Starting phenix.real_space_refine (version: dev) on Wed Feb 22 16:12:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqu_21357/02_2023/6vqu_21357.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqu_21357/02_2023/6vqu_21357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqu_21357/02_2023/6vqu_21357.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqu_21357/02_2023/6vqu_21357.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqu_21357/02_2023/6vqu_21357.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqu_21357/02_2023/6vqu_21357.pdb" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8895 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A ASP 226": "OD1" <-> "OD2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 316": "OD1" <-> "OD2" Residue "A ASP 340": "OD1" <-> "OD2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A ASP 468": "OD1" <-> "OD2" Residue "A ASP 478": "OD1" <-> "OD2" Residue "A ASP 522": "OD1" <-> "OD2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B ASP 226": "OD1" <-> "OD2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 316": "OD1" <-> "OD2" Residue "B ASP 340": "OD1" <-> "OD2" Residue "B GLU 344": "OE1" <-> "OE2" Residue "B PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B GLU 415": "OE1" <-> "OE2" Residue "B ASP 468": "OD1" <-> "OD2" Residue "B ASP 478": "OD1" <-> "OD2" Residue "B ASP 522": "OD1" <-> "OD2" Residue "B GLU 523": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 9156 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4578 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 15, 'TRANS': 573} Chain: "B" Number of atoms: 4578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4578 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 15, 'TRANS': 573} Time building chain proxies: 5.29, per 1000 atoms: 0.58 Number of scatterers: 9156 At special positions: 0 Unit cell: (110.922, 86.736, 140.946, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1662 8.00 N 1624 7.00 C 5846 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: 3.50 Conformation dependent library (CDL) restraints added in 1.5 seconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2184 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 73.5% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 15 through 28 Proline residue: A 25 - end of helix Processing helix chain 'A' and resid 32 through 69 Proline residue: A 57 - end of helix Processing helix chain 'A' and resid 75 through 127 removed outlier: 4.534A pdb=" N ARG A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL A 108 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 135 removed outlier: 3.878A pdb=" N HIS A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 161 Processing helix chain 'A' and resid 161 through 178 Processing helix chain 'A' and resid 181 through 230 removed outlier: 3.962A pdb=" N VAL A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 238 Processing helix chain 'A' and resid 239 through 293 Processing helix chain 'A' and resid 298 through 312 removed outlier: 4.021A pdb=" N VAL A 302 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.929A pdb=" N ASP A 316 " --> pdb=" O ARG A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 317 through 341 Processing helix chain 'A' and resid 401 through 408 removed outlier: 4.535A pdb=" N ARG A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 450 through 456 Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 485 through 489 removed outlier: 3.546A pdb=" N THR A 489 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 515 Processing helix chain 'A' and resid 529 through 544 removed outlier: 4.389A pdb=" N SER A 538 " --> pdb=" O GLN A 534 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 539 " --> pdb=" O ASP A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 587 through 602 Processing helix chain 'B' and resid 15 through 28 Proline residue: B 25 - end of helix Processing helix chain 'B' and resid 32 through 69 Proline residue: B 57 - end of helix Processing helix chain 'B' and resid 75 through 127 removed outlier: 4.533A pdb=" N ARG B 107 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 135 removed outlier: 3.879A pdb=" N HIS B 132 " --> pdb=" O SER B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 161 Processing helix chain 'B' and resid 161 through 178 Processing helix chain 'B' and resid 181 through 230 removed outlier: 3.962A pdb=" N VAL B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 238 Processing helix chain 'B' and resid 239 through 293 Processing helix chain 'B' and resid 298 through 312 removed outlier: 4.020A pdb=" N VAL B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 316 removed outlier: 3.928A pdb=" N ASP B 316 " --> pdb=" O ARG B 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 313 through 316' Processing helix chain 'B' and resid 317 through 341 Processing helix chain 'B' and resid 401 through 408 removed outlier: 4.535A pdb=" N ARG B 405 " --> pdb=" O SER B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 450 through 456 Processing helix chain 'B' and resid 457 through 459 No H-bonds generated for 'chain 'B' and resid 457 through 459' Processing helix chain 'B' and resid 463 through 474 Processing helix chain 'B' and resid 476 through 483 Processing helix chain 'B' and resid 485 through 489 removed outlier: 3.546A pdb=" N THR B 489 " --> pdb=" O GLY B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 515 Processing helix chain 'B' and resid 529 through 544 removed outlier: 4.389A pdb=" N SER B 538 " --> pdb=" O GLN B 534 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR B 539 " --> pdb=" O ASP B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 578 through 586 Processing helix chain 'B' and resid 587 through 602 Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 384 removed outlier: 4.166A pdb=" N GLY A 379 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N VAL A 366 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N SER A 381 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASP A 364 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU A 383 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR A 362 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHE A 363 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 419 " --> pdb=" O PHE A 363 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASN A 365 " --> pdb=" O ARG A 417 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ARG A 417 " --> pdb=" O ASN A 365 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 437 through 440 removed outlier: 6.724A pdb=" N GLY A 438 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ASP A 522 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A 440 " --> pdb=" O ASP A 522 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU A 519 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE A 552 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N PHE A 521 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ARG A 389 " --> pdb=" O THR A 564 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LEU A 566 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALA A 391 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU A 568 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A 393 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP A 569 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N LEU A 573 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 377 through 384 removed outlier: 4.166A pdb=" N GLY B 379 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N VAL B 366 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER B 381 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP B 364 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU B 383 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR B 362 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHE B 363 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 419 " --> pdb=" O PHE B 363 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASN B 365 " --> pdb=" O ARG B 417 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ARG B 417 " --> pdb=" O ASN B 365 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 437 through 440 removed outlier: 6.725A pdb=" N GLY B 438 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASP B 522 " --> pdb=" O GLY B 438 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL B 440 " --> pdb=" O ASP B 522 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU B 519 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE B 552 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N PHE B 521 " --> pdb=" O ILE B 552 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ARG B 389 " --> pdb=" O THR B 564 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LEU B 566 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALA B 391 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B 568 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 393 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP B 569 " --> pdb=" O LEU B 573 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU B 573 " --> pdb=" O ASP B 569 " (cutoff:3.500A) 668 hydrogen bonds defined for protein. 1962 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: 2.81 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2965 1.34 - 1.45: 1418 1.45 - 1.57: 4895 1.57 - 1.69: 0 1.69 - 1.80: 48 Bond restraints: 9326 Sorted by residual: bond pdb=" CB PRO B 57 " pdb=" CG PRO B 57 " ideal model delta sigma weight residual 1.492 1.384 0.108 5.00e-02 4.00e+02 4.68e+00 bond pdb=" CB PRO A 57 " pdb=" CG PRO A 57 " ideal model delta sigma weight residual 1.492 1.384 0.108 5.00e-02 4.00e+02 4.66e+00 bond pdb=" C GLN B 74 " pdb=" N PRO B 75 " ideal model delta sigma weight residual 1.334 1.381 -0.048 2.34e-02 1.83e+03 4.13e+00 bond pdb=" C GLN A 74 " pdb=" N PRO A 75 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.08e+00 bond pdb=" CA LEU A 56 " pdb=" C LEU A 56 " ideal model delta sigma weight residual 1.522 1.545 -0.023 1.26e-02 6.30e+03 3.47e+00 ... (remaining 9321 not shown) Histogram of bond angle deviations from ideal: 98.89 - 105.91: 142 105.91 - 112.93: 5135 112.93 - 119.94: 3197 119.94 - 126.96: 4094 126.96 - 133.98: 100 Bond angle restraints: 12668 Sorted by residual: angle pdb=" CA ARG A 494 " pdb=" CB ARG A 494 " pdb=" CG ARG A 494 " ideal model delta sigma weight residual 114.10 121.37 -7.27 2.00e+00 2.50e-01 1.32e+01 angle pdb=" CA ARG B 494 " pdb=" CB ARG B 494 " pdb=" CG ARG B 494 " ideal model delta sigma weight residual 114.10 121.36 -7.26 2.00e+00 2.50e-01 1.32e+01 angle pdb=" C ASP B 569 " pdb=" N GLN B 570 " pdb=" CA GLN B 570 " ideal model delta sigma weight residual 122.46 127.56 -5.10 1.41e+00 5.03e-01 1.31e+01 angle pdb=" C ASP A 569 " pdb=" N GLN A 570 " pdb=" CA GLN A 570 " ideal model delta sigma weight residual 122.46 127.49 -5.03 1.41e+00 5.03e-01 1.27e+01 angle pdb=" C GLU B 493 " pdb=" N ARG B 494 " pdb=" CA ARG B 494 " ideal model delta sigma weight residual 122.08 127.09 -5.01 1.47e+00 4.63e-01 1.16e+01 ... (remaining 12663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.89: 4673 13.89 - 27.78: 621 27.78 - 41.66: 174 41.66 - 55.55: 50 55.55 - 69.44: 18 Dihedral angle restraints: 5536 sinusoidal: 2140 harmonic: 3396 Sorted by residual: dihedral pdb=" CA PHE A 368 " pdb=" C PHE A 368 " pdb=" N GLY A 369 " pdb=" CA GLY A 369 " ideal model delta harmonic sigma weight residual 180.00 153.61 26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA PHE B 368 " pdb=" C PHE B 368 " pdb=" N GLY B 369 " pdb=" CA GLY B 369 " ideal model delta harmonic sigma weight residual 180.00 153.70 26.30 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA ALA A 76 " pdb=" C ALA A 76 " pdb=" N LEU A 77 " pdb=" CA LEU A 77 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 5533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1079 0.053 - 0.106: 279 0.106 - 0.160: 111 0.160 - 0.213: 9 0.213 - 0.266: 6 Chirality restraints: 1484 Sorted by residual: chirality pdb=" CB VAL B 543 " pdb=" CA VAL B 543 " pdb=" CG1 VAL B 543 " pdb=" CG2 VAL B 543 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB VAL A 543 " pdb=" CA VAL A 543 " pdb=" CG1 VAL A 543 " pdb=" CG2 VAL A 543 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB ILE A 559 " pdb=" CA ILE A 559 " pdb=" CG1 ILE A 559 " pdb=" CG2 ILE A 559 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1481 not shown) Planarity restraints: 1616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 543 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C VAL A 543 " -0.063 2.00e-02 2.50e+03 pdb=" O VAL A 543 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA A 544 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 543 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C VAL B 543 " 0.062 2.00e-02 2.50e+03 pdb=" O VAL B 543 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA B 544 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 303 " 0.024 2.00e-02 2.50e+03 1.70e-02 5.03e+00 pdb=" CG PHE A 303 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 303 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 303 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 303 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 303 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 303 " 0.013 2.00e-02 2.50e+03 ... (remaining 1613 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2554 2.80 - 3.33: 9066 3.33 - 3.85: 15907 3.85 - 4.38: 17055 4.38 - 4.90: 28934 Nonbonded interactions: 73516 Sorted by model distance: nonbonded pdb=" O THR A 199 " pdb=" OG1 THR A 203 " model vdw 2.276 2.440 nonbonded pdb=" O THR B 199 " pdb=" OG1 THR B 203 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR B 429 " pdb=" OG SER B 432 " model vdw 2.293 2.440 nonbonded pdb=" O ASP B 15 " pdb=" OG1 THR B 19 " model vdw 2.293 2.440 nonbonded pdb=" O ASP A 15 " pdb=" OG1 THR A 19 " model vdw 2.293 2.440 ... (remaining 73511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 5846 2.51 5 N 1624 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 13.540 Check model and map are aligned: 0.130 Process input model: 25.910 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 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 : 0.007 0.108 9326 Z= 0.438 Angle : 0.942 8.779 12668 Z= 0.539 Chirality : 0.056 0.266 1484 Planarity : 0.007 0.054 1616 Dihedral : 14.622 69.440 3352 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 1.70 % 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: -2.26 (0.21), residues: 1174 helix: -1.29 (0.15), residues: 788 sheet: -1.53 (0.62), residues: 72 loop : -1.51 (0.31), residues: 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 61 time to evaluate : 1.059 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 2 residues processed: 74 average time/residue: 0.2798 time to fit residues: 27.5320 Evaluate side-chains 41 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1161 time to fit residues: 1.8744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.0170 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 chunk 30 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 125 HIS A 305 ASN A 504 GLN B 14 HIS B 74 GLN B 119 ASN B 125 HIS B 504 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 9326 Z= 0.154 Angle : 0.568 7.443 12668 Z= 0.298 Chirality : 0.038 0.149 1484 Planarity : 0.005 0.117 1616 Dihedral : 4.125 20.622 1306 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.23), residues: 1174 helix: 0.81 (0.17), residues: 790 sheet: -1.29 (0.61), residues: 72 loop : -0.94 (0.33), residues: 312 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 48 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 67 average time/residue: 0.1991 time to fit residues: 19.5287 Evaluate side-chains 42 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.999 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0811 time to fit residues: 2.8400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 87 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A 74 GLN A 119 ASN A 125 HIS B 119 ASN B 125 HIS B 305 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 9326 Z= 0.260 Angle : 0.609 8.490 12668 Z= 0.322 Chirality : 0.039 0.136 1484 Planarity : 0.004 0.039 1616 Dihedral : 3.905 17.103 1306 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 1.81 % 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: 1.37 (0.24), residues: 1174 helix: 1.65 (0.18), residues: 788 sheet: -1.09 (0.61), residues: 72 loop : -0.39 (0.35), residues: 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 34 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 1 residues processed: 51 average time/residue: 0.2112 time to fit residues: 16.5128 Evaluate side-chains 34 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 1.138 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0752 time to fit residues: 1.6401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.3980 chunk 79 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 0.0980 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN B 119 ASN B 125 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 9326 Z= 0.161 Angle : 0.581 13.092 12668 Z= 0.292 Chirality : 0.039 0.165 1484 Planarity : 0.003 0.042 1616 Dihedral : 3.746 16.487 1306 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 1.17 % 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: 1.69 (0.24), residues: 1174 helix: 1.82 (0.18), residues: 800 sheet: -0.86 (0.62), residues: 72 loop : -0.15 (0.37), residues: 302 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 36 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 47 average time/residue: 0.1670 time to fit residues: 13.2739 Evaluate side-chains 36 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 1.190 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0838 time to fit residues: 1.8445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 0.0770 chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN B 119 ASN B 125 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9326 Z= 0.173 Angle : 0.578 10.014 12668 Z= 0.291 Chirality : 0.039 0.151 1484 Planarity : 0.003 0.023 1616 Dihedral : 3.699 16.958 1306 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 1.38 % 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: 1.87 (0.25), residues: 1174 helix: 1.95 (0.18), residues: 796 sheet: -0.80 (0.62), residues: 72 loop : -0.03 (0.36), residues: 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 36 time to evaluate : 0.864 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 46 average time/residue: 0.1937 time to fit residues: 14.1213 Evaluate side-chains 39 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 1.001 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0937 time to fit residues: 2.2631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 6.9990 chunk 100 optimal weight: 0.0470 chunk 22 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS A 442 GLN B 442 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 9326 Z= 0.233 Angle : 0.614 10.670 12668 Z= 0.311 Chirality : 0.040 0.170 1484 Planarity : 0.003 0.031 1616 Dihedral : 3.799 20.997 1306 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 1.06 % 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: 1.90 (0.25), residues: 1174 helix: 1.97 (0.18), residues: 794 sheet: -0.66 (0.62), residues: 72 loop : -0.05 (0.36), residues: 308 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 1.131 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 40 average time/residue: 0.1740 time to fit residues: 11.7664 Evaluate side-chains 36 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 1.094 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1253 time to fit residues: 2.0640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 44 optimal weight: 0.0980 chunk 66 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 9326 Z= 0.156 Angle : 0.588 11.040 12668 Z= 0.294 Chirality : 0.040 0.177 1484 Planarity : 0.003 0.030 1616 Dihedral : 3.735 21.765 1306 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 1.17 % 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: 2.01 (0.25), residues: 1174 helix: 2.00 (0.18), residues: 796 sheet: -0.48 (0.63), residues: 72 loop : 0.12 (0.37), residues: 306 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 36 time to evaluate : 1.056 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 0 residues processed: 45 average time/residue: 0.1714 time to fit residues: 12.7876 Evaluate side-chains 34 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 0.3980 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS A 442 GLN B 125 HIS B 442 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9326 Z= 0.167 Angle : 0.619 13.999 12668 Z= 0.301 Chirality : 0.040 0.204 1484 Planarity : 0.003 0.024 1616 Dihedral : 3.668 19.391 1306 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 0.64 % 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: 2.08 (0.25), residues: 1174 helix: 2.01 (0.18), residues: 800 sheet: -0.42 (0.63), residues: 72 loop : 0.24 (0.38), residues: 302 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 1.090 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 42 average time/residue: 0.1731 time to fit residues: 12.1597 Evaluate side-chains 36 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 1.096 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1198 time to fit residues: 1.5109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 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 125 HIS B 125 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9326 Z= 0.181 Angle : 0.633 12.714 12668 Z= 0.311 Chirality : 0.040 0.199 1484 Planarity : 0.003 0.023 1616 Dihedral : 3.711 18.046 1306 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.32 % 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: 2.04 (0.25), residues: 1174 helix: 1.97 (0.18), residues: 800 sheet: -0.34 (0.63), residues: 72 loop : 0.23 (0.38), residues: 302 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 1.011 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 43 average time/residue: 0.1613 time to fit residues: 11.7549 Evaluate side-chains 40 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 1.003 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0815 time to fit residues: 1.4606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 92 optimal weight: 0.0770 chunk 9 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS B 125 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9326 Z= 0.178 Angle : 0.637 11.156 12668 Z= 0.316 Chirality : 0.040 0.199 1484 Planarity : 0.003 0.024 1616 Dihedral : 3.731 22.564 1306 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 0.43 % 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: 2.02 (0.25), residues: 1174 helix: 1.97 (0.18), residues: 794 sheet: -0.29 (0.63), residues: 72 loop : 0.20 (0.37), residues: 308 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 1.067 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 43 average time/residue: 0.1693 time to fit residues: 12.1885 Evaluate side-chains 40 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 92 optimal weight: 0.4980 chunk 38 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS B 125 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.035145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.026578 restraints weight = 86471.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.027472 restraints weight = 52247.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.028100 restraints weight = 37630.120| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 9326 Z= 0.186 Angle : 0.684 11.586 12668 Z= 0.341 Chirality : 0.041 0.195 1484 Planarity : 0.003 0.026 1616 Dihedral : 3.760 23.077 1306 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.32 % 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 (0.25), residues: 1174 helix: 1.98 (0.18), residues: 788 sheet: -0.14 (0.64), residues: 70 loop : 0.13 (0.37), residues: 316 =============================================================================== Job complete usr+sys time: 1570.04 seconds wall clock time: 29 minutes 31.85 seconds (1771.85 seconds total)