Starting phenix.real_space_refine on Thu Sep 10 23:42:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5ttp_8467/09_2026/5ttp_8467.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ttp_8467/09_2026/5ttp_8467.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5ttp_8467/09_2026/5ttp_8467.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ttp_8467/09_2026/5ttp_8467.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5ttp_8467/09_2026/5ttp_8467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ttp_8467/09_2026/5ttp_8467.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 3 Type Number sf(0) Gaussians C 3340 2.51 5 N 1138 2.21 5 O 1138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5616 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 2808 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 484} Link IDs: {'PTRANS': 13, 'TRANS': 555} Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1665 Unresolved non-hydrogen angles: 2123 Unresolved non-hydrogen dihedrals: 1347 Unresolved non-hydrogen chiralities: 188 Planarities with less than four sites: {'GLN:plan1': 24, 'PHE:plan': 22, 'ARG:plan': 38, 'TRP:plan': 4, 'ASN:plan1': 20, 'ASP:plan': 28, 'TYR:plan': 13, 'HIS:plan': 8, 'GLU:plan': 28} Unresolved non-hydrogen planarities: 841 Restraints were copied for chains: B Time building chain proxies: 2.16, per 1000 atoms: 0.38 Number of scatterers: 5616 At special positions: 0 Unit cell: (77.49, 71.34, 135.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1138 8.00 N 1138 7.00 C 3340 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 - 3.00 Amino acid : True - 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: 0.59 Conformation dependent library (CDL) restraints added in 454.7 milliseconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 2 sheets defined 67.8% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 12 through 17 Processing helix chain 'A' and resid 20 through 54 removed outlier: 3.872A pdb=" N LYS A 24 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 58 through 109 Proline residue: A 68 - end of helix Processing helix chain 'A' and resid 112 through 117 removed outlier: 3.790A pdb=" N PHE A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 removed outlier: 4.035A pdb=" N ARG A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 161 removed outlier: 3.807A pdb=" N ARG A 148 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA A 151 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 214 Proline residue: A 176 - end of helix removed outlier: 4.388A pdb=" N GLN A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N HIS A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 221 Processing helix chain 'A' and resid 223 through 276 removed outlier: 4.593A pdb=" N THR A 227 " --> pdb=" O GLN A 223 " (cutoff:3.500A) Proline residue: A 253 - end of helix Proline residue: A 273 - end of helix Processing helix chain 'A' and resid 280 through 296 removed outlier: 4.380A pdb=" N ILE A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER A 290 " --> pdb=" O VAL A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 321 removed outlier: 3.686A pdb=" N LEU A 301 " --> pdb=" O PRO A 297 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.191A pdb=" N SER A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.871A pdb=" N TYR A 410 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 446 through 455 Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 483 through 497 removed outlier: 4.940A pdb=" N ALA A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 495 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 496 " --> pdb=" O ALA A 492 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG A 497 " --> pdb=" O ARG A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 527 Processing helix chain 'A' and resid 538 through 545 removed outlier: 4.571A pdb=" N ILE A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 569 removed outlier: 4.444A pdb=" N GLU A 567 " --> pdb=" O ASN A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 579 removed outlier: 4.198A pdb=" N ALA A 573 " --> pdb=" O ARG A 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 20 through 54 removed outlier: 3.872A pdb=" N LYS B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 58 through 109 Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.790A pdb=" N PHE B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 130 removed outlier: 4.035A pdb=" N ARG B 127 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 161 removed outlier: 3.807A pdb=" N ARG B 148 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU B 149 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY B 150 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA B 151 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 214 Proline residue: B 176 - end of helix removed outlier: 4.387A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL B 203 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS B 214 " --> pdb=" O MET B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 221 Processing helix chain 'B' and resid 223 through 276 removed outlier: 4.594A pdb=" N THR B 227 " --> pdb=" O GLN B 223 " (cutoff:3.500A) Proline residue: B 253 - end of helix Proline residue: B 273 - end of helix Processing helix chain 'B' and resid 280 through 296 removed outlier: 4.380A pdb=" N ILE B 284 " --> pdb=" O THR B 280 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL B 287 " --> pdb=" O THR B 283 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE B 288 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 321 removed outlier: 3.686A pdb=" N LEU B 301 " --> pdb=" O PRO B 297 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN B 303 " --> pdb=" O LYS B 299 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET B 312 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N CYS B 315 " --> pdb=" O GLY B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.191A pdb=" N SER B 387 " --> pdb=" O SER B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.871A pdb=" N TYR B 410 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 417 Processing helix chain 'B' and resid 446 through 455 Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 483 through 497 removed outlier: 4.940A pdb=" N ALA B 494 " --> pdb=" O ALA B 490 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 495 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU B 496 " --> pdb=" O ALA B 492 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG B 497 " --> pdb=" O ARG B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 527 Processing helix chain 'B' and resid 538 through 545 removed outlier: 4.572A pdb=" N ILE B 542 " --> pdb=" O ARG B 538 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 569 removed outlier: 4.445A pdb=" N GLU B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 579 removed outlier: 4.199A pdb=" N ALA B 573 " --> pdb=" O ARG B 569 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 372 through 375 removed outlier: 5.555A pdb=" N ALA A 373 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A 551 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL A 375 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 548 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG A 559 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A 550 " --> pdb=" O VAL A 557 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 372 through 375 removed outlier: 5.555A pdb=" N ALA B 373 " --> pdb=" O VAL B 549 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL B 551 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL B 375 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE B 548 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG B 559 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL B 550 " --> pdb=" O VAL B 557 " (cutoff:3.500A) 508 hydrogen bonds defined for protein. 1512 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: 0.80 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 1138 1.29 - 1.36: 1136 1.36 - 1.43: 1 1.43 - 1.50: 1147 1.50 - 1.57: 2192 Bond restraints: 5614 Sorted by residual: bond pdb=" CA LEU B 36 " pdb=" C LEU B 36 " ideal model delta sigma weight residual 1.522 1.574 -0.051 1.37e-02 5.33e+03 1.41e+01 bond pdb=" CA LEU A 36 " pdb=" C LEU A 36 " ideal model delta sigma weight residual 1.522 1.573 -0.051 1.37e-02 5.33e+03 1.39e+01 bond pdb=" CA GLN B 326 " pdb=" C GLN B 326 " ideal model delta sigma weight residual 1.525 1.492 0.033 1.28e-02 6.10e+03 6.53e+00 bond pdb=" CA GLN A 326 " pdb=" C GLN A 326 " ideal model delta sigma weight residual 1.525 1.492 0.033 1.28e-02 6.10e+03 6.52e+00 bond pdb=" CA LEU B 211 " pdb=" C LEU B 211 " ideal model delta sigma weight residual 1.524 1.498 0.027 1.28e-02 6.10e+03 4.35e+00 ... (remaining 5609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 7347 2.59 - 5.19: 413 5.19 - 7.78: 35 7.78 - 10.37: 15 10.37 - 12.97: 2 Bond angle restraints: 7812 Sorted by residual: angle pdb=" C ILE A 20 " pdb=" N ALA A 21 " pdb=" CA ALA A 21 " ideal model delta sigma weight residual 119.78 129.54 -9.76 1.24e+00 6.50e-01 6.20e+01 angle pdb=" C ILE B 20 " pdb=" N ALA B 21 " pdb=" CA ALA B 21 " ideal model delta sigma weight residual 119.78 129.48 -9.70 1.24e+00 6.50e-01 6.12e+01 angle pdb=" N VAL A 173 " pdb=" CA VAL A 173 " pdb=" C VAL A 173 " ideal model delta sigma weight residual 111.00 103.01 7.99 1.09e+00 8.42e-01 5.37e+01 angle pdb=" N VAL B 173 " pdb=" CA VAL B 173 " pdb=" C VAL B 173 " ideal model delta sigma weight residual 111.00 103.04 7.96 1.09e+00 8.42e-01 5.34e+01 angle pdb=" N GLN A 326 " pdb=" CA GLN A 326 " pdb=" C GLN A 326 " ideal model delta sigma weight residual 108.20 98.07 10.13 1.71e+00 3.42e-01 3.51e+01 ... (remaining 7807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.35: 2934 11.35 - 22.70: 268 22.70 - 34.04: 46 34.04 - 45.39: 14 45.39 - 56.74: 2 Dihedral angle restraints: 3264 sinusoidal: 0 harmonic: 3264 Sorted by residual: dihedral pdb=" CA MET B 111 " pdb=" C MET B 111 " pdb=" N PRO B 112 " pdb=" CA PRO B 112 " ideal model delta harmonic sigma weight residual 180.00 -123.26 -56.74 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CA MET A 111 " pdb=" C MET A 111 " pdb=" N PRO A 112 " pdb=" CA PRO A 112 " ideal model delta harmonic sigma weight residual -180.00 -123.31 -56.69 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CA GLU A 325 " pdb=" C GLU A 325 " pdb=" N GLN A 326 " pdb=" CA GLN A 326 " ideal model delta harmonic sigma weight residual 180.00 135.29 44.71 0 5.00e+00 4.00e-02 7.99e+01 ... (remaining 3261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 667 0.054 - 0.108: 309 0.108 - 0.162: 75 0.162 - 0.217: 9 0.217 - 0.271: 4 Chirality restraints: 1064 Sorted by residual: chirality pdb=" CA PRO B 112 " pdb=" N PRO B 112 " pdb=" C PRO B 112 " pdb=" CB PRO B 112 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA PRO A 112 " pdb=" N PRO A 112 " pdb=" C PRO A 112 " pdb=" CB PRO A 112 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA GLU A 325 " pdb=" N GLU A 325 " pdb=" C GLU A 325 " pdb=" CB GLU A 325 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1061 not shown) Planarity restraints: 1136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 100 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.08e+00 pdb=" C MET A 100 " 0.049 2.00e-02 2.50e+03 pdb=" O MET A 100 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG A 101 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 100 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.00e+00 pdb=" C MET B 100 " -0.049 2.00e-02 2.50e+03 pdb=" O MET B 100 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG B 101 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 303 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.82e+00 pdb=" C ASN A 303 " 0.038 2.00e-02 2.50e+03 pdb=" O ASN A 303 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL A 304 " -0.013 2.00e-02 2.50e+03 ... (remaining 1133 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 268 2.65 - 3.21: 7019 3.21 - 3.77: 8714 3.77 - 4.34: 10473 4.34 - 4.90: 14646 Nonbonded interactions: 41120 Sorted by model distance: nonbonded pdb=" O ASN A 435 " pdb=" N TYR A 439 " model vdw 2.086 3.120 nonbonded pdb=" O ASN B 435 " pdb=" N TYR B 439 " model vdw 2.087 3.120 nonbonded pdb=" O PHE A 56 " pdb=" N ARG A 61 " model vdw 2.184 3.120 nonbonded pdb=" O PHE B 56 " pdb=" N ARG B 61 " model vdw 2.184 3.120 nonbonded pdb=" O MET B 196 " pdb=" N THR B 199 " model vdw 2.227 3.120 ... (remaining 41115 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.040 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 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 0.051 5614 Z= 0.463 Angle : 1.358 12.968 7812 Z= 0.898 Chirality : 0.063 0.271 1064 Planarity : 0.006 0.028 1136 Dihedral : 11.703 56.740 1136 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 24.92 Ramachandran Plot: Outliers : 0.71 % Allowed : 14.11 % Favored : 85.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 1.62 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.87 (0.16), residues: 1134 helix: -4.21 (0.10), residues: 630 sheet: -3.46 (0.39), residues: 44 loop : -3.22 (0.23), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 83 PHE 0.000 0.000 PHE A 13 TRP 0.000 0.000 TRP A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.46 ( 5614) covalent geometry : angle 1.35844 / 0.90 ( 7812) hydrogen bonds : bond 0.23360 / 18.03 ( 508) hydrogen bonds : angle 12.70726 / 9.74 ( 1512) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.109 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0146 time to fit residues: 0.8147 Evaluate side-chains 25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 50.0000 chunk 49 optimal weight: 0.0980 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 50.0000 chunk 5 optimal weight: 30.0000 chunk 33 optimal weight: 30.0000 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 30.0000 chunk 100 optimal weight: 40.0000 chunk 106 optimal weight: 30.0000 overall best weight: 13.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.060651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.051843 restraints weight = 31935.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.051931 restraints weight = 30469.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.051931 restraints weight = 29555.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.051931 restraints weight = 29555.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.051931 restraints weight = 29555.316| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 5614 Z= 0.367 Angle : 0.908 9.903 7812 Z= 0.559 Chirality : 0.047 0.202 1064 Planarity : 0.006 0.021 1136 Dihedral : 9.069 41.515 1136 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.58 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 1.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.22), residues: 1134 helix: -1.51 (0.17), residues: 686 sheet: -3.39 (0.59), residues: 44 loop : -2.81 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 83 PHE 0.000 0.000 PHE A 13 TRP 0.000 0.000 TRP A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.37 ( 5614) covalent geometry : angle 0.90783 / 0.56 ( 7812) hydrogen bonds : bond 0.06588 / 5.11 ( 508) hydrogen bonds : angle 6.66432 / 5.23 ( 1512) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.102 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0117 time to fit residues: 0.6531 Evaluate side-chains 25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 30.0000 chunk 74 optimal weight: 30.0000 chunk 87 optimal weight: 30.0000 chunk 21 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 chunk 99 optimal weight: 40.0000 chunk 38 optimal weight: 30.0000 chunk 102 optimal weight: 0.0070 chunk 111 optimal weight: 5.9990 overall best weight: 2.7204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.065212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.055880 restraints weight = 30885.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.055993 restraints weight = 29191.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.056170 restraints weight = 28126.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.056334 restraints weight = 27064.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.056334 restraints weight = 26264.421| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.6229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 5614 Z= 0.123 Angle : 0.569 7.323 7812 Z= 0.334 Chirality : 0.043 0.192 1064 Planarity : 0.003 0.011 1136 Dihedral : 6.131 39.047 1136 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.26), residues: 1134 helix: 1.20 (0.19), residues: 722 sheet: -3.08 (0.64), residues: 44 loop : -2.23 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 83 PHE 0.000 0.000 PHE A 13 TRP 0.000 0.000 TRP A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00163 / 0.12 ( 5614) covalent geometry : angle 0.56908 / 0.33 ( 7812) hydrogen bonds : bond 0.03895 / 3.05 ( 508) hydrogen bonds : angle 4.34940 / 3.41 ( 1512) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.127 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0138 time to fit residues: 0.7957 Evaluate side-chains 25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 104 optimal weight: 40.0000 chunk 39 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 88 optimal weight: 0.0040 chunk 9 optimal weight: 9.9990 chunk 91 optimal weight: 40.0000 chunk 55 optimal weight: 5.9990 chunk 110 optimal weight: 30.0000 chunk 43 optimal weight: 30.0000 chunk 95 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 overall best weight: 5.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.063241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.054338 restraints weight = 30429.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.054569 restraints weight = 28231.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.054786 restraints weight = 26625.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.054908 restraints weight = 25348.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.054908 restraints weight = 24443.481| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.7027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 5614 Z= 0.173 Angle : 0.592 6.966 7812 Z= 0.350 Chirality : 0.043 0.209 1064 Planarity : 0.003 0.012 1136 Dihedral : 6.046 37.930 1136 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.26), residues: 1134 helix: 2.02 (0.19), residues: 712 sheet: -2.78 (0.72), residues: 44 loop : -2.00 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 83 PHE 0.000 0.000 PHE A 13 TRP 0.000 0.000 TRP A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.17 ( 5614) covalent geometry : angle 0.59203 / 0.35 ( 7812) hydrogen bonds : bond 0.04244 / 3.31 ( 508) hydrogen bonds : angle 4.45678 / 3.54 ( 1512) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.126 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0136 time to fit residues: 0.7849 Evaluate side-chains 25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 0.0670 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 99 optimal weight: 30.0000 chunk 33 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 108 optimal weight: 50.0000 chunk 102 optimal weight: 0.0030 chunk 93 optimal weight: 6.9990 overall best weight: 2.2134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.065277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.056207 restraints weight = 29221.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.056460 restraints weight = 27378.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 13)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.056597 restraints weight = 25827.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.056788 restraints weight = 24690.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.056788 restraints weight = 23844.400| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.7523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 5614 Z= 0.098 Angle : 0.476 6.736 7812 Z= 0.278 Chirality : 0.042 0.171 1064 Planarity : 0.002 0.009 1136 Dihedral : 4.912 31.988 1136 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.27), residues: 1134 helix: 2.98 (0.20), residues: 724 sheet: -2.80 (0.73), residues: 44 loop : -1.81 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 83 PHE 0.000 0.000 PHE A 13 TRP 0.000 0.000 TRP A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00131 / 0.10 ( 5614) covalent geometry : angle 0.47559 / 0.28 ( 7812) hydrogen bonds : bond 0.03288 / 2.57 ( 508) hydrogen bonds : angle 3.41159 / 2.68 ( 1512) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.134 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0136 time to fit residues: 0.7376 Evaluate side-chains 25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 7.9990 chunk 40 optimal weight: 30.0000 chunk 50 optimal weight: 30.0000 chunk 86 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 75 optimal weight: 0.8980 chunk 31 optimal weight: 20.0000 chunk 104 optimal weight: 30.0000 chunk 48 optimal weight: 30.0000 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.062386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.050710 restraints weight = 33345.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.051077 restraints weight = 30451.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.051260 restraints weight = 28196.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.051565 restraints weight = 26861.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.051698 restraints weight = 25381.211| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.7981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 5614 Z= 0.184 Angle : 0.566 6.357 7812 Z= 0.338 Chirality : 0.042 0.194 1064 Planarity : 0.002 0.011 1136 Dihedral : 5.548 35.307 1136 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.27), residues: 1134 helix: 2.88 (0.19), residues: 706 sheet: -2.26 (0.79), residues: 24 loop : -2.04 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 83 PHE 0.000 0.000 PHE A 13 TRP 0.000 0.000 TRP A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.18 ( 5614) covalent geometry : angle 0.56624 / 0.34 ( 7812) hydrogen bonds : bond 0.04194 / 3.28 ( 508) hydrogen bonds : angle 4.07521 / 3.22 ( 1512) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.106 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0124 time to fit residues: 0.7100 Evaluate side-chains 25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 59 optimal weight: 30.0000 chunk 55 optimal weight: 8.9990 chunk 41 optimal weight: 30.0000 chunk 26 optimal weight: 30.0000 chunk 68 optimal weight: 30.0000 chunk 48 optimal weight: 30.0000 chunk 42 optimal weight: 20.0000 chunk 4 optimal weight: 0.3980 chunk 108 optimal weight: 50.0000 overall best weight: 10.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.058921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.047195 restraints weight = 31390.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.047455 restraints weight = 29210.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.047748 restraints weight = 27444.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.047748 restraints weight = 25453.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.047748 restraints weight = 25453.540| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.9224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 5614 Z= 0.274 Angle : 0.701 8.289 7812 Z= 0.429 Chirality : 0.044 0.209 1064 Planarity : 0.003 0.015 1136 Dihedral : 7.004 40.056 1136 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.99 % Favored : 87.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.54 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.25), residues: 1134 helix: 1.50 (0.19), residues: 722 sheet: -2.57 (0.93), residues: 20 loop : -2.79 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 83 PHE 0.000 0.000 PHE A 13 TRP 0.000 0.000 TRP A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.27 ( 5614) covalent geometry : angle 0.70067 / 0.43 ( 7812) hydrogen bonds : bond 0.05433 / 4.24 ( 508) hydrogen bonds : angle 5.14467 / 4.04 ( 1512) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.107 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0121 time to fit residues: 0.6830 Evaluate side-chains 25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 20.0000 chunk 18 optimal weight: 30.0000 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 30.0000 chunk 91 optimal weight: 6.9990 chunk 47 optimal weight: 30.0000 chunk 97 optimal weight: 30.0000 chunk 64 optimal weight: 9.9990 chunk 40 optimal weight: 30.0000 chunk 72 optimal weight: 20.0000 chunk 70 optimal weight: 8.9990 overall best weight: 9.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.056185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.044775 restraints weight = 34689.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.045139 restraints weight = 31250.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.045364 restraints weight = 28772.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.045622 restraints weight = 26992.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.045797 restraints weight = 25509.769| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.9770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 5614 Z= 0.238 Angle : 0.644 9.781 7812 Z= 0.388 Chirality : 0.043 0.184 1064 Planarity : 0.003 0.015 1136 Dihedral : 6.526 33.707 1136 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.25), residues: 1134 helix: 1.79 (0.19), residues: 718 sheet: -2.71 (0.92), residues: 20 loop : -2.80 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 83 PHE 0.000 0.000 PHE A 13 TRP 0.000 0.000 TRP A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.24 ( 5614) covalent geometry : angle 0.64442 / 0.39 ( 7812) hydrogen bonds : bond 0.04878 / 3.81 ( 508) hydrogen bonds : angle 4.57192 / 3.58 ( 1512) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.108 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0131 time to fit residues: 0.7431 Evaluate side-chains 25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 0.0270 chunk 35 optimal weight: 50.0000 chunk 25 optimal weight: 30.0000 chunk 84 optimal weight: 30.0000 chunk 31 optimal weight: 8.9990 chunk 39 optimal weight: 0.0020 chunk 109 optimal weight: 40.0000 chunk 14 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 47 optimal weight: 30.0000 chunk 51 optimal weight: 30.0000 overall best weight: 5.8052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.057704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.046332 restraints weight = 34729.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 14)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.046650 restraints weight = 31300.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.046974 restraints weight = 28922.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.047164 restraints weight = 27057.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.047404 restraints weight = 25628.002| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 1.0100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 5614 Z= 0.166 Angle : 0.537 6.434 7812 Z= 0.324 Chirality : 0.042 0.157 1064 Planarity : 0.002 0.011 1136 Dihedral : 5.696 33.577 1136 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.27), residues: 1134 helix: 2.45 (0.19), residues: 732 sheet: -3.67 (0.51), residues: 44 loop : -2.82 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 83 PHE 0.000 0.000 PHE A 13 TRP 0.000 0.000 TRP A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.17 ( 5614) covalent geometry : angle 0.53686 / 0.32 ( 7812) hydrogen bonds : bond 0.04109 / 3.21 ( 508) hydrogen bonds : angle 3.96709 / 3.09 ( 1512) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.102 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0140 time to fit residues: 0.7777 Evaluate side-chains 25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 15 optimal weight: 20.0000 chunk 45 optimal weight: 30.0000 chunk 110 optimal weight: 40.0000 chunk 106 optimal weight: 30.0000 chunk 44 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 54 optimal weight: 40.0000 chunk 97 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 108 optimal weight: 50.0000 chunk 93 optimal weight: 0.0870 overall best weight: 13.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.053767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.042686 restraints weight = 33908.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.042965 restraints weight = 30724.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.043268 restraints weight = 28226.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 14)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.043438 restraints weight = 26572.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.043609 restraints weight = 25326.116| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 1.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 5614 Z= 0.334 Angle : 0.764 10.070 7812 Z= 0.469 Chirality : 0.045 0.191 1064 Planarity : 0.004 0.015 1136 Dihedral : 7.543 36.898 1136 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.23 % Favored : 86.42 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.54 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.24), residues: 1134 helix: 0.82 (0.18), residues: 718 sheet: -2.88 (0.93), residues: 20 loop : -3.30 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 83 PHE 0.000 0.000 PHE A 13 TRP 0.000 0.000 TRP A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.33 ( 5614) covalent geometry : angle 0.76437 / 0.47 ( 7812) hydrogen bonds : bond 0.06143 / 4.79 ( 508) hydrogen bonds : angle 5.60677 / 4.38 ( 1512) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.106 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0134 time to fit residues: 0.7571 Evaluate side-chains 25 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 93 optimal weight: 0.0870 chunk 77 optimal weight: 30.0000 chunk 55 optimal weight: 0.7980 chunk 97 optimal weight: 0.0060 chunk 94 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 109 optimal weight: 50.0000 overall best weight: 3.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.058038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.046808 restraints weight = 33339.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.047111 restraints weight = 30287.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.047412 restraints weight = 28142.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.047591 restraints weight = 26433.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.047803 restraints weight = 25111.713| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 1.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 5614 Z= 0.122 Angle : 0.512 6.764 7812 Z= 0.302 Chirality : 0.042 0.147 1064 Planarity : 0.002 0.010 1136 Dihedral : 5.639 35.203 1136 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.27), residues: 1134 helix: 2.49 (0.19), residues: 734 sheet: -4.00 (0.50), residues: 44 loop : -2.76 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 83 PHE 0.000 0.000 PHE A 13 TRP 0.000 0.000 TRP A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00164 / 0.12 ( 5614) covalent geometry : angle 0.51226 / 0.30 ( 7812) hydrogen bonds : bond 0.03866 / 3.02 ( 508) hydrogen bonds : angle 3.73405 / 2.87 ( 1512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 637.74 seconds wall clock time: 12 minutes 6.97 seconds (726.97 seconds total)