.387 2.520 ... (remaining 48537 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: 3.810 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: 0.000 Extract box with map and model: 7.610 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.290 Find NCS groups from input model: 0.210 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 : 0.005 0.082 6631 Z= 0.306 Angle : 0.669 10.589 9082 Z= 0.406 Chirality : 0.042 0.196 1096 Planarity : 0.005 0.077 1132 Dihedral : 13.445 114.370 2110 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.17 % Allowed : 0.69 % Favored : 99.13 % 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: 875 helix: 2.00 (0.28), residues: 387 sheet: 0.65 (0.42), residues: 173 loop : -0.72 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 211 HIS 0.006 0.001 HIS B 183 PHE 0.010 0.001 PHE B 199 TYR 0.023 0.001 TYR A 253 ARG 0.002 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 0.731 Fit side-chains REVERT: G 48 ASP cc_start: 0.7982 (p0) cc_final: 0.7777 (p0) REVERT: R 103 ASN cc_start: 0.6069 (m-40) cc_final: 0.5818 (m-40) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.1976 time to fit residues: 29.1559 Evaluate side-chains 91 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 9.9990 chunk 66 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 30.0000 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 ASN R 296 HIS R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6631 Z= 0.189 Angle : 0.489 6.979 9082 Z= 0.260 Chirality : 0.041 0.166 1096 Planarity : 0.004 0.059 1132 Dihedral : 8.287 116.230 977 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.38 % Allowed : 9.52 % Favored : 89.10 % 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: 1.35 (0.29), residues: 875 helix: 2.32 (0.27), residues: 378 sheet: 0.48 (0.40), residues: 176 loop : -0.58 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.006 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.011 0.001 TYR A 311 ARG 0.002 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.762 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 100 average time/residue: 0.2077 time to fit residues: 27.3719 Evaluate side-chains 95 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain R residue 190 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 30.0000 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 6631 Z= 0.411 Angle : 0.604 6.848 9082 Z= 0.324 Chirality : 0.045 0.163 1096 Planarity : 0.005 0.072 1132 Dihedral : 8.344 114.709 977 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.77 % Allowed : 11.76 % Favored : 85.47 % 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: 0.65 (0.28), residues: 875 helix: 1.64 (0.27), residues: 388 sheet: 0.18 (0.40), residues: 170 loop : -0.91 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.009 0.002 HIS A 357 PHE 0.016 0.002 PHE A 273 TYR 0.012 0.002 TYR A 339 ARG 0.003 0.001 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 0.694 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 92 average time/residue: 0.2002 time to fit residues: 24.3126 Evaluate side-chains 92 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 237 GLU Chi-restraints excluded: chain R residue 295 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 30.0000 chunk 70 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6631 Z= 0.163 Angle : 0.471 6.283 9082 Z= 0.251 Chirality : 0.040 0.185 1096 Planarity : 0.004 0.075 1132 Dihedral : 8.016 119.507 977 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.25 % Allowed : 15.05 % Favored : 82.70 % 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: 1.02 (0.29), residues: 875 helix: 2.05 (0.28), residues: 380 sheet: 0.16 (0.39), residues: 176 loop : -0.69 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 277 HIS 0.005 0.001 HIS A 220 PHE 0.013 0.001 PHE B 199 TYR 0.021 0.001 TYR A 253 ARG 0.006 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.716 Fit side-chains REVERT: B 59 TYR cc_start: 0.8477 (m-80) cc_final: 0.7731 (m-80) REVERT: G 38 MET cc_start: 0.7830 (ttp) cc_final: 0.7610 (ttp) outliers start: 13 outliers final: 11 residues processed: 87 average time/residue: 0.1989 time to fit residues: 22.9527 Evaluate side-chains 86 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 190 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.0040 chunk 1 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6631 Z= 0.139 Angle : 0.444 6.258 9082 Z= 0.236 Chirality : 0.040 0.188 1096 Planarity : 0.004 0.074 1132 Dihedral : 7.715 123.651 977 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.42 % Allowed : 15.40 % Favored : 82.18 % 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: 1.20 (0.30), residues: 875 helix: 2.34 (0.28), residues: 366 sheet: 0.13 (0.39), residues: 176 loop : -0.57 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.004 0.001 HIS A 220 PHE 0.012 0.001 PHE B 199 TYR 0.021 0.001 TYR A 253 ARG 0.001 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.713 Fit side-chains REVERT: B 59 TYR cc_start: 0.8419 (m-80) cc_final: 0.7689 (m-80) outliers start: 14 outliers final: 8 residues processed: 91 average time/residue: 0.1950 time to fit residues: 23.5930 Evaluate side-chains 87 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 237 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 0.0770 chunk 7 optimal weight: 0.0980 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6631 Z= 0.123 Angle : 0.435 6.341 9082 Z= 0.229 Chirality : 0.039 0.190 1096 Planarity : 0.003 0.072 1132 Dihedral : 7.620 127.231 977 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.90 % Allowed : 16.61 % Favored : 81.49 % 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: 1.26 (0.30), residues: 875 helix: 2.36 (0.28), residues: 367 sheet: 0.20 (0.39), residues: 176 loop : -0.53 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 277 HIS 0.004 0.001 HIS A 220 PHE 0.013 0.001 PHE A 212 TYR 0.022 0.001 TYR A 253 ARG 0.002 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.773 Fit side-chains REVERT: B 59 TYR cc_start: 0.8350 (m-80) cc_final: 0.7656 (m-80) outliers start: 11 outliers final: 9 residues processed: 92 average time/residue: 0.1977 time to fit residues: 24.1687 Evaluate side-chains 88 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 237 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 0.0670 chunk 33 optimal weight: 2.9990 overall best weight: 1.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 6631 Z= 0.320 Angle : 0.525 6.950 9082 Z= 0.281 Chirality : 0.042 0.179 1096 Planarity : 0.004 0.075 1132 Dihedral : 7.822 127.690 977 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.25 % Allowed : 16.61 % Favored : 81.14 % 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: 0.86 (0.29), residues: 875 helix: 1.95 (0.28), residues: 372 sheet: 0.10 (0.40), residues: 169 loop : -0.73 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.006 0.001 HIS A 357 PHE 0.015 0.002 PHE A 212 TYR 0.023 0.002 TYR A 253 ARG 0.004 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.740 Fit side-chains REVERT: A 270 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8496 (mp) REVERT: B 234 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.7643 (t80) REVERT: B 331 SER cc_start: 0.9310 (p) cc_final: 0.9108 (p) outliers start: 13 outliers final: 9 residues processed: 92 average time/residue: 0.1994 time to fit residues: 24.3217 Evaluate side-chains 92 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 237 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6631 Z= 0.252 Angle : 0.495 6.760 9082 Z= 0.265 Chirality : 0.041 0.191 1096 Planarity : 0.004 0.076 1132 Dihedral : 7.812 128.101 977 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.25 % Allowed : 17.47 % Favored : 80.28 % 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: 0.77 (0.29), residues: 875 helix: 1.87 (0.28), residues: 372 sheet: -0.02 (0.39), residues: 175 loop : -0.73 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 211 HIS 0.005 0.001 HIS A 220 PHE 0.014 0.001 PHE A 212 TYR 0.023 0.001 TYR A 253 ARG 0.003 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 0.702 Fit side-chains REVERT: A 270 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8463 (mp) REVERT: B 59 TYR cc_start: 0.8518 (m-80) cc_final: 0.7836 (m-80) REVERT: B 234 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.7638 (t80) REVERT: B 331 SER cc_start: 0.9325 (p) cc_final: 0.9050 (p) REVERT: G 27 ARG cc_start: 0.8376 (mpt180) cc_final: 0.8007 (mmt180) outliers start: 13 outliers final: 11 residues processed: 88 average time/residue: 0.1902 time to fit residues: 22.5440 Evaluate side-chains 92 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 237 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6631 Z= 0.214 Angle : 0.481 6.845 9082 Z= 0.256 Chirality : 0.041 0.186 1096 Planarity : 0.004 0.075 1132 Dihedral : 7.713 128.348 977 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.08 % Allowed : 17.99 % Favored : 79.93 % 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: 0.81 (0.29), residues: 875 helix: 1.88 (0.28), residues: 373 sheet: -0.04 (0.39), residues: 176 loop : -0.67 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 211 HIS 0.005 0.001 HIS A 220 PHE 0.014 0.001 PHE A 212 TYR 0.022 0.001 TYR A 253 ARG 0.003 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.848 Fit side-chains REVERT: A 270 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8503 (mp) REVERT: B 59 TYR cc_start: 0.8507 (m-80) cc_final: 0.7798 (m-80) REVERT: B 234 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.7620 (t80) REVERT: B 331 SER cc_start: 0.9321 (p) cc_final: 0.9082 (p) outliers start: 12 outliers final: 9 residues processed: 88 average time/residue: 0.2056 time to fit residues: 24.0171 Evaluate side-chains 92 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 237 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.1980 chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 55 optimal weight: 0.0070 chunk 74 optimal weight: 6.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6631 Z= 0.127 Angle : 0.446 6.572 9082 Z= 0.233 Chirality : 0.039 0.199 1096 Planarity : 0.004 0.074 1132 Dihedral : 7.459 129.894 977 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.56 % Allowed : 19.20 % Favored : 79.24 % 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: 0.98 (0.29), residues: 875 helix: 2.06 (0.29), residues: 372 sheet: 0.03 (0.39), residues: 176 loop : -0.60 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 277 HIS 0.003 0.001 HIS A 220 PHE 0.013 0.001 PHE A 212 TYR 0.022 0.001 TYR A 253 ARG 0.009 0.000 ARG R 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.702 Fit side-chains REVERT: A 270 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8485 (mp) REVERT: B 59 TYR cc_start: 0.8434 (m-80) cc_final: 0.7725 (m-80) REVERT: B 331 SER cc_start: 0.9310 (p) cc_final: 0.9076 (p) outliers start: 9 outliers final: 8 residues processed: 93 average time/residue: 0.1824 time to fit residues: 22.7866 Evaluate side-chains 93 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain R residue 195 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.123235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.100386 restraints weight = 11314.040| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.63 r_work: 0.3202 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6631 Z= 0.166 Angle : 0.461 6.975 9082 Z= 0.241 Chirality : 0.040 0.190 1096 Planarity : 0.004 0.074 1132 Dihedral : 7.400 129.514 977 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.38 % Allowed : 19.72 % Favored : 78.89 % 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: 0.98 (0.29), residues: 875 helix: 2.06 (0.28), residues: 372 sheet: 0.06 (0.39), residues: 176 loop : -0.63 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 277 HIS 0.005 0.001 HIS A 220 PHE 0.012 0.001 PHE B 199 TYR 0.026 0.001 TYR A 253 ARG 0.008 0.000 ARG R 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1705.92 seconds wall clock time: 32 minutes 2.08 seconds (1922.08 seconds total)