Starting phenix.real_space_refine on Fri Jul 19 22:50:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo8_14843/07_2024/7zo8_14843.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo8_14843/07_2024/7zo8_14843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo8_14843/07_2024/7zo8_14843.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo8_14843/07_2024/7zo8_14843.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo8_14843/07_2024/7zo8_14843.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo8_14843/07_2024/7zo8_14843.cif" } resolution = 3.6 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= 0.004 sd= 0.120 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 44 5.16 5 C 5678 2.51 5 N 1582 2.21 5 O 1646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 307": "OE1" <-> "OE2" Residue "B GLU 307": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8952 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4437 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 570, 4422 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 11, 'TRANS': 558} Conformer: "B" Number of residues, atoms: 570, 4422 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 11, 'TRANS': 558} bond proxies already assigned to first conformer: 4478 Chain: "B" Number of atoms: 4437 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 570, 4422 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 11, 'TRANS': 558} Conformer: "B" Number of residues, atoms: 570, 4422 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 11, 'TRANS': 558} bond proxies already assigned to first conformer: 4478 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 9.76, per 1000 atoms: 1.09 Number of scatterers: 8952 At special positions: 0 Unit cell: (74.825, 109.675, 135.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 2 15.00 O 1646 8.00 N 1582 7.00 C 5678 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: 3.67 Conformation dependent library (CDL) restraints added in 3.1 seconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 4 sheets defined 71.7% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 1 through 17 removed outlier: 4.002A pdb=" N TYR A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 14 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU A 17 " --> pdb=" O TYR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 48 removed outlier: 3.762A pdb=" N THR A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 55 through 100 removed outlier: 3.625A pdb=" N MET A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.949A pdb=" N HIS A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 155 removed outlier: 3.616A pdb=" N MET A 134 " --> pdb=" O TRP A 130 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 155 through 204 removed outlier: 3.640A pdb=" N GLY A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N HIS A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 211 Processing helix chain 'A' and resid 213 through 233 Processing helix chain 'A' and resid 235 through 267 removed outlier: 5.257A pdb=" N ASN A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ARG A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 267 " --> pdb=" O TYR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 316 removed outlier: 3.505A pdb=" N PHE A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 280 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 400 through 402 No H-bonds generated for 'chain 'A' and resid 400 through 402' Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.890A pdb=" N HIS A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 431 removed outlier: 3.688A pdb=" N VAL A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 448 removed outlier: 4.253A pdb=" N HIS A 442 " --> pdb=" O HIS A 438 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 456 removed outlier: 4.379A pdb=" N ALA A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 463 removed outlier: 4.150A pdb=" N ASP A 462 " --> pdb=" O GLU A 459 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR A 463 " --> pdb=" O GLY A 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 463' Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 473 through 489 Processing helix chain 'A' and resid 503 through 518 removed outlier: 3.877A pdb=" N LYS A 509 " --> pdb=" O GLU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 570 Processing helix chain 'B' and resid 2 through 17 removed outlier: 4.002A pdb=" N TYR B 13 " --> pdb=" O ARG B 9 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU B 14 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU B 17 " --> pdb=" O TYR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 48 removed outlier: 3.761A pdb=" N THR B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 55 through 100 removed outlier: 3.624A pdb=" N MET B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.950A pdb=" N HIS B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 155 removed outlier: 3.616A pdb=" N MET B 134 " --> pdb=" O TRP B 130 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Proline residue: B 149 - end of helix Processing helix chain 'B' and resid 155 through 204 removed outlier: 3.639A pdb=" N GLY B 183 " --> pdb=" O LYS B 179 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N HIS B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 211 Processing helix chain 'B' and resid 213 through 233 Processing helix chain 'B' and resid 235 through 267 removed outlier: 5.257A pdb=" N ASN B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ARG B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 267 " --> pdb=" O TYR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 316 removed outlier: 3.504A pdb=" N PHE B 278 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 280 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.889A pdb=" N HIS B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 431 removed outlier: 3.689A pdb=" N VAL B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 removed outlier: 4.252A pdb=" N HIS B 442 " --> pdb=" O HIS B 438 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 456 removed outlier: 4.380A pdb=" N ALA B 456 " --> pdb=" O ASP B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 463 removed outlier: 4.150A pdb=" N ASP B 462 " --> pdb=" O GLU B 459 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR B 463 " --> pdb=" O GLY B 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 459 through 463' Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 473 through 489 Processing helix chain 'B' and resid 503 through 518 removed outlier: 3.877A pdb=" N LYS B 509 " --> pdb=" O GLU B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 570 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 5.363A pdb=" N VAL A 354 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL A 340 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA A 389 " --> pdb=" O VAL A 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 411 through 414 removed outlier: 7.216A pdb=" N VAL A 539 " --> pdb=" O SER A 550 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N SER A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHE A 541 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358 removed outlier: 5.363A pdb=" N VAL B 354 " --> pdb=" O ASN B 339 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL B 340 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA B 389 " --> pdb=" O VAL B 340 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 411 through 414 removed outlier: 7.215A pdb=" N VAL B 539 " --> pdb=" O SER B 550 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N PHE B 541 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) 641 hydrogen bonds defined for protein. 1883 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: 2.57 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1470 1.31 - 1.43: 2282 1.43 - 1.55: 5262 1.55 - 1.68: 4 1.68 - 1.80: 86 Bond restraints: 9104 Sorted by residual: bond pdb=" CB PLC A 601 " pdb=" O3 PLC A 601 " ideal model delta sigma weight residual 1.327 1.414 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" CB PLC B 601 " pdb=" O3 PLC B 601 " ideal model delta sigma weight residual 1.327 1.414 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C' PLC A 601 " pdb=" O2 PLC A 601 " ideal model delta sigma weight residual 1.332 1.416 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C' PLC B 601 " pdb=" O2 PLC B 601 " ideal model delta sigma weight residual 1.332 1.415 -0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" N PLC A 601 " pdb=" C5 PLC A 601 " ideal model delta sigma weight residual 1.508 1.450 0.058 2.00e-02 2.50e+03 8.35e+00 ... (remaining 9099 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.65: 114 105.65 - 112.72: 5050 112.72 - 119.80: 2895 119.80 - 126.88: 4173 126.88 - 133.96: 86 Bond angle restraints: 12318 Sorted by residual: angle pdb=" O1P PLC A 601 " pdb=" P PLC A 601 " pdb=" O2P PLC A 601 " ideal model delta sigma weight residual 119.61 100.95 18.66 3.00e+00 1.11e-01 3.87e+01 angle pdb=" O1P PLC B 601 " pdb=" P PLC B 601 " pdb=" O2P PLC B 601 " ideal model delta sigma weight residual 119.61 101.00 18.61 3.00e+00 1.11e-01 3.85e+01 angle pdb=" O3P PLC A 601 " pdb=" P PLC A 601 " pdb=" O4P PLC A 601 " ideal model delta sigma weight residual 93.62 110.31 -16.69 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O3P PLC B 601 " pdb=" P PLC B 601 " pdb=" O4P PLC B 601 " ideal model delta sigma weight residual 93.62 110.28 -16.66 3.00e+00 1.11e-01 3.09e+01 angle pdb=" C ARG A 135 " pdb=" N GLN A 136 " pdb=" CA GLN A 136 " ideal model delta sigma weight residual 120.58 114.67 5.91 1.71e+00 3.42e-01 1.20e+01 ... (remaining 12313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.06: 5159 27.06 - 54.11: 283 54.11 - 81.17: 36 81.17 - 108.23: 6 108.23 - 135.28: 6 Dihedral angle restraints: 5490 sinusoidal: 2184 harmonic: 3306 Sorted by residual: dihedral pdb=" CA SER A 50 " pdb=" C SER A 50 " pdb=" N ASP A 51 " pdb=" CA ASP A 51 " ideal model delta harmonic sigma weight residual 180.00 155.41 24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA SER B 50 " pdb=" C SER B 50 " pdb=" N ASP B 51 " pdb=" CA ASP B 51 " ideal model delta harmonic sigma weight residual 180.00 155.46 24.54 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" C3 PLC B 601 " pdb=" C1 PLC B 601 " pdb=" C2 PLC B 601 " pdb=" O3P PLC B 601 " ideal model delta sinusoidal sigma weight residual 67.16 -157.56 -135.28 1 3.00e+01 1.11e-03 1.82e+01 ... (remaining 5487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 968 0.035 - 0.069: 349 0.069 - 0.104: 79 0.104 - 0.139: 34 0.139 - 0.174: 10 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CA PRO A 103 " pdb=" N PRO A 103 " pdb=" C PRO A 103 " pdb=" CB PRO A 103 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA PRO B 103 " pdb=" N PRO B 103 " pdb=" C PRO B 103 " pdb=" CB PRO B 103 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA HIS B 137 " pdb=" N HIS B 137 " pdb=" C HIS B 137 " pdb=" CB HIS B 137 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 1437 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 134 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C MET B 134 " -0.061 2.00e-02 2.50e+03 pdb=" O MET B 134 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG B 135 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 134 " -0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C MET A 134 " 0.061 2.00e-02 2.50e+03 pdb=" O MET A 134 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG A 135 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 359 " 0.038 5.00e-02 4.00e+02 5.74e-02 5.26e+00 pdb=" N PRO B 360 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 360 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 360 " 0.032 5.00e-02 4.00e+02 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1892 2.79 - 3.31: 9249 3.31 - 3.84: 14444 3.84 - 4.37: 15461 4.37 - 4.90: 28189 Nonbonded interactions: 69235 Sorted by model distance: nonbonded pdb=" OG SER A 490 " pdb=" O ILE A 492 " model vdw 2.257 2.440 nonbonded pdb=" OG SER B 490 " pdb=" O ILE B 492 " model vdw 2.258 2.440 nonbonded pdb=" O GLY B 561 " pdb=" OG SER B 564 " model vdw 2.319 2.440 nonbonded pdb=" O GLY A 561 " pdb=" OG SER A 564 " model vdw 2.319 2.440 nonbonded pdb=" NH2 ARG A 423 " pdb=" OE2 GLU B 217 " model vdw 2.346 2.520 ... (remaining 69230 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 87 or resid 89 through 116 or resid 118 through \ 570 or resid 601)) selection = (chain 'B' and (resid 1 through 87 or resid 89 through 116 or resid 118 through \ 570 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.420 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 34.040 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 0.004 0.087 9104 Z= 0.273 Angle : 0.704 18.665 12318 Z= 0.336 Chirality : 0.041 0.174 1440 Planarity : 0.004 0.057 1572 Dihedral : 16.849 135.282 3350 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.75 % Favored : 94.89 % Rotamer: Outliers : 0.42 % Allowed : 0.21 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.26), residues: 1140 helix: 2.12 (0.19), residues: 782 sheet: 0.61 (0.58), residues: 70 loop : -1.58 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 106 HIS 0.005 0.001 HIS B 137 PHE 0.018 0.001 PHE A 195 TYR 0.007 0.001 TYR A 461 ARG 0.007 0.000 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.076 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1653 time to fit residues: 27.9742 Evaluate side-chains 90 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 47 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 54 optimal weight: 30.0000 chunk 66 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9104 Z= 0.279 Angle : 0.595 8.231 12318 Z= 0.311 Chirality : 0.042 0.176 1440 Planarity : 0.004 0.040 1572 Dihedral : 12.300 129.570 1320 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.58 % Favored : 95.07 % Rotamer: Outliers : 1.38 % Allowed : 6.90 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.26), residues: 1140 helix: 2.01 (0.19), residues: 788 sheet: 0.65 (0.57), residues: 70 loop : -1.67 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 238 HIS 0.007 0.001 HIS A 137 PHE 0.017 0.001 PHE A 195 TYR 0.023 0.001 TYR A 263 ARG 0.003 0.000 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 1.017 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 103 average time/residue: 0.1655 time to fit residues: 26.1734 Evaluate side-chains 102 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 422 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 103 optimal weight: 10.0000 chunk 112 optimal weight: 30.0000 chunk 92 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9104 Z= 0.259 Angle : 0.580 8.477 12318 Z= 0.300 Chirality : 0.042 0.173 1440 Planarity : 0.004 0.037 1572 Dihedral : 11.505 115.027 1320 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.58 % Favored : 95.07 % Rotamer: Outliers : 1.70 % Allowed : 8.49 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.26), residues: 1140 helix: 2.06 (0.19), residues: 782 sheet: 0.62 (0.56), residues: 70 loop : -1.69 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 238 HIS 0.006 0.001 HIS A 137 PHE 0.017 0.001 PHE A 195 TYR 0.023 0.001 TYR A 263 ARG 0.003 0.000 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 1.010 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 103 average time/residue: 0.1669 time to fit residues: 26.3257 Evaluate side-chains 104 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 53 optimal weight: 0.0370 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9104 Z= 0.277 Angle : 0.577 7.278 12318 Z= 0.299 Chirality : 0.042 0.174 1440 Planarity : 0.004 0.037 1572 Dihedral : 10.608 96.678 1320 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.23 % Favored : 95.42 % Rotamer: Outliers : 2.12 % Allowed : 9.87 % Favored : 88.00 % 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: 1.61 (0.26), residues: 1140 helix: 2.08 (0.19), residues: 780 sheet: 0.60 (0.56), residues: 70 loop : -1.74 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 106 HIS 0.006 0.001 HIS A 137 PHE 0.017 0.001 PHE A 195 TYR 0.007 0.001 TYR A 461 ARG 0.003 0.000 ARG B 288 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 1.059 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 102 average time/residue: 0.1699 time to fit residues: 26.9518 Evaluate side-chains 104 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9104 Z= 0.264 Angle : 0.580 8.641 12318 Z= 0.298 Chirality : 0.041 0.179 1440 Planarity : 0.004 0.037 1572 Dihedral : 9.951 79.053 1320 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.40 % Favored : 95.25 % Rotamer: Outliers : 1.70 % Allowed : 12.00 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.26), residues: 1140 helix: 2.12 (0.19), residues: 780 sheet: 0.68 (0.59), residues: 70 loop : -1.73 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 238 HIS 0.006 0.001 HIS B 137 PHE 0.017 0.001 PHE A 195 TYR 0.024 0.001 TYR A 263 ARG 0.003 0.000 ARG B 288 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.935 Fit side-chains REVERT: B 393 MET cc_start: 0.7097 (tpp) cc_final: 0.6875 (tmm) outliers start: 12 outliers final: 12 residues processed: 100 average time/residue: 0.1670 time to fit residues: 25.4146 Evaluate side-chains 105 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 110 optimal weight: 0.0020 chunk 91 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9104 Z= 0.271 Angle : 0.580 7.733 12318 Z= 0.298 Chirality : 0.041 0.177 1440 Planarity : 0.004 0.037 1572 Dihedral : 9.455 72.044 1320 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.05 % Favored : 95.60 % Rotamer: Outliers : 1.91 % Allowed : 11.89 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.26), residues: 1140 helix: 2.12 (0.19), residues: 780 sheet: 0.69 (0.58), residues: 70 loop : -1.73 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 238 HIS 0.006 0.001 HIS B 137 PHE 0.017 0.001 PHE A 195 TYR 0.006 0.001 TYR A 461 ARG 0.003 0.000 ARG B 288 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 1.043 Fit side-chains REVERT: A 108 GLN cc_start: 0.8484 (mp10) cc_final: 0.7773 (mp10) REVERT: A 270 MET cc_start: 0.8597 (ttt) cc_final: 0.8338 (mtp) REVERT: B 108 GLN cc_start: 0.8487 (mp10) cc_final: 0.7819 (mp10) REVERT: B 270 MET cc_start: 0.8563 (ttt) cc_final: 0.8283 (mtp) outliers start: 14 outliers final: 14 residues processed: 99 average time/residue: 0.1587 time to fit residues: 24.4630 Evaluate side-chains 106 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 62 optimal weight: 0.0870 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 30.0000 chunk 67 optimal weight: 0.9980 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9104 Z= 0.200 Angle : 0.549 9.928 12318 Z= 0.280 Chirality : 0.040 0.173 1440 Planarity : 0.004 0.036 1572 Dihedral : 9.024 64.242 1320 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.40 % Favored : 95.25 % Rotamer: Outliers : 1.80 % Allowed : 12.53 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.26), residues: 1140 helix: 2.27 (0.19), residues: 780 sheet: 0.75 (0.60), residues: 70 loop : -1.70 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 106 HIS 0.004 0.001 HIS B 137 PHE 0.017 0.001 PHE B 195 TYR 0.023 0.001 TYR A 263 ARG 0.001 0.000 ARG B 288 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 1.119 Fit side-chains REVERT: A 108 GLN cc_start: 0.8432 (mp10) cc_final: 0.7745 (mp10) REVERT: A 248 MET cc_start: 0.8388 (mmm) cc_final: 0.7941 (mmm) REVERT: B 104 LEU cc_start: 0.8199 (mp) cc_final: 0.7283 (mp) REVERT: B 108 GLN cc_start: 0.8467 (mp10) cc_final: 0.7833 (mp10) REVERT: B 248 MET cc_start: 0.8402 (mmm) cc_final: 0.7947 (mmm) outliers start: 13 outliers final: 12 residues processed: 102 average time/residue: 0.1588 time to fit residues: 26.1700 Evaluate side-chains 102 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 69 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9104 Z= 0.351 Angle : 0.624 10.739 12318 Z= 0.320 Chirality : 0.042 0.181 1440 Planarity : 0.004 0.044 1572 Dihedral : 9.113 69.743 1320 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.05 % Favored : 95.60 % Rotamer: Outliers : 2.12 % Allowed : 12.95 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.26), residues: 1140 helix: 2.03 (0.19), residues: 786 sheet: 0.65 (0.59), residues: 70 loop : -1.73 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 238 HIS 0.007 0.001 HIS B 137 PHE 0.017 0.002 PHE A 195 TYR 0.006 0.001 TYR A 461 ARG 0.003 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.920 Fit side-chains REVERT: A 108 GLN cc_start: 0.8467 (mp10) cc_final: 0.7716 (mp10) REVERT: B 108 GLN cc_start: 0.8479 (mp10) cc_final: 0.7810 (mp10) outliers start: 16 outliers final: 14 residues processed: 98 average time/residue: 0.1479 time to fit residues: 22.9619 Evaluate side-chains 104 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.7980 chunk 102 optimal weight: 0.0070 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 0.0270 chunk 92 optimal weight: 0.0670 chunk 67 optimal weight: 0.0020 chunk 108 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 overall best weight: 0.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9104 Z= 0.156 Angle : 0.544 11.016 12318 Z= 0.274 Chirality : 0.039 0.169 1440 Planarity : 0.004 0.038 1572 Dihedral : 8.660 59.659 1320 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.31 % Favored : 95.33 % Rotamer: Outliers : 1.17 % Allowed : 13.91 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.26), residues: 1140 helix: 2.32 (0.19), residues: 784 sheet: 0.73 (0.59), residues: 70 loop : -1.49 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 106 HIS 0.004 0.001 HIS A 191 PHE 0.016 0.001 PHE B 195 TYR 0.020 0.001 TYR B 263 ARG 0.002 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.981 Fit side-chains REVERT: A 104 LEU cc_start: 0.8279 (mp) cc_final: 0.7272 (mp) REVERT: A 108 GLN cc_start: 0.8404 (mp10) cc_final: 0.7721 (mp10) REVERT: B 104 LEU cc_start: 0.8197 (mp) cc_final: 0.7350 (mp) REVERT: B 108 GLN cc_start: 0.8444 (mp10) cc_final: 0.7817 (mp10) outliers start: 7 outliers final: 6 residues processed: 102 average time/residue: 0.1601 time to fit residues: 25.2286 Evaluate side-chains 102 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 90 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 0.0970 chunk 55 optimal weight: 0.0070 chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9104 Z= 0.196 Angle : 0.566 11.241 12318 Z= 0.282 Chirality : 0.039 0.167 1440 Planarity : 0.004 0.038 1572 Dihedral : 8.577 57.024 1320 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.87 % Favored : 95.77 % Rotamer: Outliers : 1.06 % Allowed : 14.01 % Favored : 84.93 % 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: 2.00 (0.26), residues: 1140 helix: 2.36 (0.19), residues: 782 sheet: 0.68 (0.58), residues: 70 loop : -1.55 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 106 HIS 0.006 0.001 HIS B 191 PHE 0.016 0.001 PHE B 453 TYR 0.006 0.001 TYR A 96 ARG 0.002 0.000 ARG B 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.961 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 96 average time/residue: 0.1591 time to fit residues: 23.7458 Evaluate side-chains 98 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 0.0870 chunk 37 optimal weight: 7.9990 chunk 93 optimal weight: 0.6980 chunk 11 optimal weight: 0.0670 chunk 16 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.209720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.157305 restraints weight = 27237.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.157143 restraints weight = 34005.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.153796 restraints weight = 15595.486| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9104 Z= 0.173 Angle : 0.561 11.192 12318 Z= 0.276 Chirality : 0.039 0.174 1440 Planarity : 0.003 0.035 1572 Dihedral : 8.401 58.544 1320 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.40 % Favored : 95.25 % Rotamer: Outliers : 1.06 % Allowed : 14.33 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.26), residues: 1140 helix: 2.42 (0.19), residues: 782 sheet: 0.71 (0.58), residues: 70 loop : -1.50 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 106 HIS 0.005 0.001 HIS B 191 PHE 0.015 0.001 PHE B 453 TYR 0.021 0.001 TYR A 263 ARG 0.001 0.000 ARG A 433 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1745.96 seconds wall clock time: 32 minutes 10.50 seconds (1930.50 seconds total)