Starting phenix.real_space_refine (version: dev) on Sun Dec 11 16:52:54 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ttp_8467/12_2022/5ttp_8467.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ttp_8467/12_2022/5ttp_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_8467/12_2022/5ttp_8467.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ttp_8467/12_2022/5ttp_8467.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ttp_8467/12_2022/5ttp_8467.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ttp_8467/12_2022/5ttp_8467.pdb" } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 5616 Number of models: 1 Model: "" Number of chains: 2 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 Chain: "B" 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 Time building chain proxies: 4.22, per 1000 atoms: 0.75 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.5 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: 0.35 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: 1.73 Time building geometry restraints manager: 2.95 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: 98.07 - 104.37: 36 104.37 - 110.66: 1709 110.66 - 116.95: 2151 116.95 - 123.25: 3667 123.25 - 129.54: 249 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 2.520 nonbonded pdb=" O ASN B 435 " pdb=" N TYR B 439 " model vdw 2.087 2.520 nonbonded pdb=" O PHE A 56 " pdb=" N ARG A 61 " model vdw 2.184 2.520 nonbonded pdb=" O PHE B 56 " pdb=" N ARG B 61 " model vdw 2.184 2.520 nonbonded pdb=" O MET B 196 " pdb=" N THR B 199 " model vdw 2.227 2.520 ... (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 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. 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. 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: 0.270 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.190 Check model and map are aligned: 0.090 Convert atoms to be neutral: 0.050 Process input model: 21.360 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.020 ------------------------------------------------------------------------------- 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= 0.459 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 % 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 *********************** 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 : 0.341 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0328 time to fit residues: 1.8831 Evaluate side-chains 25 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.424 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4363 ------------------------------------------------------------------------------- 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: 40.0000 chunk 84 optimal weight: 30.0000 chunk 47 optimal weight: 30.0000 chunk 28 optimal weight: 30.0000 chunk 57 optimal weight: 20.0000 chunk 45 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 chunk 33 optimal weight: 30.0000 chunk 53 optimal weight: 50.0000 chunk 65 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 overall best weight: 19.9998 ------------------------------------------------------------------------------- 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: 0.6525 moved from start: 0.6400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.046 5614 Z= 0.501 Angle : 1.074 11.449 7812 Z= 0.672 Chirality : 0.050 0.260 1064 Planarity : 0.007 0.029 1136 Dihedral : 10.297 46.392 1136 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 24.19 Ramachandran Plot: Outliers : 0.53 % Allowed : 14.99 % Favored : 84.48 % Rotamer Outliers : 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: -4.12 (0.21), residues: 1134 helix: -2.18 (0.16), residues: 672 sheet: -3.60 (1.00), residues: 20 loop : -3.47 (0.25), residues: 442 *********************** 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 : 0.329 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0288 time to fit residues: 1.7481 Evaluate side-chains 25 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.313 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4276 ------------------------------------------------------------------------------- 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: 30.0000 chunk 31 optimal weight: 0.0970 chunk 84 optimal weight: 30.0000 chunk 69 optimal weight: 0.0040 chunk 28 optimal weight: 30.0000 chunk 101 optimal weight: 30.0000 chunk 110 optimal weight: 30.0000 chunk 90 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 81 optimal weight: 30.0000 chunk 100 optimal weight: 30.0000 overall best weight: 6.2594 ------------------------------------------------------------------------------- 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: 0.6379 moved from start: 0.6834 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= 0.179 Angle : 0.645 8.390 7812 Z= 0.385 Chirality : 0.044 0.228 1064 Planarity : 0.003 0.012 1136 Dihedral : 6.970 39.725 1136 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.53 % Allowed : 11.82 % Favored : 87.65 % Rotamer Outliers : 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 (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: -1.81 (0.24), residues: 1134 helix: 0.09 (0.19), residues: 680 sheet: -3.56 (0.47), residues: 64 loop : -3.13 (0.28), residues: 390 *********************** 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 : 0.358 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0299 time to fit residues: 1.8330 Evaluate side-chains 25 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.356 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4447 ------------------------------------------------------------------------------- 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: 50.0000 chunk 11 optimal weight: 0.3980 chunk 48 optimal weight: 30.0000 chunk 68 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 108 optimal weight: 50.0000 chunk 53 optimal weight: 30.0000 chunk 96 optimal weight: 30.0000 chunk 29 optimal weight: 20.0000 chunk 90 optimal weight: 0.3980 overall best weight: 10.1592 ------------------------------------------------------------------------------- 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: 0.6523 moved from start: 0.8363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.016 5614 Z= 0.263 Angle : 0.728 9.987 7812 Z= 0.441 Chirality : 0.045 0.253 1064 Planarity : 0.003 0.018 1136 Dihedral : 7.679 43.819 1136 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.53 % Allowed : 15.70 % Favored : 83.77 % Rotamer Outliers : 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: -2.15 (0.23), residues: 1134 helix: -0.25 (0.18), residues: 686 sheet: -3.85 (0.89), residues: 20 loop : -3.30 (0.27), residues: 428 *********************** 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 : 0.335 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0294 time to fit residues: 1.7881 Evaluate side-chains 25 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.334 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4970 ------------------------------------------------------------------------------- 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: 20.0000 chunk 44 optimal weight: 30.0000 chunk 92 optimal weight: 30.0000 chunk 74 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 55 optimal weight: 0.2980 chunk 97 optimal weight: 20.0000 chunk 27 optimal weight: 0.2980 chunk 36 optimal weight: 30.0000 overall best weight: 12.1192 ------------------------------------------------------------------------------- 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: 0.6616 moved from start: 1.0231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.019 5614 Z= 0.293 Angle : 0.737 11.894 7812 Z= 0.451 Chirality : 0.045 0.249 1064 Planarity : 0.004 0.016 1136 Dihedral : 7.858 41.586 1136 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.35 % Allowed : 16.58 % Favored : 83.07 % Rotamer Outliers : 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: -2.97 (0.22), residues: 1134 helix: -0.81 (0.18), residues: 686 sheet: None (None), residues: 0 loop : -3.93 (0.23), residues: 448 *********************** 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 : 0.474 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0294 time to fit residues: 1.8019 Evaluate side-chains 25 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.356 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4461 ------------------------------------------------------------------------------- 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: 4.9990 chunk 63 optimal weight: 30.0000 chunk 26 optimal weight: 40.0000 chunk 108 optimal weight: 50.0000 chunk 89 optimal weight: 30.0000 chunk 50 optimal weight: 40.0000 chunk 9 optimal weight: 10.0000 chunk 35 optimal weight: 0.0670 chunk 56 optimal weight: 30.0000 chunk 104 optimal weight: 30.0000 overall best weight: 15.0132 ------------------------------------------------------------------------------- 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: 0.6699 moved from start: 1.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.025 5614 Z= 0.358 Angle : 0.826 12.111 7812 Z= 0.509 Chirality : 0.046 0.264 1064 Planarity : 0.004 0.016 1136 Dihedral : 8.493 41.701 1136 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.88 % Allowed : 19.58 % Favored : 79.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.90 % 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: -3.47 (0.22), residues: 1134 helix: -1.23 (0.18), residues: 686 sheet: -3.64 (0.77), residues: 20 loop : -4.06 (0.25), residues: 428 *********************** 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 : 0.292 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0252 time to fit residues: 1.5328 Evaluate side-chains 25 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.290 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3658 ------------------------------------------------------------------------------- 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: 20.0000 chunk 61 optimal weight: 40.0000 chunk 79 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 60 optimal weight: 30.0000 chunk 107 optimal weight: 30.0000 chunk 67 optimal weight: 0.0970 chunk 65 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 66 optimal weight: 0.0040 chunk 43 optimal weight: 40.0000 overall best weight: 6.6198 ------------------------------------------------------------------------------- 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: 0.6582 moved from start: 1.1112 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= 0.179 Angle : 0.613 10.199 7812 Z= 0.364 Chirality : 0.043 0.208 1064 Planarity : 0.003 0.012 1136 Dihedral : 6.834 32.395 1136 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 1.06 % Allowed : 15.70 % Favored : 83.25 % Rotamer Outliers : 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: -1.70 (0.24), residues: 1134 helix: 0.30 (0.19), residues: 706 sheet: -3.53 (0.81), residues: 20 loop : -3.69 (0.27), residues: 408 *********************** 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 : 0.344 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0298 time to fit residues: 1.8324 Evaluate side-chains 25 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.344 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4314 ------------------------------------------------------------------------------- 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: 5.9990 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 30.0000 chunk 73 optimal weight: 30.0000 chunk 53 optimal weight: 50.0000 chunk 10 optimal weight: 0.9990 chunk 84 optimal weight: 30.0000 chunk 98 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- 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: 0.6535 moved from start: 1.1320 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= 0.149 Angle : 0.551 8.998 7812 Z= 0.326 Chirality : 0.043 0.186 1064 Planarity : 0.002 0.012 1136 Dihedral : 5.989 27.780 1136 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.35 % Allowed : 15.34 % Favored : 84.30 % Rotamer Outliers : 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: -0.62 (0.26), residues: 1134 helix: 1.23 (0.20), residues: 716 sheet: -3.56 (0.78), residues: 20 loop : -3.52 (0.28), residues: 398 *********************** 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 : 0.362 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0297 time to fit residues: 1.8195 Evaluate side-chains 25 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.361 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4237 ------------------------------------------------------------------------------- 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: 30.0000 chunk 100 optimal weight: 30.0000 chunk 103 optimal weight: 8.9990 chunk 60 optimal weight: 30.0000 chunk 43 optimal weight: 30.0000 chunk 78 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 0.0050 chunk 95 optimal weight: 0.0170 chunk 66 optimal weight: 0.2980 chunk 106 optimal weight: 40.0000 overall best weight: 3.4636 ------------------------------------------------------------------------------- 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: 0.6466 moved from start: 1.1430 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= 0.116 Angle : 0.494 7.754 7812 Z= 0.289 Chirality : 0.042 0.164 1064 Planarity : 0.002 0.011 1136 Dihedral : 5.309 27.533 1136 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.87 % Favored : 86.95 % Rotamer Outliers : 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: 0.00 (0.27), residues: 1134 helix: 1.68 (0.20), residues: 746 sheet: -4.62 (0.44), residues: 40 loop : -3.36 (0.32), residues: 348 *********************** 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 : 0.313 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0310 time to fit residues: 2.0157 Evaluate side-chains 25 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.361 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4586 ------------------------------------------------------------------------------- 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: 10.0000 chunk 50 optimal weight: 30.0000 chunk 73 optimal weight: 30.0000 chunk 111 optimal weight: 0.8980 chunk 102 optimal weight: 20.0000 chunk 88 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 68 optimal weight: 20.0000 chunk 54 optimal weight: 0.0050 chunk 70 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 overall best weight: 5.3802 ------------------------------------------------------------------------------- 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: 0.6523 moved from start: 1.1621 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= 0.148 Angle : 0.528 8.439 7812 Z= 0.312 Chirality : 0.042 0.173 1064 Planarity : 0.002 0.012 1136 Dihedral : 5.580 26.557 1136 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.35 % Allowed : 15.17 % Favored : 84.48 % Rotamer Outliers : 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: -0.13 (0.26), residues: 1134 helix: 1.57 (0.19), residues: 732 sheet: -4.63 (0.44), residues: 40 loop : -3.18 (0.32), residues: 362 ********************** 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 : 0.335 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0282 time to fit residues: 1.7405 Evaluate side-chains 25 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.338 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4253 ------------------------------------------------------------------------------- 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: 0.9980 chunk 81 optimal weight: 20.0000 chunk 13 optimal weight: 0.0030 chunk 24 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 0.0980 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 5 optimal weight: 40.0000 overall best weight: 2.8194 ------------------------------------------------------------------------------- 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 = 0.3234 r_free = 0.3234 target = 0.058778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.047106 restraints weight = 33347.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.047427 restraints weight = 30569.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.047650 restraints weight = 28444.243| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 1.1718 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= 0.097 Angle : 0.457 6.766 7812 Z= 0.267 Chirality : 0.041 0.149 1064 Planarity : 0.002 0.011 1136 Dihedral : 4.868 27.099 1136 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.17 % Favored : 87.65 % Rotamer Outliers : 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: 2.08 (0.20), residues: 748 sheet: -4.65 (0.44), residues: 40 loop : -3.24 (0.33), residues: 346 =============================================================================== Job complete usr+sys time: 852.63 seconds wall clock time: 15 minutes 57.76 seconds (957.76 seconds total)