Starting phenix.real_space_refine on Mon Sep 23 21:41:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ttp_8467/09_2024/5ttp_8467.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ttp_8467/09_2024/5ttp_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ttp_8467/09_2024/5ttp_8467.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ttp_8467/09_2024/5ttp_8467.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ttp_8467/09_2024/5ttp_8467.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ttp_8467/09_2024/5ttp_8467.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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, 'HIS:plan': 8, 'TYR:plan': 13, 'ASN:plan1': 20, 'TRP:plan': 4, 'ASP:plan': 28, 'PHE:plan': 22, 'GLU:plan': 28, 'ARG:plan': 38} Unresolved non-hydrogen planarities: 841 Restraints were copied for chains: B Time building chain proxies: 4.67, per 1000 atoms: 0.83 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: 1.86 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.70 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: 1.62 Time building geometry restraints manager: 2.08 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: 0.00 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: 0.480 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: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.810 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 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= 0.459 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 (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: -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 TRP 0.000 0.000 TRP A 17 PHE 0.000 0.000 PHE A 13 TYR 0.000 0.000 TYR A 83 *********************** 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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.325 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0321 time to fit residues: 1.8881 Evaluate side-chains 25 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0770 chunk 84 optimal weight: 30.0000 chunk 47 optimal weight: 40.0000 chunk 28 optimal weight: 30.0000 chunk 57 optimal weight: 0.0870 chunk 45 optimal weight: 30.0000 chunk 87 optimal weight: 0.0980 chunk 33 optimal weight: 30.0000 chunk 53 optimal weight: 50.0000 chunk 65 optimal weight: 9.9990 chunk 101 optimal weight: 30.0000 overall best weight: 8.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6264 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 5614 Z= 0.242 Angle : 0.750 7.501 7812 Z= 0.457 Chirality : 0.045 0.175 1064 Planarity : 0.004 0.018 1136 Dihedral : 7.611 34.629 1136 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.23 % Favored : 92.42 % 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 (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: -2.32 (0.23), residues: 1134 helix: -0.87 (0.17), residues: 686 sheet: -3.71 (0.49), residues: 44 loop : -2.29 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 17 PHE 0.000 0.000 PHE A 13 TYR 0.000 0.000 TYR A 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.310 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0300 time to fit residues: 1.7962 Evaluate side-chains 25 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 84 optimal weight: 30.0000 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 30.0000 chunk 101 optimal weight: 30.0000 chunk 110 optimal weight: 50.0000 chunk 90 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 81 optimal weight: 30.0000 chunk 100 optimal weight: 8.9990 overall best weight: 13.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.7679 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= 0.356 Angle : 0.837 8.885 7812 Z= 0.514 Chirality : 0.046 0.232 1064 Planarity : 0.004 0.017 1136 Dihedral : 8.426 43.603 1136 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 1.23 % Allowed : 13.76 % Favored : 85.01 % 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 (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: -3.11 (0.22), residues: 1134 helix: -1.23 (0.18), residues: 702 sheet: -4.21 (0.65), residues: 44 loop : -3.21 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 17 PHE 0.000 0.000 PHE A 13 TYR 0.000 0.000 TYR A 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.323 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0237 time to fit residues: 1.4773 Evaluate side-chains 25 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 20.0000 chunk 52 optimal weight: 0.0980 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 30.0000 chunk 68 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 0.0980 chunk 53 optimal weight: 50.0000 chunk 96 optimal weight: 30.0000 chunk 29 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.7762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.008 5614 Z= 0.117 Angle : 0.541 6.938 7812 Z= 0.317 Chirality : 0.043 0.193 1064 Planarity : 0.002 0.011 1136 Dihedral : 5.867 33.835 1136 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.05 % Favored : 89.77 % 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 : 0.00 % 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: -0.50 (0.26), residues: 1134 helix: 1.04 (0.19), residues: 708 sheet: -4.01 (0.51), residues: 44 loop : -2.56 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 17 PHE 0.000 0.000 PHE A 13 TYR 0.000 0.000 TYR A 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.276 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0305 time to fit residues: 1.7653 Evaluate side-chains 25 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 40.0000 chunk 1 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 92 optimal weight: 30.0000 chunk 74 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 27 optimal weight: 0.3980 chunk 36 optimal weight: 30.0000 overall best weight: 10.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.8628 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= 0.270 Angle : 0.699 8.735 7812 Z= 0.425 Chirality : 0.045 0.248 1064 Planarity : 0.003 0.015 1136 Dihedral : 7.130 39.240 1136 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.96 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 : 0.72 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.24), residues: 1134 helix: 0.08 (0.19), residues: 686 sheet: -3.12 (1.03), residues: 20 loop : -2.93 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 17 PHE 0.000 0.000 PHE A 13 TYR 0.000 0.000 TYR A 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.291 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0279 time to fit residues: 1.6603 Evaluate side-chains 25 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 30.0000 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 30.0000 chunk 26 optimal weight: 30.0000 chunk 108 optimal weight: 50.0000 chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 35 optimal weight: 0.0370 chunk 56 optimal weight: 30.0000 chunk 104 optimal weight: 30.0000 overall best weight: 9.2068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.9729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 5614 Z= 0.225 Angle : 0.619 8.679 7812 Z= 0.376 Chirality : 0.043 0.219 1064 Planarity : 0.003 0.011 1136 Dihedral : 6.297 32.352 1136 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.99 % Favored : 84.83 % 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 : 0.00 % 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: -1.54 (0.25), residues: 1134 helix: 0.43 (0.19), residues: 712 sheet: -4.93 (0.43), residues: 40 loop : -3.46 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 17 PHE 0.000 0.000 PHE A 13 TYR 0.000 0.000 TYR A 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.281 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0297 time to fit residues: 1.7567 Evaluate side-chains 25 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 30.0000 chunk 61 optimal weight: 40.0000 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 0.0010 chunk 60 optimal weight: 20.0000 chunk 107 optimal weight: 30.0000 chunk 67 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 49 optimal weight: 30.0000 chunk 66 optimal weight: 4.9990 chunk 43 optimal weight: 30.0000 overall best weight: 5.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 1.0004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 5614 Z= 0.152 Angle : 0.538 6.750 7812 Z= 0.320 Chirality : 0.043 0.182 1064 Planarity : 0.002 0.010 1136 Dihedral : 5.609 27.344 1136 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.93 % Favored : 85.89 % 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 : 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: -0.37 (0.26), residues: 1134 helix: 1.25 (0.19), residues: 722 sheet: -3.95 (0.67), residues: 20 loop : -3.04 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 17 PHE 0.000 0.000 PHE A 13 TYR 0.000 0.000 TYR A 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.287 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0292 time to fit residues: 1.7381 Evaluate side-chains 25 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 21 optimal weight: 0.0040 chunk 20 optimal weight: 0.0970 chunk 68 optimal weight: 20.0000 chunk 73 optimal weight: 30.0000 chunk 53 optimal weight: 50.0000 chunk 10 optimal weight: 0.3980 chunk 84 optimal weight: 30.0000 chunk 98 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 overall best weight: 3.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 1.0223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.012 5614 Z= 0.103 Angle : 0.462 5.995 7812 Z= 0.271 Chirality : 0.041 0.148 1064 Planarity : 0.002 0.009 1136 Dihedral : 4.818 26.298 1136 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.82 % Favored : 88.01 % 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 : 0.00 % 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 (0.27), residues: 1134 helix: 1.97 (0.19), residues: 738 sheet: -4.35 (0.58), residues: 20 loop : -2.99 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 17 PHE 0.000 0.000 PHE A 13 TYR 0.000 0.000 TYR A 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.323 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0298 time to fit residues: 1.7605 Evaluate side-chains 25 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 103 optimal weight: 30.0000 chunk 60 optimal weight: 30.0000 chunk 43 optimal weight: 30.0000 chunk 78 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.0670 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 0.0370 chunk 106 optimal weight: 30.0000 overall best weight: 3.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 1.0429 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= 0.114 Angle : 0.463 5.725 7812 Z= 0.273 Chirality : 0.041 0.146 1064 Planarity : 0.002 0.010 1136 Dihedral : 4.740 26.562 1136 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.05 % Favored : 86.77 % 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 : 0.00 % 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: 0.60 (0.27), residues: 1134 helix: 2.12 (0.19), residues: 738 sheet: -4.59 (0.51), residues: 20 loop : -3.06 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 17 PHE 0.000 0.000 PHE A 13 TYR 0.000 0.000 TYR A 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.300 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0289 time to fit residues: 1.7455 Evaluate side-chains 25 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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: 4.9990 chunk 50 optimal weight: 30.0000 chunk 73 optimal weight: 30.0000 chunk 111 optimal weight: 8.9990 chunk 102 optimal weight: 30.0000 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 chunk 54 optimal weight: 0.0370 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 overall best weight: 3.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 1.0673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.013 5614 Z= 0.100 Angle : 0.439 5.794 7812 Z= 0.258 Chirality : 0.041 0.134 1064 Planarity : 0.002 0.010 1136 Dihedral : 4.433 26.217 1136 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.29 % 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 : 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 (0.27), residues: 1134 helix: 2.48 (0.19), residues: 728 sheet: -5.75 (0.22), residues: 42 loop : -2.66 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 17 PHE 0.000 0.000 PHE A 13 TYR 0.000 0.000 TYR A 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.316 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0288 time to fit residues: 1.7477 Evaluate side-chains 25 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 20.0000 chunk 88 optimal weight: 0.0670 chunk 37 optimal weight: 10.0000 chunk 91 optimal weight: 50.0000 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 30.0000 chunk 78 optimal weight: 20.0000 chunk 5 optimal weight: 40.0000 overall best weight: 5.3728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.057378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.046370 restraints weight = 34055.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.046552 restraints weight = 31720.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.046829 restraints weight = 30160.622| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 1.0917 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= 0.144 Angle : 0.487 6.472 7812 Z= 0.290 Chirality : 0.041 0.141 1064 Planarity : 0.002 0.011 1136 Dihedral : 4.951 27.670 1136 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.11 % Favored : 85.71 % 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 : 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: 0.39 (0.27), residues: 1134 helix: 1.98 (0.19), residues: 734 sheet: -5.74 (0.26), residues: 30 loop : -2.97 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 17 PHE 0.000 0.000 PHE A 13 TYR 0.000 0.000 TYR A 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 882.35 seconds wall clock time: 16 minutes 9.13 seconds (969.13 seconds total)