Starting phenix.real_space_refine on Fri Apr 5 21:54:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgh_41236/04_2024/8tgh_41236_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgh_41236/04_2024/8tgh_41236.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgh_41236/04_2024/8tgh_41236_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgh_41236/04_2024/8tgh_41236_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgh_41236/04_2024/8tgh_41236_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgh_41236/04_2024/8tgh_41236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgh_41236/04_2024/8tgh_41236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgh_41236/04_2024/8tgh_41236_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgh_41236/04_2024/8tgh_41236_trim_updated.pdb" } resolution = 3.5 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= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 3843 2.51 5 N 900 2.21 5 O 978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5778 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2860 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 360} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2864 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 21, 'TRANS': 361} Chain breaks: 2 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'1WE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.46, per 1000 atoms: 0.60 Number of scatterers: 5778 At special positions: 0 Unit cell: (77.688, 62.416, 114.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 978 8.00 N 900 7.00 C 3843 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: 2.52 Conformation dependent library (CDL) restraints added in 1.2 seconds 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 1WE A 601 " Number of C-beta restraints generated: 1370 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 0 sheets defined 85.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 20 through 50 removed outlier: 4.036A pdb=" N LEU A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Proline residue: A 43 - end of helix Proline residue: A 46 - end of helix removed outlier: 3.828A pdb=" N TYR A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 164 removed outlier: 3.506A pdb=" N LEU A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LYS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ALA A 147 " --> pdb=" O PHE A 143 " (cutoff:3.500A) Proline residue: A 155 - end of helix Proline residue: A 159 - end of helix removed outlier: 4.041A pdb=" N ASN A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 186 Processing helix chain 'A' and resid 190 through 218 removed outlier: 3.766A pdb=" N VAL A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 253 removed outlier: 4.524A pdb=" N ALA A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Proline residue: A 245 - end of helix Processing helix chain 'A' and resid 257 through 277 Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.793A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 293 through 298' Processing helix chain 'A' and resid 300 through 330 removed outlier: 3.715A pdb=" N LEU A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) Proline residue: A 321 - end of helix Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 335 through 341 removed outlier: 4.385A pdb=" N GLY A 339 " --> pdb=" O TRP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 363 removed outlier: 4.367A pdb=" N GLY A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 389 through 420 removed outlier: 3.574A pdb=" N ILE A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLY A 394 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Proline residue: A 395 - end of helix removed outlier: 3.534A pdb=" N SER A 408 " --> pdb=" O MET A 405 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N MET A 411 " --> pdb=" O SER A 408 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 427 through 454 removed outlier: 4.321A pdb=" N GLY A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) Proline residue: A 445 - end of helix removed outlier: 4.941A pdb=" N GLY A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ALA A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 478 Proline residue: A 473 - end of helix removed outlier: 4.810A pdb=" N TYR A 476 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TYR A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LEU A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 53 removed outlier: 3.769A pdb=" N LEU B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Proline residue: B 43 - end of helix Proline residue: B 46 - end of helix removed outlier: 3.768A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 164 removed outlier: 3.603A pdb=" N ILE B 136 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR B 137 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS B 146 " --> pdb=" O PHE B 143 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN B 154 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Proline residue: B 155 - end of helix removed outlier: 4.366A pdb=" N GLY B 158 " --> pdb=" O PRO B 155 " (cutoff:3.500A) Proline residue: B 159 - end of helix removed outlier: 3.886A pdb=" N ILE B 164 " --> pdb=" O THR B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 186 removed outlier: 3.540A pdb=" N GLY B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 174 " --> pdb=" O MET B 170 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 218 removed outlier: 3.540A pdb=" N PHE B 194 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 195 " --> pdb=" O THR B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 241 removed outlier: 4.019A pdb=" N LEU B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 253 removed outlier: 4.348A pdb=" N SER B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL B 249 " --> pdb=" O PRO B 245 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE B 253 " --> pdb=" O VAL B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 Processing helix chain 'B' and resid 293 through 296 No H-bonds generated for 'chain 'B' and resid 293 through 296' Processing helix chain 'B' and resid 300 through 330 removed outlier: 3.797A pdb=" N ALA B 305 " --> pdb=" O TYR B 301 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 319 " --> pdb=" O GLY B 315 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 320 " --> pdb=" O VAL B 316 " (cutoff:3.500A) Proline residue: B 321 - end of helix Proline residue: B 324 - end of helix Processing helix chain 'B' and resid 340 through 363 Proline residue: B 344 - end of helix removed outlier: 4.808A pdb=" N SER B 348 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE B 356 " --> pdb=" O THR B 353 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ALA B 360 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASN B 361 " --> pdb=" O VAL B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 385 Proline residue: B 384 - end of helix Processing helix chain 'B' and resid 389 through 421 removed outlier: 3.538A pdb=" N ILE B 393 " --> pdb=" O PHE B 390 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY B 394 " --> pdb=" O GLY B 391 " (cutoff:3.500A) Proline residue: B 395 - end of helix removed outlier: 3.533A pdb=" N ASP B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET B 410 " --> pdb=" O ASP B 407 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N MET B 411 " --> pdb=" O SER B 408 " (cutoff:3.500A) Proline residue: B 412 - end of helix removed outlier: 3.805A pdb=" N ARG B 421 " --> pdb=" O VAL B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 454 removed outlier: 3.552A pdb=" N ILE B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Proline residue: B 445 - end of helix removed outlier: 3.879A pdb=" N ALA B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 478 removed outlier: 3.554A pdb=" N MET B 461 " --> pdb=" O PHE B 457 " (cutoff:3.500A) Proline residue: B 473 - end of helix removed outlier: 5.118A pdb=" N TYR B 476 " --> pdb=" O ALA B 472 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N TYR B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 984 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: 1.47 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 861 1.28 - 1.41: 1471 1.41 - 1.54: 3480 1.54 - 1.68: 10 1.68 - 1.81: 100 Bond restraints: 5922 Sorted by residual: bond pdb=" C ALA B 244 " pdb=" O ALA B 244 " ideal model delta sigma weight residual 1.244 1.157 0.087 1.00e-02 1.00e+04 7.62e+01 bond pdb=" C10 YHR B 601 " pdb=" C11 YHR B 601 " ideal model delta sigma weight residual 1.572 1.429 0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" C LEU B 238 " pdb=" O LEU B 238 " ideal model delta sigma weight residual 1.237 1.161 0.075 1.17e-02 7.31e+03 4.13e+01 bond pdb=" C PRO B 245 " pdb=" O PRO B 245 " ideal model delta sigma weight residual 1.236 1.144 0.092 1.76e-02 3.23e+03 2.71e+01 bond pdb=" C GLY B 243 " pdb=" O GLY B 243 " ideal model delta sigma weight residual 1.235 1.166 0.069 1.35e-02 5.49e+03 2.62e+01 ... (remaining 5917 not shown) Histogram of bond angle deviations from ideal: 98.63 - 106.26: 208 106.26 - 113.89: 3385 113.89 - 121.53: 3399 121.53 - 129.16: 1040 129.16 - 136.80: 34 Bond angle restraints: 8066 Sorted by residual: angle pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C9 YHR B 601 " ideal model delta sigma weight residual 99.45 130.32 -30.87 3.00e+00 1.11e-01 1.06e+02 angle pdb=" CA ALA B 244 " pdb=" C ALA B 244 " pdb=" O ALA B 244 " ideal model delta sigma weight residual 118.79 110.51 8.28 9.60e-01 1.09e+00 7.45e+01 angle pdb=" N GLY A 243 " pdb=" CA GLY A 243 " pdb=" C GLY A 243 " ideal model delta sigma weight residual 112.50 119.23 -6.73 1.16e+00 7.43e-01 3.36e+01 angle pdb=" C12 YHR B 601 " pdb=" C13 YHR B 601 " pdb=" N8 YHR B 601 " ideal model delta sigma weight residual 117.31 100.47 16.84 3.00e+00 1.11e-01 3.15e+01 angle pdb=" C VAL B 242 " pdb=" CA VAL B 242 " pdb=" CB VAL B 242 " ideal model delta sigma weight residual 112.19 106.43 5.76 1.15e+00 7.56e-01 2.51e+01 ... (remaining 8061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.24: 3059 22.24 - 44.48: 327 44.48 - 66.73: 36 66.73 - 88.97: 5 88.97 - 111.21: 1 Dihedral angle restraints: 3428 sinusoidal: 1272 harmonic: 2156 Sorted by residual: dihedral pdb=" CA VAL B 358 " pdb=" C VAL B 358 " pdb=" N LEU B 359 " pdb=" CA LEU B 359 " ideal model delta harmonic sigma weight residual 180.00 -160.14 -19.86 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA PRO A 43 " pdb=" C PRO A 43 " pdb=" N ILE A 44 " pdb=" CA ILE A 44 " ideal model delta harmonic sigma weight residual 180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C13 YHR B 601 " pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C6 YHR B 601 " ideal model delta sinusoidal sigma weight residual 53.17 -58.04 111.21 1 3.00e+01 1.11e-03 1.45e+01 ... (remaining 3425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 857 0.072 - 0.143: 103 0.143 - 0.215: 7 0.215 - 0.287: 1 0.287 - 0.358: 1 Chirality restraints: 969 Sorted by residual: chirality pdb=" CG LEU A 381 " pdb=" CB LEU A 381 " pdb=" CD1 LEU A 381 " pdb=" CD2 LEU A 381 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA VAL B 242 " pdb=" N VAL B 242 " pdb=" C VAL B 242 " pdb=" CB VAL B 242 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C16 YHR B 601 " pdb=" C15 YHR B 601 " pdb=" C17 YHR B 601 " pdb=" C3 YHR B 601 " both_signs ideal model delta sigma weight residual False 2.75 2.54 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 966 not shown) Planarity restraints: 983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 42 " 0.088 5.00e-02 4.00e+02 1.31e-01 2.76e+01 pdb=" N PRO A 43 " -0.227 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 244 " -0.022 2.00e-02 2.50e+03 4.53e-02 2.05e+01 pdb=" C ALA B 244 " 0.078 2.00e-02 2.50e+03 pdb=" O ALA B 244 " -0.028 2.00e-02 2.50e+03 pdb=" N PRO B 245 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 472 " -0.056 5.00e-02 4.00e+02 8.48e-02 1.15e+01 pdb=" N PRO A 473 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " -0.047 5.00e-02 4.00e+02 ... (remaining 980 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1564 2.80 - 3.32: 5582 3.32 - 3.85: 9404 3.85 - 4.37: 10181 4.37 - 4.90: 18701 Nonbonded interactions: 45432 Sorted by model distance: nonbonded pdb=" O MET A 183 " pdb=" OG SER A 187 " model vdw 2.269 2.440 nonbonded pdb=" OE1 GLU B 135 " pdb=" NH1 ARG B 138 " model vdw 2.285 2.520 nonbonded pdb=" OD1 ASP A 299 " pdb=" NH1 ARG A 421 " model vdw 2.291 2.520 nonbonded pdb=" OD2 ASP A 299 " pdb=" NE2 HIS A 422 " model vdw 2.299 2.520 nonbonded pdb=" OD1 ASN A 313 " pdb=" N 1WE A 601 " model vdw 2.309 2.520 ... (remaining 45427 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 278 or resid 289 through 482)) selection = (chain 'B' and (resid 19 through 51 or resid 136 through 482)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.380 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: 13.020 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.500 Find NCS groups from input model: 0.320 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 0.007 0.143 5922 Z= 0.424 Angle : 0.931 30.867 8066 Z= 0.477 Chirality : 0.048 0.358 969 Planarity : 0.010 0.131 983 Dihedral : 16.886 111.208 2058 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.98 % Allowed : 29.92 % Favored : 69.11 % 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: 0.62 (0.29), residues: 757 helix: 0.97 (0.21), residues: 577 sheet: None (None), residues: 0 loop : -1.28 (0.40), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 336 HIS 0.001 0.001 HIS A 167 PHE 0.033 0.002 PHE B 131 TYR 0.029 0.002 TYR B 190 ARG 0.006 0.001 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 0.622 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 128 average time/residue: 0.1191 time to fit residues: 22.3060 Evaluate side-chains 124 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 241 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.9990 chunk 57 optimal weight: 0.0020 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.0770 chunk 59 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 overall best weight: 0.3146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 274 GLN B 313 ASN B 329 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5922 Z= 0.215 Angle : 0.634 7.330 8066 Z= 0.318 Chirality : 0.043 0.218 969 Planarity : 0.008 0.077 983 Dihedral : 6.722 82.188 826 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.58 % Allowed : 26.83 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.30), residues: 757 helix: 1.29 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -1.13 (0.45), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 336 HIS 0.002 0.001 HIS A 416 PHE 0.012 0.001 PHE B 246 TYR 0.012 0.001 TYR A 430 ARG 0.003 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 143 time to evaluate : 0.534 Fit side-chains REVERT: A 200 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: B 149 MET cc_start: 0.7759 (tpp) cc_final: 0.7387 (tpt) REVERT: B 168 ILE cc_start: 0.8340 (mp) cc_final: 0.8106 (mt) outliers start: 22 outliers final: 9 residues processed: 159 average time/residue: 0.1146 time to fit residues: 26.4919 Evaluate side-chains 145 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 387 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 57 optimal weight: 0.4980 chunk 46 optimal weight: 0.3980 chunk 19 optimal weight: 0.0060 chunk 69 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 55 optimal weight: 0.5980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5922 Z= 0.204 Angle : 0.599 6.473 8066 Z= 0.297 Chirality : 0.041 0.138 969 Planarity : 0.006 0.061 983 Dihedral : 6.191 76.423 824 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.41 % Allowed : 27.64 % Favored : 68.94 % 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: 1.05 (0.31), residues: 757 helix: 1.25 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -1.26 (0.46), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.001 0.000 HIS A 416 PHE 0.018 0.001 PHE A 206 TYR 0.012 0.001 TYR B 471 ARG 0.002 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 0.557 Fit side-chains REVERT: A 200 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7494 (tm-30) REVERT: B 149 MET cc_start: 0.7729 (tpp) cc_final: 0.7357 (tpt) REVERT: B 168 ILE cc_start: 0.8259 (mp) cc_final: 0.8040 (mt) REVERT: B 421 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.6963 (mtp180) outliers start: 21 outliers final: 12 residues processed: 147 average time/residue: 0.1204 time to fit residues: 25.2905 Evaluate side-chains 146 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 421 ARG Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.5980 chunk 51 optimal weight: 0.0030 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 0.0050 chunk 46 optimal weight: 0.3980 chunk 69 optimal weight: 0.0170 chunk 73 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 overall best weight: 0.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5922 Z= 0.158 Angle : 0.569 6.850 8066 Z= 0.280 Chirality : 0.040 0.132 969 Planarity : 0.006 0.053 983 Dihedral : 5.963 73.104 824 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.07 % Allowed : 26.02 % Favored : 69.92 % 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: 1.23 (0.32), residues: 757 helix: 1.37 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -1.14 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 336 HIS 0.001 0.000 HIS A 422 PHE 0.015 0.001 PHE B 131 TYR 0.010 0.001 TYR A 430 ARG 0.002 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 177 MET cc_start: 0.7833 (ttp) cc_final: 0.7618 (ttp) REVERT: B 34 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7873 (t0) REVERT: B 149 MET cc_start: 0.7773 (tpp) cc_final: 0.7477 (tpp) REVERT: B 153 VAL cc_start: 0.7696 (t) cc_final: 0.7465 (p) REVERT: B 421 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.6862 (mtp180) REVERT: B 479 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.6656 (ptt-90) outliers start: 25 outliers final: 13 residues processed: 151 average time/residue: 0.1303 time to fit residues: 27.5866 Evaluate side-chains 141 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 421 ARG Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 479 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 0.4980 chunk 37 optimal weight: 0.2980 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 468 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5922 Z= 0.260 Angle : 0.598 6.785 8066 Z= 0.295 Chirality : 0.042 0.138 969 Planarity : 0.006 0.055 983 Dihedral : 5.854 73.141 824 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.58 % Allowed : 26.83 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.31), residues: 757 helix: 1.31 (0.22), residues: 589 sheet: None (None), residues: 0 loop : -1.21 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 366 HIS 0.002 0.001 HIS A 416 PHE 0.021 0.001 PHE A 206 TYR 0.012 0.001 TYR A 430 ARG 0.003 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 128 time to evaluate : 0.483 Fit side-chains REVERT: A 38 PHE cc_start: 0.8602 (t80) cc_final: 0.8376 (t80) REVERT: A 240 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8438 (mp) REVERT: B 40 VAL cc_start: 0.7870 (OUTLIER) cc_final: 0.7646 (p) REVERT: B 52 MET cc_start: 0.7698 (mmm) cc_final: 0.7385 (tpp) outliers start: 22 outliers final: 12 residues processed: 143 average time/residue: 0.1267 time to fit residues: 25.9696 Evaluate side-chains 140 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 70 optimal weight: 0.0670 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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: 0.7831 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5922 Z= 0.242 Angle : 0.592 7.805 8066 Z= 0.292 Chirality : 0.042 0.136 969 Planarity : 0.006 0.055 983 Dihedral : 5.781 72.696 824 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.07 % Allowed : 26.50 % Favored : 69.43 % 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: 1.13 (0.31), residues: 757 helix: 1.35 (0.22), residues: 583 sheet: None (None), residues: 0 loop : -1.23 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 336 HIS 0.002 0.000 HIS A 416 PHE 0.018 0.001 PHE A 206 TYR 0.012 0.001 TYR A 430 ARG 0.003 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 0.461 Fit side-chains REVERT: A 174 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7573 (t80) REVERT: A 212 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7917 (mt) REVERT: A 240 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8429 (mp) REVERT: B 40 VAL cc_start: 0.7872 (OUTLIER) cc_final: 0.7666 (p) REVERT: B 52 MET cc_start: 0.7705 (mmm) cc_final: 0.7370 (tpp) REVERT: B 149 MET cc_start: 0.7805 (tpp) cc_final: 0.7264 (tpp) REVERT: B 421 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7102 (mtp180) REVERT: B 479 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6662 (ptt-90) outliers start: 25 outliers final: 11 residues processed: 146 average time/residue: 0.1253 time to fit residues: 25.7793 Evaluate side-chains 140 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 421 ARG Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 479 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7850 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5922 Z= 0.296 Angle : 0.621 8.073 8066 Z= 0.305 Chirality : 0.044 0.145 969 Planarity : 0.006 0.056 983 Dihedral : 5.787 74.688 824 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.07 % Allowed : 26.34 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.31), residues: 757 helix: 1.26 (0.22), residues: 583 sheet: None (None), residues: 0 loop : -1.29 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 366 HIS 0.002 0.001 HIS A 416 PHE 0.019 0.002 PHE A 206 TYR 0.016 0.002 TYR B 471 ARG 0.004 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 38 PHE cc_start: 0.8602 (t80) cc_final: 0.8371 (t80) REVERT: A 212 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7994 (mt) REVERT: A 240 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8427 (mp) REVERT: B 40 VAL cc_start: 0.7951 (OUTLIER) cc_final: 0.7565 (t) REVERT: B 149 MET cc_start: 0.7813 (tpp) cc_final: 0.7289 (tpp) REVERT: B 421 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7187 (mtp180) outliers start: 25 outliers final: 17 residues processed: 147 average time/residue: 0.1289 time to fit residues: 26.7201 Evaluate side-chains 149 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 421 ARG Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 57 optimal weight: 0.0670 chunk 66 optimal weight: 0.0980 chunk 70 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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: 0.7821 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5922 Z= 0.210 Angle : 0.604 9.588 8066 Z= 0.293 Chirality : 0.042 0.153 969 Planarity : 0.006 0.055 983 Dihedral : 5.710 73.669 824 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.58 % Allowed : 26.50 % Favored : 69.92 % 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: 1.06 (0.31), residues: 757 helix: 1.33 (0.22), residues: 580 sheet: None (None), residues: 0 loop : -1.32 (0.44), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 326 HIS 0.001 0.000 HIS A 416 PHE 0.016 0.001 PHE A 206 TYR 0.011 0.001 TYR A 430 ARG 0.003 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 0.606 Fit side-chains REVERT: A 240 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8448 (mp) REVERT: B 40 VAL cc_start: 0.7954 (OUTLIER) cc_final: 0.7613 (t) REVERT: B 52 MET cc_start: 0.7704 (mmm) cc_final: 0.7361 (tpp) REVERT: B 149 MET cc_start: 0.7782 (tpp) cc_final: 0.7259 (tpp) REVERT: B 314 MET cc_start: 0.7942 (ttm) cc_final: 0.7740 (mtp) REVERT: B 370 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7750 (tt) REVERT: B 421 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7026 (mtp180) REVERT: B 479 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6708 (ptt-90) outliers start: 22 outliers final: 15 residues processed: 143 average time/residue: 0.1278 time to fit residues: 25.8395 Evaluate side-chains 143 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 421 ARG Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 479 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.4980 chunk 53 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.0870 chunk 64 optimal weight: 0.6980 chunk 68 optimal weight: 0.3980 chunk 44 optimal weight: 0.0570 chunk 72 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 overall best weight: 0.2676 ------------------------------------------------------------------------------- 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: 0.7796 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5922 Z= 0.184 Angle : 0.592 7.552 8066 Z= 0.289 Chirality : 0.041 0.164 969 Planarity : 0.006 0.054 983 Dihedral : 5.647 72.746 824 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.41 % Allowed : 27.48 % Favored : 69.11 % 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: 1.17 (0.31), residues: 757 helix: 1.43 (0.22), residues: 579 sheet: None (None), residues: 0 loop : -1.35 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 326 HIS 0.001 0.000 HIS A 416 PHE 0.017 0.001 PHE A 246 TYR 0.015 0.001 TYR B 471 ARG 0.002 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 0.595 Fit side-chains REVERT: A 41 VAL cc_start: 0.8056 (t) cc_final: 0.7830 (t) REVERT: A 240 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8458 (mp) REVERT: B 40 VAL cc_start: 0.7935 (OUTLIER) cc_final: 0.7575 (t) REVERT: B 149 MET cc_start: 0.7779 (tpp) cc_final: 0.7290 (tpp) REVERT: B 370 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7740 (tt) REVERT: B 421 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.6959 (mtp180) REVERT: B 479 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6664 (ptt-90) outliers start: 21 outliers final: 15 residues processed: 136 average time/residue: 0.1342 time to fit residues: 25.7272 Evaluate side-chains 136 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 421 ARG Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 479 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.0170 chunk 60 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5922 Z= 0.215 Angle : 0.612 10.818 8066 Z= 0.296 Chirality : 0.042 0.148 969 Planarity : 0.006 0.073 983 Dihedral : 5.650 73.614 824 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.25 % Allowed : 28.13 % Favored : 68.62 % 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: 1.22 (0.31), residues: 757 helix: 1.47 (0.22), residues: 574 sheet: None (None), residues: 0 loop : -1.29 (0.43), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.001 0.000 HIS A 416 PHE 0.023 0.001 PHE A 246 TYR 0.015 0.001 TYR B 471 ARG 0.003 0.000 ARG B 479 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 0.751 Fit side-chains REVERT: A 41 VAL cc_start: 0.8087 (t) cc_final: 0.7879 (t) REVERT: A 240 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8431 (mp) REVERT: B 149 MET cc_start: 0.7793 (tpp) cc_final: 0.7257 (tpp) REVERT: B 421 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7032 (mtp180) REVERT: B 479 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6767 (ptt-90) outliers start: 20 outliers final: 15 residues processed: 132 average time/residue: 0.1250 time to fit residues: 23.5232 Evaluate side-chains 136 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 421 ARG Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 479 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.0980 chunk 25 optimal weight: 0.0000 chunk 62 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 chunk 3 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 0.2980 chunk 40 optimal weight: 0.2980 chunk 51 optimal weight: 0.8980 overall best weight: 0.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.094853 restraints weight = 8164.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.097842 restraints weight = 3697.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.099755 restraints weight = 2044.910| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5922 Z= 0.165 Angle : 0.577 7.916 8066 Z= 0.281 Chirality : 0.040 0.131 969 Planarity : 0.006 0.054 983 Dihedral : 5.602 71.610 824 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.74 % Allowed : 27.64 % Favored : 68.62 % 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: 1.41 (0.32), residues: 757 helix: 1.59 (0.22), residues: 575 sheet: None (None), residues: 0 loop : -1.18 (0.45), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 336 HIS 0.001 0.000 HIS B 387 PHE 0.020 0.001 PHE A 38 TYR 0.014 0.001 TYR B 471 ARG 0.001 0.000 ARG A 421 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1627.54 seconds wall clock time: 30 minutes 0.55 seconds (1800.55 seconds total)