Starting phenix.real_space_refine on Fri Apr 5 22:14:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgm_41241/04_2024/8tgm_41241_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgm_41241/04_2024/8tgm_41241.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgm_41241/04_2024/8tgm_41241_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/8tgm_41241/04_2024/8tgm_41241_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgm_41241/04_2024/8tgm_41241_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgm_41241/04_2024/8tgm_41241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgm_41241/04_2024/8tgm_41241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgm_41241/04_2024/8tgm_41241_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgm_41241/04_2024/8tgm_41241_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= 0.023 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 3878 2.51 5 N 900 2.21 5 O 990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 224": "OE1" <-> "OE2" 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: 5826 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2869 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 21, 'TRANS': 362} Chain breaks: 2 Chain: "B" Number of atoms: 2869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2869 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 21, 'TRANS': 362} Chain breaks: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 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: 4.36, per 1000 atoms: 0.75 Number of scatterers: 5826 At special positions: 0 Unit cell: (73.04, 65.736, 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 58 16.00 O 990 8.00 N 900 7.00 C 3878 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: 2.37 Conformation dependent library (CDL) restraints added in 1.7 seconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 0 sheets defined 84.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 21 through 39 removed outlier: 3.738A pdb=" N VAL A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 53 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 132 through 164 removed outlier: 4.783A pdb=" N THR A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ARG A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LYS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ALA A 147 " --> pdb=" O PHE A 143 " (cutoff:3.500A) Proline residue: A 155 - end of helix removed outlier: 4.369A pdb=" N GLY A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Proline residue: A 159 - end of helix Processing helix chain 'A' and resid 167 through 186 Processing helix chain 'A' and resid 190 through 218 Processing helix chain 'A' and resid 224 through 253 removed outlier: 3.526A pdb=" N ALA A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Proline residue: A 245 - end of helix removed outlier: 4.051A pdb=" N SER A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 275 Processing helix chain 'A' and resid 293 through 298 removed outlier: 4.191A pdb=" N LYS A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 330 removed outlier: 3.895A pdb=" N ALA A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 320 " --> pdb=" O VAL A 316 " (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 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 339 through 363 removed outlier: 3.626A pdb=" N LEU A 343 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Proline residue: A 344 - end of helix removed outlier: 4.639A pdb=" N SER A 348 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 356 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ALA A 360 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASN A 361 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.542A pdb=" N LEU A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 376 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 377 " --> pdb=" O MET A 373 " (cutoff:3.500A) Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 389 through 421 removed outlier: 3.742A pdb=" N ILE A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY A 394 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Proline residue: A 395 - end of helix removed outlier: 4.391A pdb=" N MET A 410 " --> pdb=" O ASP A 407 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N MET A 411 " --> pdb=" O SER A 408 " (cutoff:3.500A) Proline residue: A 412 - end of helix removed outlier: 3.959A pdb=" N ARG A 421 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 454 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 457 through 478 removed outlier: 3.703A pdb=" N MET A 461 " --> pdb=" O PHE A 457 " (cutoff:3.500A) Proline residue: A 473 - end of helix removed outlier: 4.814A pdb=" N TYR A 476 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N TYR A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 40 removed outlier: 3.715A pdb=" N LEU B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 53 Proline residue: B 46 - end of helix removed outlier: 3.720A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 164 removed outlier: 3.511A pdb=" N ILE B 136 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N THR B 137 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 144 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 145 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS B 146 " --> pdb=" O PHE B 143 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN B 154 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Proline residue: B 155 - end of helix removed outlier: 4.221A pdb=" N GLY B 158 " --> pdb=" O PRO B 155 " (cutoff:3.500A) Proline residue: B 159 - end of helix removed outlier: 3.830A pdb=" N ILE B 164 " --> pdb=" O THR B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 186 Processing helix chain 'B' and resid 190 through 218 Processing helix chain 'B' and resid 223 through 243 removed outlier: 3.805A pdb=" N ARG B 227 " --> pdb=" O HIS B 223 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.782A pdb=" N GLU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.618A 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: 3.511A pdb=" N ALA B 305 " --> pdb=" O TYR B 301 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 319 " --> pdb=" O GLY B 315 " (cutoff:3.500A) removed outlier: 3.508A 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 339 through 359 Proline residue: B 344 - end of helix removed outlier: 4.756A pdb=" N SER B 348 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 355 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE B 356 " --> pdb=" O THR B 353 " (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: 4.180A pdb=" N GLY B 394 " --> pdb=" O GLY B 391 " (cutoff:3.500A) Proline residue: B 395 - end of helix removed outlier: 3.507A pdb=" N ILE B 403 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET B 410 " --> pdb=" O ASP B 407 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N MET B 411 " --> pdb=" O SER B 408 " (cutoff:3.500A) Proline residue: B 412 - end of helix removed outlier: 3.885A pdb=" N ARG B 421 " --> pdb=" O VAL B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 454 removed outlier: 3.681A pdb=" N ILE B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Proline residue: B 445 - end of helix removed outlier: 3.875A pdb=" N ALA B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 478 Proline residue: B 473 - end of helix removed outlier: 4.960A pdb=" N TYR B 476 " --> pdb=" O ALA B 472 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N TYR B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 948 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: 1.55 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 868 1.29 - 1.42: 1554 1.42 - 1.55: 3447 1.55 - 1.68: 3 1.68 - 1.81: 102 Bond restraints: 5974 Sorted by residual: bond pdb=" C10 YHR A 601 " pdb=" C11 YHR A 601 " ideal model delta sigma weight residual 1.572 1.428 0.144 2.00e-02 2.50e+03 5.21e+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 PRO A 481 " pdb=" O PRO A 481 " ideal model delta sigma weight residual 1.240 1.161 0.080 1.12e-02 7.97e+03 5.06e+01 bond pdb=" C13 YHR B 601 " pdb=" C14 YHR B 601 " ideal model delta sigma weight residual 1.567 1.493 0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C13 YHR A 601 " pdb=" C14 YHR A 601 " ideal model delta sigma weight residual 1.567 1.493 0.074 2.00e-02 2.50e+03 1.35e+01 ... (remaining 5969 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.74: 228 106.74 - 114.20: 3430 114.20 - 121.67: 3420 121.67 - 129.13: 1023 129.13 - 136.60: 39 Bond angle restraints: 8140 Sorted by residual: angle pdb=" C7 YHR A 601 " pdb=" N8 YHR A 601 " pdb=" C9 YHR A 601 " ideal model delta sigma weight residual 99.45 130.73 -31.28 3.00e+00 1.11e-01 1.09e+02 angle pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C9 YHR B 601 " ideal model delta sigma weight residual 99.45 130.67 -31.22 3.00e+00 1.11e-01 1.08e+02 angle pdb=" C PRO B 482 " pdb=" CA PRO B 482 " pdb=" CB PRO B 482 " ideal model delta sigma weight residual 111.46 102.41 9.05 1.29e+00 6.01e-01 4.92e+01 angle pdb=" N ARG B 225 " pdb=" CA ARG B 225 " pdb=" C ARG B 225 " ideal model delta sigma weight residual 111.28 104.37 6.91 1.09e+00 8.42e-01 4.02e+01 angle pdb=" C12 YHR A 601 " pdb=" C13 YHR A 601 " pdb=" N8 YHR A 601 " ideal model delta sigma weight residual 117.31 100.43 16.88 3.00e+00 1.11e-01 3.16e+01 ... (remaining 8135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.99: 3040 21.99 - 43.98: 344 43.98 - 65.97: 45 65.97 - 87.96: 7 87.96 - 109.95: 2 Dihedral angle restraints: 3438 sinusoidal: 1284 harmonic: 2154 Sorted by residual: dihedral pdb=" C PRO B 482 " pdb=" N PRO B 482 " pdb=" CA PRO B 482 " pdb=" CB PRO B 482 " ideal model delta harmonic sigma weight residual -120.70 -110.63 -10.07 0 2.50e+00 1.60e-01 1.62e+01 dihedral pdb=" CA VAL A 358 " pdb=" C VAL A 358 " pdb=" N LEU A 359 " pdb=" CA LEU A 359 " ideal model delta harmonic sigma weight residual -180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 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 -161.00 -19.00 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 3435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 766 0.056 - 0.111: 175 0.111 - 0.167: 26 0.167 - 0.222: 5 0.222 - 0.278: 2 Chirality restraints: 974 Sorted by residual: chirality pdb=" CA PHE A 131 " pdb=" N PHE A 131 " pdb=" C PHE A 131 " pdb=" CB PHE A 131 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C15 YHR B 601 " pdb=" C14 YHR B 601 " pdb=" C16 YHR B 601 " pdb=" C6 YHR B 601 " both_signs ideal model delta sigma weight residual False 2.66 2.44 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA MET A 149 " pdb=" N MET A 149 " pdb=" C MET A 149 " pdb=" CB MET A 149 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 971 not shown) Planarity restraints: 988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 472 " 0.062 5.00e-02 4.00e+02 9.41e-02 1.42e+01 pdb=" N PRO B 473 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO B 473 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 473 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 426 " 0.015 2.00e-02 2.50e+03 2.16e-02 9.33e+00 pdb=" CG TYR A 426 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 426 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 426 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR A 426 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 426 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 426 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 426 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 42 " 0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO B 43 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 43 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 43 " 0.041 5.00e-02 4.00e+02 ... (remaining 985 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1655 2.80 - 3.33: 5652 3.33 - 3.85: 9551 3.85 - 4.38: 10343 4.38 - 4.90: 18589 Nonbonded interactions: 45790 Sorted by model distance: nonbonded pdb=" O THR B 291 " pdb=" OG1 THR B 291 " model vdw 2.279 2.440 nonbonded pdb=" OE1 GLU A 135 " pdb=" NH1 ARG A 138 " model vdw 2.283 2.520 nonbonded pdb=" O ARG A 365 " pdb=" OG SER A 409 " model vdw 2.309 2.440 nonbonded pdb=" O GLY A 158 " pdb=" OG1 THR A 161 " model vdw 2.325 2.440 nonbonded pdb=" OG1 THR A 291 " pdb=" O THR A 423 " model vdw 2.347 2.440 ... (remaining 45785 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' selection = chain 'B' } 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: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.870 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.730 Find NCS groups from input model: 0.350 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: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.144 5974 Z= 0.408 Angle : 1.170 31.283 8140 Z= 0.566 Chirality : 0.050 0.278 974 Planarity : 0.009 0.094 988 Dihedral : 17.435 109.951 2070 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.04 % Favored : 96.83 % Rotamer: Outliers : 0.65 % Allowed : 32.41 % Favored : 66.94 % Cbeta Deviations : 0.15 % 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: 0.63 (0.30), residues: 756 helix: 1.09 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -1.73 (0.41), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.005 0.001 HIS A 387 PHE 0.019 0.002 PHE B 265 TYR 0.052 0.002 TYR A 426 ARG 0.010 0.001 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 137 time to evaluate : 0.551 Fit side-chains REVERT: A 439 MET cc_start: 0.8235 (tpp) cc_final: 0.7662 (mpp) REVERT: B 163 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7453 (mtp180) REVERT: B 229 MET cc_start: 0.7887 (mmm) cc_final: 0.7625 (mmm) REVERT: B 373 MET cc_start: 0.7738 (mtp) cc_final: 0.7413 (mtp) REVERT: B 482 PRO cc_start: 0.8860 (Cg_exo) cc_final: 0.8607 (Cg_endo) outliers start: 4 outliers final: 3 residues processed: 138 average time/residue: 0.1203 time to fit residues: 24.0043 Evaluate side-chains 130 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 163 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.0170 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 0.0870 chunk 69 optimal weight: 0.5980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 313 ASN A 329 GLN B 35 ASN B 329 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5974 Z= 0.195 Angle : 0.674 7.160 8140 Z= 0.323 Chirality : 0.043 0.169 974 Planarity : 0.007 0.058 988 Dihedral : 7.261 76.534 848 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 5.37 % Allowed : 28.01 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.31), residues: 756 helix: 1.25 (0.22), residues: 582 sheet: None (None), residues: 0 loop : -1.45 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 459 HIS 0.003 0.001 HIS A 416 PHE 0.010 0.001 PHE A 437 TYR 0.010 0.001 TYR A 190 ARG 0.004 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 134 time to evaluate : 0.614 Fit side-chains REVERT: A 174 PHE cc_start: 0.8029 (t80) cc_final: 0.7755 (t80) REVERT: A 381 LEU cc_start: 0.8304 (mp) cc_final: 0.7895 (mp) REVERT: B 229 MET cc_start: 0.7892 (mmm) cc_final: 0.7394 (mmm) REVERT: B 245 PRO cc_start: 0.8496 (Cg_endo) cc_final: 0.8286 (Cg_exo) REVERT: B 261 LEU cc_start: 0.7942 (mm) cc_final: 0.7685 (mm) REVERT: B 274 GLN cc_start: 0.7757 (pt0) cc_final: 0.7128 (pt0) REVERT: B 373 MET cc_start: 0.7728 (mtp) cc_final: 0.7406 (mtp) outliers start: 33 outliers final: 10 residues processed: 154 average time/residue: 0.1189 time to fit residues: 26.2355 Evaluate side-chains 137 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 127 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 447 THR 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: 0.9980 chunk 57 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5974 Z= 0.264 Angle : 0.645 6.630 8140 Z= 0.312 Chirality : 0.044 0.208 974 Planarity : 0.006 0.050 988 Dihedral : 6.725 82.340 840 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.40 % Allowed : 26.87 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.31), residues: 756 helix: 0.98 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -2.08 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 366 HIS 0.001 0.000 HIS A 416 PHE 0.015 0.001 PHE B 356 TYR 0.012 0.001 TYR A 190 ARG 0.004 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 0.593 Fit side-chains REVERT: A 381 LEU cc_start: 0.8320 (mp) cc_final: 0.8019 (mp) REVERT: B 229 MET cc_start: 0.7849 (mmm) cc_final: 0.7611 (mmm) REVERT: B 245 PRO cc_start: 0.8510 (Cg_endo) cc_final: 0.8282 (Cg_exo) REVERT: B 261 LEU cc_start: 0.7967 (mm) cc_final: 0.7715 (mm) REVERT: B 274 GLN cc_start: 0.7832 (pt0) cc_final: 0.7272 (pt0) REVERT: B 353 THR cc_start: 0.8254 (t) cc_final: 0.8038 (t) REVERT: B 373 MET cc_start: 0.7745 (mtp) cc_final: 0.7462 (mtp) outliers start: 27 outliers final: 15 residues processed: 140 average time/residue: 0.1092 time to fit residues: 22.5135 Evaluate side-chains 138 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 387 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 0.0670 chunk 7 optimal weight: 0.2980 chunk 32 optimal weight: 0.0050 chunk 46 optimal weight: 0.3980 chunk 69 optimal weight: 0.2980 chunk 73 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 overall best weight: 0.2132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 200 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5974 Z= 0.161 Angle : 0.585 7.089 8140 Z= 0.283 Chirality : 0.041 0.157 974 Planarity : 0.005 0.045 988 Dihedral : 6.548 76.322 840 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.89 % Allowed : 27.36 % Favored : 67.75 % 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: 0.55 (0.31), residues: 756 helix: 1.05 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -2.07 (0.42), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.001 0.000 HIS A 387 PHE 0.011 0.001 PHE B 356 TYR 0.008 0.001 TYR B 190 ARG 0.003 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 0.697 Fit side-chains REVERT: A 40 VAL cc_start: 0.7984 (OUTLIER) cc_final: 0.7762 (p) REVERT: A 381 LEU cc_start: 0.8340 (mp) cc_final: 0.8013 (mp) REVERT: B 261 LEU cc_start: 0.7886 (mm) cc_final: 0.7672 (mm) REVERT: B 353 THR cc_start: 0.8218 (t) cc_final: 0.7977 (t) REVERT: B 373 MET cc_start: 0.7754 (mtp) cc_final: 0.7428 (mtp) outliers start: 30 outliers final: 13 residues processed: 151 average time/residue: 0.1112 time to fit residues: 25.3552 Evaluate side-chains 142 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 370 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.0020 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5974 Z= 0.239 Angle : 0.616 7.163 8140 Z= 0.297 Chirality : 0.043 0.177 974 Planarity : 0.006 0.063 988 Dihedral : 6.496 74.640 840 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.70 % Allowed : 27.20 % Favored : 67.10 % 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: 0.61 (0.31), residues: 756 helix: 1.05 (0.22), residues: 600 sheet: None (None), residues: 0 loop : -2.03 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 366 HIS 0.001 0.000 HIS A 387 PHE 0.019 0.001 PHE B 356 TYR 0.012 0.001 TYR B 476 ARG 0.002 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 131 time to evaluate : 0.509 Fit side-chains REVERT: A 149 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7456 (ttm) REVERT: A 381 LEU cc_start: 0.8357 (mp) cc_final: 0.8056 (mp) REVERT: B 261 LEU cc_start: 0.7955 (mm) cc_final: 0.7743 (mm) REVERT: B 295 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.6957 (mpp) REVERT: B 353 THR cc_start: 0.8164 (t) cc_final: 0.7939 (t) REVERT: B 373 MET cc_start: 0.7757 (mtp) cc_final: 0.7474 (mtp) outliers start: 35 outliers final: 24 residues processed: 152 average time/residue: 0.1135 time to fit residues: 25.7857 Evaluate side-chains 163 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 137 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 447 THR 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: 0.2980 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 18 optimal weight: 7.9990 chunk 73 optimal weight: 0.6980 chunk 61 optimal weight: 0.0770 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 70 optimal weight: 0.0170 overall best weight: 0.1776 ------------------------------------------------------------------------------- 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: 0.7692 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5974 Z= 0.157 Angle : 0.577 7.823 8140 Z= 0.280 Chirality : 0.040 0.137 974 Planarity : 0.006 0.057 988 Dihedral : 6.456 69.152 840 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.89 % Allowed : 28.18 % Favored : 66.94 % 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: 1.01 (0.31), residues: 756 helix: 1.24 (0.22), residues: 584 sheet: None (None), residues: 0 loop : -1.21 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 326 HIS 0.001 0.000 HIS A 387 PHE 0.012 0.001 PHE B 356 TYR 0.008 0.001 TYR B 190 ARG 0.002 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 0.615 Fit side-chains REVERT: A 174 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7728 (t80) REVERT: A 381 LEU cc_start: 0.8359 (mp) cc_final: 0.8030 (mp) REVERT: B 261 LEU cc_start: 0.7886 (mm) cc_final: 0.7673 (mm) REVERT: B 295 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6982 (mpp) REVERT: B 370 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7550 (tt) REVERT: B 373 MET cc_start: 0.7722 (mtp) cc_final: 0.7421 (mtp) REVERT: B 423 THR cc_start: 0.8312 (m) cc_final: 0.7877 (p) outliers start: 30 outliers final: 18 residues processed: 160 average time/residue: 0.1109 time to fit residues: 26.4180 Evaluate side-chains 159 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 138 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 73 optimal weight: 0.1980 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 22 optimal weight: 0.0060 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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: 0.7723 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5974 Z= 0.202 Angle : 0.593 7.403 8140 Z= 0.286 Chirality : 0.042 0.146 974 Planarity : 0.006 0.060 988 Dihedral : 6.526 72.901 840 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.72 % Allowed : 29.15 % Favored : 66.12 % 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: 0.74 (0.31), residues: 756 helix: 1.13 (0.22), residues: 600 sheet: None (None), residues: 0 loop : -1.95 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 326 HIS 0.001 0.000 HIS A 416 PHE 0.017 0.001 PHE B 356 TYR 0.011 0.001 TYR B 476 ARG 0.002 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 0.589 Fit side-chains REVERT: A 174 PHE cc_start: 0.7897 (t80) cc_final: 0.7671 (t80) REVERT: A 381 LEU cc_start: 0.8379 (mp) cc_final: 0.8063 (mp) REVERT: A 479 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6786 (ptt-90) REVERT: B 261 LEU cc_start: 0.7962 (mm) cc_final: 0.7741 (mm) REVERT: B 295 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.6983 (mpp) REVERT: B 331 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7450 (mmt) REVERT: B 370 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7513 (tt) REVERT: B 373 MET cc_start: 0.7752 (mtp) cc_final: 0.7478 (mtp) REVERT: B 423 THR cc_start: 0.8360 (m) cc_final: 0.7898 (p) outliers start: 29 outliers final: 20 residues processed: 156 average time/residue: 0.1159 time to fit residues: 26.4379 Evaluate side-chains 165 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 447 THR 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: 0.9980 chunk 49 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 6 optimal weight: 0.0870 chunk 57 optimal weight: 0.2980 chunk 66 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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: 0.7725 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5974 Z= 0.204 Angle : 0.586 6.906 8140 Z= 0.283 Chirality : 0.042 0.181 974 Planarity : 0.006 0.058 988 Dihedral : 6.517 73.178 840 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.05 % Allowed : 29.15 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.31), residues: 756 helix: 1.10 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -1.98 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.001 0.000 HIS A 387 PHE 0.017 0.001 PHE B 356 TYR 0.011 0.001 TYR B 476 ARG 0.002 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 147 time to evaluate : 0.648 Fit side-chains REVERT: A 371 ILE cc_start: 0.7858 (mm) cc_final: 0.7455 (mt) REVERT: A 381 LEU cc_start: 0.8390 (mp) cc_final: 0.8077 (mp) REVERT: A 479 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6797 (ptt-90) REVERT: B 170 MET cc_start: 0.7795 (tpp) cc_final: 0.7587 (ttm) REVERT: B 261 LEU cc_start: 0.7972 (mm) cc_final: 0.7761 (mm) REVERT: B 295 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.6958 (mpp) REVERT: B 370 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7528 (tt) REVERT: B 371 ILE cc_start: 0.8166 (mm) cc_final: 0.7895 (mt) REVERT: B 373 MET cc_start: 0.7779 (mtp) cc_final: 0.7484 (mtp) REVERT: B 423 THR cc_start: 0.8353 (m) cc_final: 0.7880 (p) outliers start: 31 outliers final: 23 residues processed: 162 average time/residue: 0.1113 time to fit residues: 26.4347 Evaluate side-chains 177 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7753 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5974 Z= 0.265 Angle : 0.651 9.802 8140 Z= 0.306 Chirality : 0.045 0.205 974 Planarity : 0.006 0.067 988 Dihedral : 6.363 73.930 840 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.89 % Allowed : 29.15 % Favored : 65.96 % 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: 0.74 (0.31), residues: 756 helix: 1.15 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -1.85 (0.44), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 366 HIS 0.001 0.000 HIS A 416 PHE 0.021 0.001 PHE B 356 TYR 0.014 0.001 TYR B 476 ARG 0.002 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 151 time to evaluate : 0.666 Fit side-chains REVERT: A 371 ILE cc_start: 0.7893 (mm) cc_final: 0.7496 (mt) REVERT: A 381 LEU cc_start: 0.8385 (mp) cc_final: 0.8079 (mp) REVERT: A 479 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6872 (ptt-90) REVERT: B 229 MET cc_start: 0.8180 (mmm) cc_final: 0.7491 (mmm) REVERT: B 257 SER cc_start: 0.8660 (m) cc_final: 0.8295 (p) REVERT: B 261 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7808 (mm) REVERT: B 295 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.6967 (mpp) REVERT: B 371 ILE cc_start: 0.8192 (mm) cc_final: 0.7941 (mt) REVERT: B 373 MET cc_start: 0.7790 (mtp) cc_final: 0.7524 (mtp) REVERT: B 423 THR cc_start: 0.8383 (m) cc_final: 0.7876 (p) outliers start: 30 outliers final: 25 residues processed: 164 average time/residue: 0.1139 time to fit residues: 27.6462 Evaluate side-chains 171 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.6980 chunk 60 optimal weight: 0.4980 chunk 6 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 55 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7751 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5974 Z= 0.246 Angle : 0.639 9.736 8140 Z= 0.302 Chirality : 0.044 0.186 974 Planarity : 0.006 0.065 988 Dihedral : 6.417 72.913 840 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.40 % Allowed : 30.13 % Favored : 65.47 % 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: 0.73 (0.31), residues: 756 helix: 1.14 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -1.85 (0.44), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.001 0.000 HIS A 416 PHE 0.019 0.001 PHE B 356 TYR 0.013 0.001 TYR B 476 ARG 0.002 0.000 ARG A 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 142 time to evaluate : 0.626 Fit side-chains REVERT: A 371 ILE cc_start: 0.7901 (mm) cc_final: 0.7502 (mt) REVERT: A 381 LEU cc_start: 0.8383 (mp) cc_final: 0.8077 (mp) REVERT: A 479 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6907 (ptt-90) REVERT: B 229 MET cc_start: 0.8146 (mmm) cc_final: 0.7503 (mmm) REVERT: B 257 SER cc_start: 0.8594 (m) cc_final: 0.8185 (p) REVERT: B 261 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7793 (mm) REVERT: B 295 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.6961 (mpp) REVERT: B 331 MET cc_start: 0.8301 (tpp) cc_final: 0.7509 (mmt) REVERT: B 371 ILE cc_start: 0.8190 (mm) cc_final: 0.7938 (mt) REVERT: B 373 MET cc_start: 0.7791 (mtp) cc_final: 0.7531 (mtp) outliers start: 27 outliers final: 22 residues processed: 157 average time/residue: 0.1139 time to fit residues: 26.2590 Evaluate side-chains 165 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 381 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 chunk 62 optimal weight: 0.7980 chunk 7 optimal weight: 0.0270 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 40 optimal weight: 0.1980 chunk 51 optimal weight: 0.0040 overall best weight: 0.2250 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.112309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.101263 restraints weight = 8083.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.104207 restraints weight = 3924.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106132 restraints weight = 2315.221| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5974 Z= 0.167 Angle : 0.615 10.640 8140 Z= 0.288 Chirality : 0.042 0.175 974 Planarity : 0.006 0.063 988 Dihedral : 6.433 68.944 840 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.40 % Allowed : 30.13 % Favored : 65.47 % 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: 0.91 (0.31), residues: 756 helix: 1.26 (0.22), residues: 588 sheet: None (None), residues: 0 loop : -1.69 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 326 HIS 0.001 0.000 HIS A 387 PHE 0.016 0.001 PHE B 246 TYR 0.008 0.001 TYR A 190 ARG 0.002 0.000 ARG A 479 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1636.45 seconds wall clock time: 30 minutes 0.81 seconds (1800.81 seconds total)