Starting phenix.real_space_refine on Thu Dec 7 23:32:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qky_14057/12_2023/7qky_14057.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qky_14057/12_2023/7qky_14057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qky_14057/12_2023/7qky_14057.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qky_14057/12_2023/7qky_14057.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qky_14057/12_2023/7qky_14057.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qky_14057/12_2023/7qky_14057.pdb" } resolution = 1.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 S 6 5.16 5 C 1776 2.51 5 N 504 2.21 5 O 612 1.98 5 H 2862 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 391": "OE1" <-> "OE2" Residue "A ARG 406": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 391": "OE1" <-> "OE2" Residue "B ARG 406": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 391": "OE1" <-> "OE2" Residue "C ARG 406": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 391": "OE1" <-> "OE2" Residue "D ARG 406": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 391": "OE1" <-> "OE2" Residue "E ARG 406": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 391": "OE1" <-> "OE2" Residue "F ARG 406": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5760 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 960 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "B" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 960 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "C" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 960 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "D" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 960 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "E" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 960 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "F" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 960 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Time building chain proxies: 3.28, per 1000 atoms: 0.57 Number of scatterers: 5760 At special positions: 0 Unit cell: (111.231, 82.878, 39.258, 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 6 16.00 O 612 8.00 N 504 7.00 C 1776 6.00 H 2862 1.00 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: 4.67 Conformation dependent library (CDL) restraints added in 806.7 milliseconds 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 47.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 386 removed outlier: 6.570A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLU B 380 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ARG A 379 " --> pdb=" O GLU B 380 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ALA B 382 " --> pdb=" O ARG A 379 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASN A 381 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ALA B 384 " --> pdb=" O ASN A 381 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYS A 383 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR B 386 " --> pdb=" O LYS A 383 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS A 385 " --> pdb=" O THR B 386 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR B 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N GLU E 380 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ARG B 379 " --> pdb=" O GLU E 380 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ALA E 382 " --> pdb=" O ARG B 379 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASN B 381 " --> pdb=" O ALA E 382 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ALA E 384 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LYS B 383 " --> pdb=" O ALA E 384 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N THR E 386 " --> pdb=" O LYS B 383 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS B 385 " --> pdb=" O THR E 386 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 392 through 394 removed outlier: 6.290A pdb=" N VAL A 393 " --> pdb=" O TYR B 394 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL B 393 " --> pdb=" O TYR E 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 398 through 399 removed outlier: 6.809A pdb=" N VAL A 398 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL B 398 " --> pdb=" O VAL E 399 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 406 through 414 removed outlier: 6.822A pdb=" N HIS A 407 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASN B 410 " --> pdb=" O HIS A 407 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER A 409 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N SER B 412 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A 411 " --> pdb=" O SER B 412 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N THR B 414 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER A 413 " --> pdb=" O THR B 414 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N HIS B 407 " --> pdb=" O LEU E 408 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ASN E 410 " --> pdb=" O HIS B 407 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N SER B 409 " --> pdb=" O ASN E 410 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N SER E 412 " --> pdb=" O SER B 409 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL B 411 " --> pdb=" O SER E 412 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N THR E 414 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER B 413 " --> pdb=" O THR E 414 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 417 through 420 removed outlier: 6.310A pdb=" N ASP B 418 " --> pdb=" O MET E 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 424 through 429 removed outlier: 6.500A pdb=" N LEU A 425 " --> pdb=" O ALA B 426 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU B 428 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N THR A 427 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU B 425 " --> pdb=" O ALA E 426 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU E 428 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N THR B 427 " --> pdb=" O LEU E 428 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 432 through 433 Processing sheet with id=AA8, first strand: chain 'A' and resid 436 through 438 Processing sheet with id=AA9, first strand: chain 'C' and resid 377 through 386 removed outlier: 6.548A pdb=" N THR C 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N GLU D 380 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ARG C 379 " --> pdb=" O GLU D 380 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ALA D 382 " --> pdb=" O ARG C 379 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASN C 381 " --> pdb=" O ALA D 382 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ALA D 384 " --> pdb=" O ASN C 381 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LYS C 383 " --> pdb=" O ALA D 384 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N THR D 386 " --> pdb=" O LYS C 383 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS C 385 " --> pdb=" O THR D 386 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR D 377 " --> pdb=" O PHE F 378 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N GLU F 380 " --> pdb=" O THR D 377 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG D 379 " --> pdb=" O GLU F 380 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA F 382 " --> pdb=" O ARG D 379 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASN D 381 " --> pdb=" O ALA F 382 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ALA F 384 " --> pdb=" O ASN D 381 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LYS D 383 " --> pdb=" O ALA F 384 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N THR F 386 " --> pdb=" O LYS D 383 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS D 385 " --> pdb=" O THR F 386 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 392 through 394 removed outlier: 6.289A pdb=" N VAL C 393 " --> pdb=" O TYR D 394 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL D 393 " --> pdb=" O TYR F 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 398 through 399 removed outlier: 6.831A pdb=" N VAL C 398 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL D 398 " --> pdb=" O VAL F 399 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 406 through 414 removed outlier: 6.779A pdb=" N HIS C 407 " --> pdb=" O ARG D 406 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N HIS D 407 " --> pdb=" O ARG F 406 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 417 through 420 Processing sheet with id=AB5, first strand: chain 'C' and resid 424 through 429 removed outlier: 6.520A pdb=" N LEU C 425 " --> pdb=" O ALA D 426 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU D 428 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N THR C 427 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU D 425 " --> pdb=" O ALA F 426 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU F 428 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N THR D 427 " --> pdb=" O LEU F 428 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 432 through 433 Processing sheet with id=AB7, first strand: chain 'C' and resid 436 through 438 35 hydrogen bonds defined for protein. 105 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: 1.82 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 2862 1.12 - 1.29: 516 1.29 - 1.47: 956 1.47 - 1.64: 1450 1.64 - 1.81: 12 Bond restraints: 5796 Sorted by residual: bond pdb=" CE1 PHE A 378 " pdb=" HE1 PHE A 378 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N LYS E 383 " pdb=" H LYS E 383 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CE2 TYR E 394 " pdb=" HE2 TYR E 394 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NE ARG A 379 " pdb=" HE ARG A 379 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N ALA C 384 " pdb=" H ALA C 384 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 5791 not shown) Histogram of bond angle deviations from ideal: 99.38 - 105.35: 64 105.35 - 111.32: 6320 111.32 - 117.29: 1401 117.29 - 123.26: 2278 123.26 - 129.23: 431 Bond angle restraints: 10494 Sorted by residual: angle pdb=" CB HIS A 407 " pdb=" CG HIS A 407 " pdb=" CD2 HIS A 407 " ideal model delta sigma weight residual 131.20 125.26 5.94 1.30e+00 5.92e-01 2.09e+01 angle pdb=" N ALA B 429 " pdb=" CA ALA B 429 " pdb=" C ALA B 429 " ideal model delta sigma weight residual 108.99 116.02 -7.03 1.57e+00 4.06e-01 2.01e+01 angle pdb=" CB HIS E 407 " pdb=" CG HIS E 407 " pdb=" CD2 HIS E 407 " ideal model delta sigma weight residual 131.20 125.39 5.81 1.30e+00 5.92e-01 2.00e+01 angle pdb=" CB HIS C 407 " pdb=" CG HIS C 407 " pdb=" CD2 HIS C 407 " ideal model delta sigma weight residual 131.20 125.44 5.76 1.30e+00 5.92e-01 1.96e+01 angle pdb=" CB HIS D 407 " pdb=" CG HIS D 407 " pdb=" CD2 HIS D 407 " ideal model delta sigma weight residual 131.20 125.50 5.70 1.30e+00 5.92e-01 1.92e+01 ... (remaining 10489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.18: 2385 14.18 - 28.36: 227 28.36 - 42.54: 16 42.54 - 56.72: 26 56.72 - 70.89: 34 Dihedral angle restraints: 2688 sinusoidal: 1458 harmonic: 1230 Sorted by residual: dihedral pdb=" CA HIS C 388 " pdb=" C HIS C 388 " pdb=" N GLY C 389 " pdb=" CA GLY C 389 " ideal model delta harmonic sigma weight residual 180.00 151.24 28.76 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA HIS B 388 " pdb=" C HIS B 388 " pdb=" N GLY B 389 " pdb=" CA GLY B 389 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA HIS D 388 " pdb=" C HIS D 388 " pdb=" N GLY D 389 " pdb=" CA GLY D 389 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 2685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 305 0.079 - 0.157: 151 0.157 - 0.235: 24 0.235 - 0.313: 1 0.313 - 0.392: 5 Chirality restraints: 486 Sorted by residual: chirality pdb=" CA HIS D 388 " pdb=" N HIS D 388 " pdb=" C HIS D 388 " pdb=" CB HIS D 388 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA HIS C 388 " pdb=" N HIS C 388 " pdb=" C HIS C 388 " pdb=" CB HIS C 388 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA HIS B 388 " pdb=" N HIS B 388 " pdb=" C HIS B 388 " pdb=" CB HIS B 388 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.40e+00 ... (remaining 483 not shown) Planarity restraints: 888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 378 " -0.227 2.00e-02 2.50e+03 9.08e-02 2.47e+02 pdb=" CG PHE C 378 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE C 378 " 0.075 2.00e-02 2.50e+03 pdb=" CD2 PHE C 378 " 0.073 2.00e-02 2.50e+03 pdb=" CE1 PHE C 378 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE C 378 " 0.045 2.00e-02 2.50e+03 pdb=" CZ PHE C 378 " -0.036 2.00e-02 2.50e+03 pdb=" HD1 PHE C 378 " 0.113 2.00e-02 2.50e+03 pdb=" HD2 PHE C 378 " 0.053 2.00e-02 2.50e+03 pdb=" HE1 PHE C 378 " -0.025 2.00e-02 2.50e+03 pdb=" HE2 PHE C 378 " 0.024 2.00e-02 2.50e+03 pdb=" HZ PHE C 378 " -0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 378 " -0.200 2.00e-02 2.50e+03 8.24e-02 2.04e+02 pdb=" CG PHE D 378 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 PHE D 378 " 0.065 2.00e-02 2.50e+03 pdb=" CD2 PHE D 378 " 0.061 2.00e-02 2.50e+03 pdb=" CE1 PHE D 378 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE D 378 " 0.041 2.00e-02 2.50e+03 pdb=" CZ PHE D 378 " -0.042 2.00e-02 2.50e+03 pdb=" HD1 PHE D 378 " 0.109 2.00e-02 2.50e+03 pdb=" HD2 PHE D 378 " 0.045 2.00e-02 2.50e+03 pdb=" HE1 PHE D 378 " -0.014 2.00e-02 2.50e+03 pdb=" HE2 PHE D 378 " 0.039 2.00e-02 2.50e+03 pdb=" HZ PHE D 378 " -0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 388 " -0.039 2.00e-02 2.50e+03 7.06e-02 4.99e+01 pdb=" N GLY D 389 " 0.122 2.00e-02 2.50e+03 pdb=" CA GLY D 389 " -0.035 2.00e-02 2.50e+03 pdb=" H GLY D 389 " -0.047 2.00e-02 2.50e+03 ... (remaining 885 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 551 2.17 - 2.78: 9561 2.78 - 3.39: 15847 3.39 - 3.99: 21842 3.99 - 4.60: 29797 Nonbonded interactions: 77598 Sorted by model distance: nonbonded pdb=" HG SER F 413 " pdb=" OD2 ASP F 418 " model vdw 1.568 1.850 nonbonded pdb=" HG SER E 413 " pdb=" OD2 ASP E 418 " model vdw 1.574 1.850 nonbonded pdb=" HG SER B 413 " pdb=" OD2 ASP B 418 " model vdw 1.579 1.850 nonbonded pdb=" HG SER D 413 " pdb=" OD2 ASP D 418 " model vdw 1.592 1.850 nonbonded pdb=" HG SER A 413 " pdb=" OD2 ASP A 418 " model vdw 1.639 1.850 ... (remaining 77593 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.930 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: 0.090 Extract box with map and model: 13.150 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 23.300 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 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 : 0.011 0.034 2934 Z= 0.756 Angle : 1.746 7.133 3978 Z= 1.129 Chirality : 0.092 0.392 486 Planarity : 0.011 0.081 516 Dihedral : 12.756 70.894 1068 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.61 % Allowed : 3.03 % Favored : 96.36 % Cbeta Deviations : 0.81 % 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: -3.08 (0.30), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.23), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 388 PHE 0.125 0.035 PHE C 378 TYR 0.027 0.009 TYR D 394 ARG 0.004 0.001 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 140 average time/residue: 1.8437 time to fit residues: 265.8415 Evaluate side-chains 117 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.541 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2934 Z= 0.164 Angle : 0.643 6.449 3978 Z= 0.332 Chirality : 0.047 0.131 486 Planarity : 0.003 0.021 516 Dihedral : 7.982 27.571 408 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.21 % Allowed : 12.73 % Favored : 86.06 % 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: -3.06 (0.30), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.23), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 407 PHE 0.015 0.002 PHE C 378 TYR 0.013 0.002 TYR C 394 ARG 0.003 0.001 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 123 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 124 average time/residue: 2.0762 time to fit residues: 264.4303 Evaluate side-chains 112 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.483 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 381 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2934 Z= 0.248 Angle : 0.686 7.005 3978 Z= 0.348 Chirality : 0.046 0.131 486 Planarity : 0.003 0.016 516 Dihedral : 7.612 25.494 408 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.82 % Allowed : 16.06 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.29), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.22), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 407 PHE 0.013 0.003 PHE C 378 TYR 0.012 0.002 TYR C 394 ARG 0.003 0.000 ARG F 406 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 113 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 114 average time/residue: 2.2047 time to fit residues: 257.7543 Evaluate side-chains 108 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.510 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0674 time to fit residues: 0.6680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 381 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2934 Z= 0.189 Angle : 0.634 5.937 3978 Z= 0.318 Chirality : 0.046 0.131 486 Planarity : 0.002 0.023 516 Dihedral : 7.315 25.825 408 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.21 % Allowed : 20.00 % Favored : 78.79 % 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: -3.16 (0.30), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.23), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 407 PHE 0.009 0.002 PHE C 378 TYR 0.013 0.002 TYR C 394 ARG 0.002 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 111 average time/residue: 2.3265 time to fit residues: 264.6480 Evaluate side-chains 106 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 0.525 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 0.0767 time to fit residues: 0.9839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN C 388 HIS D 388 HIS E 381 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2934 Z= 0.280 Angle : 0.706 6.698 3978 Z= 0.356 Chirality : 0.045 0.127 486 Planarity : 0.003 0.014 516 Dihedral : 7.425 25.407 408 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.12 % Allowed : 18.48 % Favored : 79.39 % 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: -3.21 (0.30), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.23), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 407 PHE 0.012 0.004 PHE C 378 TYR 0.013 0.002 TYR C 394 ARG 0.001 0.000 ARG F 406 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 112 average time/residue: 2.3349 time to fit residues: 267.9317 Evaluate side-chains 109 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 0.492 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0700 time to fit residues: 1.1932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.0770 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 381 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2934 Z= 0.149 Angle : 0.601 5.572 3978 Z= 0.299 Chirality : 0.046 0.128 486 Planarity : 0.002 0.008 516 Dihedral : 6.920 25.206 408 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.21 % Allowed : 19.09 % Favored : 79.70 % 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: -3.19 (0.30), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.23), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 407 PHE 0.007 0.002 PHE E 378 TYR 0.013 0.002 TYR F 394 ARG 0.001 0.000 ARG F 406 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 0.482 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 108 average time/residue: 2.3566 time to fit residues: 260.6442 Evaluate side-chains 106 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.452 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0723 time to fit residues: 0.8574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 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 388 HIS E 381 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2934 Z= 0.204 Angle : 0.651 5.783 3978 Z= 0.324 Chirality : 0.045 0.127 486 Planarity : 0.003 0.025 516 Dihedral : 6.951 23.956 408 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.91 % Allowed : 18.18 % Favored : 80.91 % 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: -3.21 (0.30), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.23), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 407 PHE 0.008 0.002 PHE E 378 TYR 0.014 0.002 TYR C 394 ARG 0.007 0.001 ARG C 406 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 105 average time/residue: 2.4795 time to fit residues: 267.3197 Evaluate side-chains 104 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 0.495 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0762 time to fit residues: 0.8822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.0370 chunk 9 optimal weight: 0.9980 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 381 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2934 Z= 0.160 Angle : 0.610 5.191 3978 Z= 0.301 Chirality : 0.046 0.127 486 Planarity : 0.002 0.020 516 Dihedral : 6.674 24.013 408 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.30 % Allowed : 20.30 % Favored : 79.39 % 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: -3.21 (0.31), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.24), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 407 PHE 0.007 0.002 PHE E 378 TYR 0.014 0.002 TYR C 394 ARG 0.002 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 2.4076 time to fit residues: 263.9201 Evaluate side-chains 102 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.575 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 23 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN E 381 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2934 Z= 0.151 Angle : 0.587 5.029 3978 Z= 0.292 Chirality : 0.046 0.127 486 Planarity : 0.002 0.008 516 Dihedral : 6.465 22.598 408 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.61 % Allowed : 19.70 % Favored : 79.70 % 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: -3.16 (0.31), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.24), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 407 PHE 0.006 0.002 PHE E 378 TYR 0.015 0.002 TYR C 394 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 108 average time/residue: 2.4449 time to fit residues: 270.3039 Evaluate side-chains 105 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 0.493 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0778 time to fit residues: 0.7259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN E 381 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2934 Z= 0.189 Angle : 0.638 5.821 3978 Z= 0.316 Chirality : 0.045 0.124 486 Planarity : 0.002 0.011 516 Dihedral : 6.638 23.063 408 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 21.52 % Favored : 78.48 % 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: -3.14 (0.31), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.24), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 407 PHE 0.007 0.002 PHE C 378 TYR 0.016 0.002 TYR C 394 ARG 0.002 0.000 ARG C 406 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Residue ALA 382 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 2.4500 time to fit residues: 258.3126 Evaluate side-chains 102 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.514 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 chunk 0 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN E 381 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.220263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.186971 restraints weight = 5440.267| |-----------------------------------------------------------------------------| r_work (start): 0.4539 rms_B_bonded: 1.37 r_work: 0.4414 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.4329 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2934 Z= 0.225 Angle : 0.660 5.543 3978 Z= 0.331 Chirality : 0.045 0.123 486 Planarity : 0.002 0.014 516 Dihedral : 6.802 23.404 408 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.30 % Allowed : 20.91 % Favored : 78.79 % 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: -3.17 (0.31), residues: 384 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.23), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 407 PHE 0.009 0.003 PHE C 378 TYR 0.016 0.002 TYR C 394 ARG 0.002 0.000 ARG C 406 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5095.28 seconds wall clock time: 89 minutes 9.72 seconds (5349.72 seconds total)