Starting phenix.real_space_refine on Sat Jul 4 03:59:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7m_44316/07_2026/9b7m_44316.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7m_44316/07_2026/9b7m_44316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b7m_44316/07_2026/9b7m_44316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7m_44316/07_2026/9b7m_44316.map" model { file = "/net/cci-nas-00/data/ceres_data/9b7m_44316/07_2026/9b7m_44316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7m_44316/07_2026/9b7m_44316.cif" } resolution = 2.82 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= 1.000 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 Ca 1 9.91 5 S 69 5.16 5 C 11810 2.51 5 N 3250 2.21 5 O 3614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18744 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3074 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 357} Chain breaks: 2 Chain: "B" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 164} Chain breaks: 1 Chain: "C" Number of atoms: 4036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4036 Classifications: {'peptide': 506} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 472} Chain breaks: 1 Chain: "D" Number of atoms: 3074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3074 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 357} Chain breaks: 2 Chain: "E" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 164} Chain breaks: 1 Chain: "F" Number of atoms: 4036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4036 Classifications: {'peptide': 506} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 472} Chain breaks: 1 Chain: "H" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 994 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain: "L" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 791 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Classifications: {'water': 1} Chain breaks: 1 Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 4.15, per 1000 atoms: 0.22 Number of scatterers: 18744 At special positions: 0 Unit cell: (155.21, 135.29, 95.45, 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) Ca 1 19.99 S 69 16.00 O 3614 8.00 N 3250 7.00 C 11810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.04 Simple disulfide: pdb=" SG CYS L 45 " - pdb=" SG CYS L 110 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 839.0 milliseconds 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4356 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 54 sheets defined 7.2% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 251 through 255 removed outlier: 4.244A pdb=" N ASN A 254 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 293 removed outlier: 4.340A pdb=" N HIS A 292 " --> pdb=" O ARG A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.584A pdb=" N ILE A 566 " --> pdb=" O GLU A 563 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N THR A 568 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 435 removed outlier: 4.051A pdb=" N LEU B 435 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 569 removed outlier: 4.329A pdb=" N THR B 568 " --> pdb=" O GLU B 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'C' and resid 288 through 292 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 396 through 400 removed outlier: 3.626A pdb=" N PHE C 400 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 496 Processing helix chain 'C' and resid 563 through 567 Processing helix chain 'D' and resid 251 through 256 removed outlier: 3.886A pdb=" N ASN D 254 " --> pdb=" O THR D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 292 Processing helix chain 'D' and resid 492 through 496 Processing helix chain 'D' and resid 554 through 556 No H-bonds generated for 'chain 'D' and resid 554 through 556' Processing helix chain 'D' and resid 563 through 567 removed outlier: 3.795A pdb=" N ILE D 566 " --> pdb=" O GLU D 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 435 removed outlier: 3.997A pdb=" N LEU E 435 " --> pdb=" O LEU E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 563 through 567 Processing helix chain 'F' and resid 262 through 266 Processing helix chain 'F' and resid 288 through 293 removed outlier: 4.250A pdb=" N HIS F 292 " --> pdb=" O ARG F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 304 removed outlier: 3.554A pdb=" N ASN F 304 " --> pdb=" O ARG F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 359 removed outlier: 3.717A pdb=" N SER F 358 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA F 359 " --> pdb=" O LEU F 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 355 through 359' Processing helix chain 'F' and resid 396 through 400 removed outlier: 3.790A pdb=" N PHE F 400 " --> pdb=" O LEU F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 496 Processing helix chain 'F' and resid 565 through 569 removed outlier: 4.130A pdb=" N THR F 568 " --> pdb=" O GLU F 565 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 51 removed outlier: 3.566A pdb=" N TYR H 51 " --> pdb=" O PHE H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.718A pdb=" N THR H 110 " --> pdb=" O ALA H 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 105 removed outlier: 3.647A pdb=" N PHE L 105 " --> pdb=" O PRO L 102 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 242 through 249 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 242 through 249 current: chain 'A' and resid 331 through 336 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 261 Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 384 Processing sheet with id=AA4, first strand: chain 'A' and resid 479 through 480 removed outlier: 6.337A pdb=" N ILE A 479 " --> pdb=" O VAL A 606 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 483 through 484 Processing sheet with id=AA6, first strand: chain 'A' and resid 488 through 490 Processing sheet with id=AA7, first strand: chain 'A' and resid 514 through 517 removed outlier: 4.106A pdb=" N GLY C 578 " --> pdb=" O VAL C 596 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 542 through 544 Processing sheet with id=AA9, first strand: chain 'A' and resid 553 through 554 removed outlier: 4.083A pdb=" N THR C 450 " --> pdb=" O THR C 460 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS C 462 " --> pdb=" O SER C 448 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 593 through 596 removed outlier: 4.102A pdb=" N GLY A 578 " --> pdb=" O VAL A 596 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 619 through 621 Processing sheet with id=AB3, first strand: chain 'A' and resid 627 through 629 removed outlier: 4.010A pdb=" N MET C 605 " --> pdb=" O PHE A 629 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE C 479 " --> pdb=" O VAL C 606 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 445 through 449 removed outlier: 6.738A pdb=" N LYS B 462 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 479 through 480 removed outlier: 6.294A pdb=" N ILE B 479 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET B 605 " --> pdb=" O PHE C 629 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 483 through 484 Processing sheet with id=AB7, first strand: chain 'B' and resid 488 through 490 Processing sheet with id=AB8, first strand: chain 'B' and resid 593 through 596 removed outlier: 4.069A pdb=" N GLY B 578 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 232 through 235 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 238 through 249 current: chain 'C' and resid 331 through 336 Processing sheet with id=AC1, first strand: chain 'C' and resid 258 through 261 Processing sheet with id=AC2, first strand: chain 'C' and resid 383 through 384 Processing sheet with id=AC3, first strand: chain 'C' and resid 427 through 428 removed outlier: 6.448A pdb=" N ALA C 427 " --> pdb=" O ARG C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 483 through 484 Processing sheet with id=AC5, first strand: chain 'C' and resid 488 through 490 Processing sheet with id=AC6, first strand: chain 'C' and resid 542 through 544 Processing sheet with id=AC7, first strand: chain 'C' and resid 619 through 621 Processing sheet with id=AC8, first strand: chain 'D' and resid 242 through 249 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 242 through 249 current: chain 'D' and resid 331 through 336 No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 258 through 261 Processing sheet with id=AD1, first strand: chain 'D' and resid 479 through 480 removed outlier: 6.361A pdb=" N ILE D 479 " --> pdb=" O VAL D 606 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'D' and resid 483 through 484 Processing sheet with id=AD3, first strand: chain 'D' and resid 488 through 490 Processing sheet with id=AD4, first strand: chain 'D' and resid 514 through 517 removed outlier: 4.084A pdb=" N GLY F 578 " --> pdb=" O VAL F 596 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 542 through 544 Processing sheet with id=AD6, first strand: chain 'D' and resid 578 through 581 removed outlier: 4.074A pdb=" N GLY D 578 " --> pdb=" O VAL D 596 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 619 through 621 removed outlier: 6.158A pdb=" N ALA D 620 " --> pdb=" O MET D 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 627 through 629 removed outlier: 4.032A pdb=" N MET F 605 " --> pdb=" O PHE D 629 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE F 479 " --> pdb=" O VAL F 606 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 445 through 451 removed outlier: 6.866A pdb=" N LYS E 462 " --> pdb=" O SER E 448 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR E 450 " --> pdb=" O THR E 460 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 479 through 480 removed outlier: 6.309A pdb=" N ILE E 479 " --> pdb=" O VAL E 606 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 483 through 484 Processing sheet with id=AE3, first strand: chain 'E' and resid 488 through 490 Processing sheet with id=AE4, first strand: chain 'E' and resid 508 through 511 Processing sheet with id=AE5, first strand: chain 'E' and resid 593 through 596 removed outlier: 4.130A pdb=" N GLY E 578 " --> pdb=" O VAL E 596 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 231 through 235 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 238 through 249 current: chain 'F' and resid 335 through 336 Processing sheet with id=AE7, first strand: chain 'F' and resid 258 through 261 Processing sheet with id=AE8, first strand: chain 'F' and resid 327 through 328 Processing sheet with id=AE9, first strand: chain 'F' and resid 427 through 428 removed outlier: 6.434A pdb=" N ALA F 427 " --> pdb=" O ARG F 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 445 through 451 removed outlier: 6.586A pdb=" N LYS F 462 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR F 450 " --> pdb=" O THR F 460 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 483 through 484 Processing sheet with id=AF3, first strand: chain 'F' and resid 488 through 490 Processing sheet with id=AF4, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AF5, first strand: chain 'F' and resid 619 through 621 removed outlier: 6.151A pdb=" N ALA F 620 " --> pdb=" O MET F 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'H' and resid 22 through 26 removed outlier: 3.604A pdb=" N SER H 97 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 30 through 31 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 30 through 31 current: chain 'H' and resid 64 through 70 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 77 through 79 current: chain 'H' and resid 135 through 138 Processing sheet with id=AF8, first strand: chain 'L' and resid 26 through 29 removed outlier: 3.506A pdb=" N ASP L 92 " --> pdb=" O SER L 89 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 32 through 34 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 32 through 34 current: chain 'L' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 75 through 76 current: chain 'L' and resid 119 through 120 240 hydrogen bonds defined for protein. 495 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: 3.04 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5529 1.33 - 1.45: 3720 1.45 - 1.57: 9911 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 19280 Sorted by residual: bond pdb=" C ASP H 92 " pdb=" O ASP H 92 " ideal model delta sigma weight residual 1.236 1.209 0.027 1.17e-02 7.31e+03 5.18e+00 bond pdb=" CA ASN D 329 " pdb=" CB ASN D 329 " ideal model delta sigma weight residual 1.522 1.563 -0.041 1.86e-02 2.89e+03 4.95e+00 bond pdb=" N ARG F 550 " pdb=" CA ARG F 550 " ideal model delta sigma weight residual 1.458 1.430 0.028 1.28e-02 6.10e+03 4.77e+00 bond pdb=" C ASN C 562 " pdb=" O ASN C 562 " ideal model delta sigma weight residual 1.235 1.211 0.024 1.23e-02 6.61e+03 3.87e+00 bond pdb=" CA LEU F 235 " pdb=" C LEU F 235 " ideal model delta sigma weight residual 1.530 1.510 0.021 1.08e-02 8.57e+03 3.62e+00 ... (remaining 19275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 25187 2.20 - 4.40: 924 4.40 - 6.59: 111 6.59 - 8.79: 25 8.79 - 10.99: 6 Bond angle restraints: 26253 Sorted by residual: angle pdb=" N GLY A 539 " pdb=" CA GLY A 539 " pdb=" C GLY A 539 " ideal model delta sigma weight residual 112.73 123.72 -10.99 1.20e+00 6.94e-01 8.39e+01 angle pdb=" N THR L 91 " pdb=" CA THR L 91 " pdb=" C THR L 91 " ideal model delta sigma weight residual 111.36 119.14 -7.78 1.09e+00 8.42e-01 5.09e+01 angle pdb=" N VAL C 493 " pdb=" CA VAL C 493 " pdb=" C VAL C 493 " ideal model delta sigma weight residual 111.05 119.84 -8.79 1.25e+00 6.40e-01 4.95e+01 angle pdb=" N GLY E 539 " pdb=" CA GLY E 539 " pdb=" C GLY E 539 " ideal model delta sigma weight residual 112.73 121.15 -8.42 1.20e+00 6.94e-01 4.92e+01 angle pdb=" C VAL L 80 " pdb=" N PRO L 81 " pdb=" CA PRO L 81 " ideal model delta sigma weight residual 119.78 126.94 -7.16 1.03e+00 9.43e-01 4.84e+01 ... (remaining 26248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 10728 17.77 - 35.53: 439 35.53 - 53.30: 81 53.30 - 71.07: 17 71.07 - 88.83: 17 Dihedral angle restraints: 11282 sinusoidal: 4452 harmonic: 6830 Sorted by residual: dihedral pdb=" C ASN D 329 " pdb=" N ASN D 329 " pdb=" CA ASN D 329 " pdb=" CB ASN D 329 " ideal model delta harmonic sigma weight residual -122.60 -138.28 15.68 0 2.50e+00 1.60e-01 3.93e+01 dihedral pdb=" N ASN D 329 " pdb=" C ASN D 329 " pdb=" CA ASN D 329 " pdb=" CB ASN D 329 " ideal model delta harmonic sigma weight residual 122.80 138.10 -15.30 0 2.50e+00 1.60e-01 3.74e+01 dihedral pdb=" C HIS F 290 " pdb=" N HIS F 290 " pdb=" CA HIS F 290 " pdb=" CB HIS F 290 " ideal model delta harmonic sigma weight residual -122.60 -134.41 11.81 0 2.50e+00 1.60e-01 2.23e+01 ... (remaining 11279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2490 0.113 - 0.225: 201 0.225 - 0.338: 16 0.338 - 0.450: 4 0.450 - 0.563: 3 Chirality restraints: 2714 Sorted by residual: chirality pdb=" CA ASN D 329 " pdb=" N ASN D 329 " pdb=" C ASN D 329 " pdb=" CB ASN D 329 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.91e+00 chirality pdb=" CA HIS F 290 " pdb=" N HIS F 290 " pdb=" C HIS F 290 " pdb=" CB HIS F 290 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CA HIS A 290 " pdb=" N HIS A 290 " pdb=" C HIS A 290 " pdb=" CB HIS A 290 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.14e+00 ... (remaining 2711 not shown) Planarity restraints: 3493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 294 " -0.062 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO A 295 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 367 " -0.039 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO D 368 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 368 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 368 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 381 " -0.012 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C THR A 381 " 0.038 2.00e-02 2.50e+03 pdb=" O THR A 381 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 382 " -0.013 2.00e-02 2.50e+03 ... (remaining 3490 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 223 2.62 - 3.19: 16343 3.19 - 3.76: 30260 3.76 - 4.33: 44838 4.33 - 4.90: 72186 Nonbonded interactions: 163850 Sorted by model distance: nonbonded pdb=" OE2 GLU C 565 " pdb="CA CA C 801 " model vdw 2.048 3.250 nonbonded pdb=" OH TYR C 252 " pdb=" O ILE C 374 " model vdw 2.207 3.040 nonbonded pdb=" N GLU C 565 " pdb=" OE1 GLU C 565 " model vdw 2.210 3.120 nonbonded pdb=" ND2 ASN C 710 " pdb=" OE1 GLN D 259 " model vdw 2.219 3.120 nonbonded pdb=" O GLU F 564 " pdb=" NZ LYS F 567 " model vdw 2.226 3.120 ... (remaining 163845 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = (chain 'C' and resid 219 through 736) 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.350 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 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 : 0.005 0.050 19282 Z= 0.307 Angle : 0.942 10.991 26257 Z= 0.600 Chirality : 0.066 0.563 2714 Planarity : 0.005 0.096 3493 Dihedral : 11.017 88.834 6920 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.56 % Allowed : 3.96 % Favored : 94.48 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.15), residues: 2341 helix: -3.36 (0.39), residues: 98 sheet: 0.21 (0.19), residues: 628 loop : -0.41 (0.13), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 730 TYR 0.022 0.002 TYR C 701 PHE 0.018 0.002 PHE A 286 TRP 0.023 0.002 TRP F 281 HIS 0.011 0.002 HIS C 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.31 (19280) covalent geometry : angle 0.94237 / 0.60 (26253) SS BOND : bond 0.00586 / 0.29 ( 2) SS BOND : angle 0.99926 / 0.59 ( 4) hydrogen bonds : bond 0.22903 / 14.44 ( 240) hydrogen bonds : angle 8.45917 / 5.84 ( 495) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 320 time to evaluate : 0.759 Fit side-chains REVERT: A 559 MET cc_start: 0.7955 (mtm) cc_final: 0.7689 (mtp) REVERT: A 579 GLN cc_start: 0.7492 (mt0) cc_final: 0.7188 (mt0) REVERT: A 586 SER cc_start: 0.8005 (p) cc_final: 0.7778 (m) REVERT: B 441 ASP cc_start: 0.8337 (m-30) cc_final: 0.7967 (m-30) REVERT: B 514 ARG cc_start: 0.7649 (mtm180) cc_final: 0.6111 (mtp85) REVERT: C 254 ASN cc_start: 0.7873 (m-40) cc_final: 0.7438 (t0) REVERT: C 406 ARG cc_start: 0.7627 (mtt180) cc_final: 0.6752 (mtm110) REVERT: D 316 LYS cc_start: 0.8338 (mtpp) cc_final: 0.7809 (mtmt) REVERT: D 419 ASN cc_start: 0.7975 (t0) cc_final: 0.7681 (t0) REVERT: D 579 GLN cc_start: 0.8076 (mt0) cc_final: 0.7861 (mt0) REVERT: D 682 GLU cc_start: 0.7654 (tt0) cc_final: 0.7190 (tm-30) REVERT: E 514 ARG cc_start: 0.7783 (mtm180) cc_final: 0.6251 (ptt180) REVERT: E 515 ASN cc_start: 0.8033 (m-40) cc_final: 0.7689 (t0) REVERT: E 533 ARG cc_start: 0.6952 (ptt-90) cc_final: 0.6607 (pmt170) REVERT: F 259 GLN cc_start: 0.7379 (tt0) cc_final: 0.6101 (pm20) REVERT: F 334 ILE cc_start: 0.8891 (mt) cc_final: 0.8605 (mp) REVERT: F 387 GLN cc_start: 0.8125 (mt0) cc_final: 0.7265 (mm-40) REVERT: F 406 ARG cc_start: 0.7712 (mtt180) cc_final: 0.6582 (mtm110) REVERT: F 412 GLN cc_start: 0.7940 (pt0) cc_final: 0.7563 (pt0) outliers start: 32 outliers final: 15 residues processed: 344 average time/residue: 0.6725 time to fit residues: 256.7450 Evaluate side-chains 220 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 205 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 703 SER Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 262 ASN Chi-restraints excluded: chain F residue 532 ASP Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 111 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 10.0000 overall best weight: 5.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 ASN A 497 ASN A 585 GLN A 588 GLN A 608 GLN A 624 HIS A 646 GLN A 651 ASN ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN B 470 ASN B 497 ASN B 608 GLN C 229 HIS C 292 HIS C 497 ASN C 552 ASN ** C 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 GLN C 673 GLN D 262 ASN D 292 HIS D 497 ASN D 624 HIS D 646 GLN D 651 ASN E 430 GLN E 456 GLN E 497 ASN E 562 ASN ** E 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 608 GLN F 304 ASN F 336 ASN F 337 ASN F 452 ASN F 590 GLN F 608 GLN F 646 GLN F 673 GLN F 710 ASN H 22 GLN L 28 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.093478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.079540 restraints weight = 30587.923| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 1.54 r_work: 0.2741 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19282 Z= 0.222 Angle : 0.629 8.797 26257 Z= 0.333 Chirality : 0.046 0.146 2714 Planarity : 0.005 0.049 3493 Dihedral : 6.132 53.281 2591 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.44 % Allowed : 8.15 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.15), residues: 2341 helix: -3.26 (0.45), residues: 86 sheet: 0.22 (0.20), residues: 554 loop : -0.18 (0.13), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 730 TYR 0.020 0.002 TYR C 731 PHE 0.014 0.002 PHE F 535 TRP 0.018 0.002 TRP F 281 HIS 0.007 0.002 HIS D 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 (19280) covalent geometry : angle 0.62933 / 0.33 (26253) SS BOND : bond 0.00564 / 0.28 ( 2) SS BOND : angle 1.30983 / 0.71 ( 4) hydrogen bonds : bond 0.03586 / 2.22 ( 240) hydrogen bonds : angle 6.56917 / 4.52 ( 495) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 212 time to evaluate : 0.821 Fit side-chains REVERT: A 579 GLN cc_start: 0.7738 (mt0) cc_final: 0.7258 (mt0) REVERT: B 441 ASP cc_start: 0.8516 (m-30) cc_final: 0.8305 (m-30) REVERT: B 485 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7887 (ttt180) REVERT: B 514 ARG cc_start: 0.7609 (mtm180) cc_final: 0.5919 (mtp85) REVERT: C 254 ASN cc_start: 0.8245 (m-40) cc_final: 0.7806 (t0) REVERT: C 406 ARG cc_start: 0.7926 (mtt180) cc_final: 0.6572 (mtm110) REVERT: C 418 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7351 (tp30) REVERT: C 641 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8404 (mttt) REVERT: D 316 LYS cc_start: 0.8295 (mtpp) cc_final: 0.7564 (mtmt) REVERT: D 349 ASP cc_start: 0.8341 (m-30) cc_final: 0.8001 (m-30) REVERT: D 416 GLU cc_start: 0.8261 (tt0) cc_final: 0.7933 (tp30) REVERT: D 419 ASN cc_start: 0.7905 (t0) cc_final: 0.7672 (t0) REVERT: D 579 GLN cc_start: 0.8401 (mt0) cc_final: 0.8105 (mt0) REVERT: D 682 GLU cc_start: 0.8014 (tt0) cc_final: 0.7390 (tm-30) REVERT: F 312 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7987 (ptp90) REVERT: F 324 GLU cc_start: 0.7305 (pp20) cc_final: 0.7079 (pp20) REVERT: F 334 ILE cc_start: 0.8885 (mt) cc_final: 0.8654 (mp) REVERT: F 387 GLN cc_start: 0.8294 (mt0) cc_final: 0.7171 (mm-40) REVERT: F 406 ARG cc_start: 0.8061 (mtt180) cc_final: 0.6226 (mtm-85) REVERT: F 412 GLN cc_start: 0.8215 (pt0) cc_final: 0.7660 (pt0) REVERT: F 579 GLN cc_start: 0.8008 (mt0) cc_final: 0.7774 (mt0) REVERT: H 38 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8373 (ttt180) REVERT: H 140 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7785 (pp30) outliers start: 50 outliers final: 20 residues processed: 246 average time/residue: 0.6777 time to fit residues: 185.3901 Evaluate side-chains 218 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 641 LYS Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 312 ARG Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 140 GLN Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 111 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 212 optimal weight: 30.0000 chunk 166 optimal weight: 10.0000 chunk 221 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 154 optimal weight: 0.4980 chunk 165 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 GLN A 588 GLN B 428 HIS B 430 GLN C 651 ASN D 262 ASN D 292 HIS E 515 ASN E 570 ASN F 304 ASN F 336 ASN F 343 GLN F 588 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.094275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.080432 restraints weight = 30569.381| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.51 r_work: 0.2759 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19282 Z= 0.142 Angle : 0.534 7.366 26257 Z= 0.279 Chirality : 0.043 0.138 2714 Planarity : 0.004 0.041 3493 Dihedral : 5.451 59.441 2584 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.90 % Allowed : 9.57 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.16), residues: 2341 helix: -3.42 (0.44), residues: 88 sheet: 0.31 (0.21), residues: 533 loop : -0.05 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 533 TYR 0.013 0.002 TYR H 69 PHE 0.011 0.001 PHE F 535 TRP 0.015 0.001 TRP E 509 HIS 0.004 0.001 HIS D 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (19280) covalent geometry : angle 0.53404 / 0.28 (26253) SS BOND : bond 0.00543 / 0.27 ( 2) SS BOND : angle 0.96403 / 0.55 ( 4) hydrogen bonds : bond 0.02917 / 1.81 ( 240) hydrogen bonds : angle 6.07480 / 4.20 ( 495) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 0.798 Fit side-chains REVERT: A 485 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7129 (ttt90) REVERT: A 579 GLN cc_start: 0.7720 (mt0) cc_final: 0.7182 (mt0) REVERT: B 485 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7884 (ttt180) REVERT: B 514 ARG cc_start: 0.7598 (mtm180) cc_final: 0.5907 (mtp85) REVERT: C 254 ASN cc_start: 0.8257 (m-40) cc_final: 0.7742 (t0) REVERT: C 406 ARG cc_start: 0.7907 (mtt180) cc_final: 0.6517 (mtm110) REVERT: C 418 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7268 (tp30) REVERT: C 524 MET cc_start: 0.9009 (mtm) cc_final: 0.8756 (mtp) REVERT: C 641 LYS cc_start: 0.8687 (mtpm) cc_final: 0.8405 (mttt) REVERT: D 316 LYS cc_start: 0.8306 (mtpp) cc_final: 0.7435 (mppt) REVERT: D 349 ASP cc_start: 0.8375 (m-30) cc_final: 0.7980 (m-30) REVERT: D 419 ASN cc_start: 0.7975 (t0) cc_final: 0.7768 (t0) REVERT: D 579 GLN cc_start: 0.8429 (mt0) cc_final: 0.8223 (mt0) REVERT: D 682 GLU cc_start: 0.7952 (tt0) cc_final: 0.7359 (tm-30) REVERT: E 485 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7860 (ttm170) REVERT: F 312 ARG cc_start: 0.8249 (mtt-85) cc_final: 0.8031 (ptp90) REVERT: F 324 GLU cc_start: 0.7347 (pp20) cc_final: 0.7070 (pp20) REVERT: F 334 ILE cc_start: 0.8852 (mt) cc_final: 0.8627 (mp) REVERT: F 387 GLN cc_start: 0.8243 (mt0) cc_final: 0.7124 (mm-40) REVERT: F 406 ARG cc_start: 0.8089 (mtt180) cc_final: 0.6378 (mtm110) REVERT: F 412 GLN cc_start: 0.8198 (pt0) cc_final: 0.7625 (pt0) REVERT: H 25 GLU cc_start: 0.8688 (mp0) cc_final: 0.8474 (mp0) REVERT: H 38 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8324 (ttt180) REVERT: H 140 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7754 (pp30) outliers start: 39 outliers final: 20 residues processed: 237 average time/residue: 0.6703 time to fit residues: 176.1814 Evaluate side-chains 218 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 532 ASP Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 140 GLN Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 111 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 176 optimal weight: 20.0000 chunk 179 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 225 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 174 optimal weight: 0.0370 chunk 33 optimal weight: 10.0000 overall best weight: 4.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 GLN A 588 GLN D 262 ASN F 304 ASN F 588 GLN F 651 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.092574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.078468 restraints weight = 30477.922| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 1.54 r_work: 0.2729 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19282 Z= 0.188 Angle : 0.559 7.933 26257 Z= 0.294 Chirality : 0.044 0.136 2714 Planarity : 0.004 0.044 3493 Dihedral : 5.493 48.218 2578 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.64 % Allowed : 9.38 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.16), residues: 2341 helix: -3.65 (0.42), residues: 88 sheet: 0.29 (0.21), residues: 536 loop : -0.11 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 533 TYR 0.016 0.002 TYR C 701 PHE 0.011 0.002 PHE F 535 TRP 0.017 0.002 TRP E 509 HIS 0.005 0.001 HIS D 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (19280) covalent geometry : angle 0.55847 / 0.29 (26253) SS BOND : bond 0.00585 / 0.29 ( 2) SS BOND : angle 0.95659 / 0.54 ( 4) hydrogen bonds : bond 0.03055 / 1.87 ( 240) hydrogen bonds : angle 6.20065 / 4.30 ( 495) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 0.680 Fit side-chains REVERT: A 485 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7318 (ttt90) REVERT: A 579 GLN cc_start: 0.7713 (mt0) cc_final: 0.7192 (mt0) REVERT: B 485 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7947 (ttt180) REVERT: B 514 ARG cc_start: 0.7539 (mtm180) cc_final: 0.5839 (mtp85) REVERT: C 254 ASN cc_start: 0.8285 (m-40) cc_final: 0.7732 (t0) REVERT: C 406 ARG cc_start: 0.7920 (mtt180) cc_final: 0.6586 (mtm110) REVERT: C 418 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7330 (tp30) REVERT: C 641 LYS cc_start: 0.8688 (mtpm) cc_final: 0.8404 (mttt) REVERT: D 316 LYS cc_start: 0.8320 (mtpp) cc_final: 0.7484 (mppt) REVERT: D 349 ASP cc_start: 0.8453 (m-30) cc_final: 0.8094 (m-30) REVERT: D 579 GLN cc_start: 0.8447 (mt0) cc_final: 0.8170 (mt0) REVERT: D 682 GLU cc_start: 0.8015 (tt0) cc_final: 0.7546 (tm-30) REVERT: E 436 MET cc_start: 0.8876 (pmm) cc_final: 0.8525 (ptp) REVERT: E 485 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7906 (ttm170) REVERT: F 324 GLU cc_start: 0.7398 (pp20) cc_final: 0.7144 (pp20) REVERT: F 334 ILE cc_start: 0.8864 (mt) cc_final: 0.8651 (mp) REVERT: F 387 GLN cc_start: 0.8277 (mt0) cc_final: 0.7095 (mm-40) REVERT: F 406 ARG cc_start: 0.8081 (mtt180) cc_final: 0.6222 (mtm110) REVERT: F 412 GLN cc_start: 0.8219 (pt0) cc_final: 0.7616 (pt0) REVERT: H 38 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8406 (ttt180) REVERT: H 140 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7767 (pp30) outliers start: 54 outliers final: 32 residues processed: 237 average time/residue: 0.6531 time to fit residues: 171.5817 Evaluate side-chains 225 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 425 SER Chi-restraints excluded: chain F residue 532 ASP Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 140 GLN Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 111 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 67 optimal weight: 20.0000 chunk 230 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 7.9990 chunk 131 optimal weight: 0.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 GLN D 262 ASN F 304 ASN F 588 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.092301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.078235 restraints weight = 30365.505| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 1.54 r_work: 0.2723 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19282 Z= 0.187 Angle : 0.549 8.268 26257 Z= 0.289 Chirality : 0.043 0.136 2714 Planarity : 0.004 0.044 3493 Dihedral : 5.439 50.322 2578 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.59 % Allowed : 9.57 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.16), residues: 2341 helix: -3.71 (0.42), residues: 86 sheet: 0.27 (0.21), residues: 536 loop : -0.13 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 550 TYR 0.016 0.002 TYR C 701 PHE 0.012 0.002 PHE B 422 TRP 0.017 0.002 TRP E 509 HIS 0.005 0.001 HIS D 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (19280) covalent geometry : angle 0.54897 / 0.29 (26253) SS BOND : bond 0.00580 / 0.29 ( 2) SS BOND : angle 0.95596 / 0.54 ( 4) hydrogen bonds : bond 0.02989 / 1.83 ( 240) hydrogen bonds : angle 6.15379 / 4.28 ( 495) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 193 time to evaluate : 0.629 Fit side-chains REVERT: A 485 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7389 (ttt90) REVERT: A 579 GLN cc_start: 0.7729 (mt0) cc_final: 0.7200 (mt0) REVERT: B 485 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7946 (ttt180) REVERT: B 514 ARG cc_start: 0.7392 (mtm180) cc_final: 0.5702 (mtp85) REVERT: C 254 ASN cc_start: 0.8294 (m-40) cc_final: 0.7724 (t0) REVERT: C 324 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6665 (mm-30) REVERT: C 406 ARG cc_start: 0.7924 (mtt180) cc_final: 0.6570 (mtm110) REVERT: C 418 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7325 (tp30) REVERT: C 641 LYS cc_start: 0.8692 (mtpm) cc_final: 0.8411 (mttt) REVERT: D 316 LYS cc_start: 0.8326 (mtpp) cc_final: 0.7655 (mtmt) REVERT: D 349 ASP cc_start: 0.8443 (m-30) cc_final: 0.8085 (m-30) REVERT: E 485 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7912 (ttm170) REVERT: F 324 GLU cc_start: 0.7374 (pp20) cc_final: 0.7151 (pp20) REVERT: F 387 GLN cc_start: 0.8417 (mt0) cc_final: 0.7177 (mm-40) REVERT: F 406 ARG cc_start: 0.8133 (mtt180) cc_final: 0.5662 (mtm110) REVERT: F 412 GLN cc_start: 0.8242 (pt0) cc_final: 0.7637 (pt0) REVERT: H 38 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8417 (ttt180) REVERT: H 140 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7731 (pp30) REVERT: L 103 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7601 (pm20) outliers start: 53 outliers final: 37 residues processed: 235 average time/residue: 0.6719 time to fit residues: 175.0891 Evaluate side-chains 228 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 183 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain E residue 449 LYS Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 425 SER Chi-restraints excluded: chain F residue 532 ASP Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 140 GLN Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 128 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 77 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 216 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 chunk 179 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 80 optimal weight: 0.9980 chunk 210 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 GLN F 304 ASN F 588 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.092934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.079015 restraints weight = 30236.911| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 1.53 r_work: 0.2735 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19282 Z= 0.155 Angle : 0.524 8.189 26257 Z= 0.274 Chirality : 0.042 0.135 2714 Planarity : 0.004 0.043 3493 Dihedral : 5.287 59.075 2578 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.39 % Allowed : 10.21 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.16), residues: 2341 helix: -3.78 (0.42), residues: 88 sheet: 0.29 (0.21), residues: 514 loop : -0.09 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 312 TYR 0.014 0.002 TYR C 701 PHE 0.011 0.001 PHE A 629 TRP 0.016 0.001 TRP E 509 HIS 0.005 0.001 HIS D 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (19280) covalent geometry : angle 0.52386 / 0.27 (26253) SS BOND : bond 0.00528 / 0.26 ( 2) SS BOND : angle 0.90531 / 0.52 ( 4) hydrogen bonds : bond 0.02808 / 1.73 ( 240) hydrogen bonds : angle 5.99512 / 4.17 ( 495) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 187 time to evaluate : 0.764 Fit side-chains REVERT: A 485 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7431 (ttt90) REVERT: A 579 GLN cc_start: 0.7713 (mt0) cc_final: 0.7200 (mt0) REVERT: B 485 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7964 (ttt180) REVERT: B 514 ARG cc_start: 0.7389 (mtm180) cc_final: 0.5761 (mtp85) REVERT: C 254 ASN cc_start: 0.8300 (m-40) cc_final: 0.7717 (t0) REVERT: C 312 ARG cc_start: 0.8145 (mtt180) cc_final: 0.7856 (ttm170) REVERT: C 324 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6684 (mm-30) REVERT: C 406 ARG cc_start: 0.7892 (mtt180) cc_final: 0.6518 (mtm110) REVERT: C 418 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7284 (tp30) REVERT: C 641 LYS cc_start: 0.8683 (mtpm) cc_final: 0.8410 (mttt) REVERT: D 349 ASP cc_start: 0.8418 (m-30) cc_final: 0.8108 (m-30) REVERT: E 485 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7824 (ttm170) REVERT: F 324 GLU cc_start: 0.7378 (pp20) cc_final: 0.7137 (pp20) REVERT: F 387 GLN cc_start: 0.8389 (mt0) cc_final: 0.7108 (mm-40) REVERT: F 406 ARG cc_start: 0.8109 (mtt180) cc_final: 0.5615 (mtm110) REVERT: F 412 GLN cc_start: 0.8232 (pt0) cc_final: 0.7522 (pp30) REVERT: H 38 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8449 (ttt180) outliers start: 49 outliers final: 34 residues processed: 227 average time/residue: 0.6921 time to fit residues: 174.5335 Evaluate side-chains 227 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain E residue 449 LYS Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 425 SER Chi-restraints excluded: chain F residue 532 ASP Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 128 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 217 optimal weight: 10.0000 chunk 148 optimal weight: 0.2980 chunk 75 optimal weight: 8.9990 chunk 208 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 GLN C 709 ASN F 304 ASN F 588 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.092532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.078613 restraints weight = 30438.311| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 1.53 r_work: 0.2729 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19282 Z= 0.176 Angle : 0.541 8.441 26257 Z= 0.284 Chirality : 0.043 0.135 2714 Planarity : 0.004 0.045 3493 Dihedral : 5.324 52.251 2578 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.39 % Allowed : 10.45 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.16), residues: 2341 helix: -3.85 (0.41), residues: 88 sheet: 0.25 (0.21), residues: 536 loop : -0.12 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 101 TYR 0.016 0.002 TYR C 701 PHE 0.012 0.001 PHE B 422 TRP 0.016 0.002 TRP E 509 HIS 0.005 0.001 HIS D 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (19280) covalent geometry : angle 0.54096 / 0.28 (26253) SS BOND : bond 0.00548 / 0.27 ( 2) SS BOND : angle 0.94341 / 0.54 ( 4) hydrogen bonds : bond 0.02924 / 1.78 ( 240) hydrogen bonds : angle 6.06656 / 4.22 ( 495) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 192 time to evaluate : 0.851 Fit side-chains REVERT: A 485 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7412 (ttt90) REVERT: A 579 GLN cc_start: 0.7727 (mt0) cc_final: 0.7203 (mt0) REVERT: B 485 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7967 (ttt180) REVERT: B 514 ARG cc_start: 0.7370 (mtm180) cc_final: 0.5737 (mtp85) REVERT: C 254 ASN cc_start: 0.8301 (m-40) cc_final: 0.7716 (t0) REVERT: C 312 ARG cc_start: 0.8132 (mtt180) cc_final: 0.7839 (ttm170) REVERT: C 406 ARG cc_start: 0.7902 (mtt180) cc_final: 0.6525 (mtm110) REVERT: C 418 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7298 (tp30) REVERT: C 419 ASN cc_start: 0.8541 (t0) cc_final: 0.8213 (t0) REVERT: C 641 LYS cc_start: 0.8683 (mtpm) cc_final: 0.8410 (mttt) REVERT: C 673 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: D 349 ASP cc_start: 0.8444 (m-30) cc_final: 0.8127 (m-30) REVERT: D 682 GLU cc_start: 0.8029 (tt0) cc_final: 0.7523 (tm-30) REVERT: E 485 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7938 (ttm170) REVERT: F 387 GLN cc_start: 0.8414 (mt0) cc_final: 0.7130 (mm-40) REVERT: F 406 ARG cc_start: 0.8078 (mtt180) cc_final: 0.6273 (mtm110) REVERT: F 412 GLN cc_start: 0.8234 (pt0) cc_final: 0.7526 (pp30) outliers start: 49 outliers final: 33 residues processed: 232 average time/residue: 0.7063 time to fit residues: 182.1895 Evaluate side-chains 223 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 673 GLN Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain E residue 449 LYS Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 425 SER Chi-restraints excluded: chain F residue 532 ASP Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 128 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 158 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 229 optimal weight: 7.9990 chunk 199 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 83 optimal weight: 0.0980 overall best weight: 5.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN A 585 GLN F 304 ASN F 588 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.091824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.077823 restraints weight = 30248.606| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 1.53 r_work: 0.2714 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 19282 Z= 0.213 Angle : 0.566 8.651 26257 Z= 0.298 Chirality : 0.044 0.135 2714 Planarity : 0.004 0.048 3493 Dihedral : 5.465 48.190 2578 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.39 % Allowed : 10.69 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.16), residues: 2341 helix: -3.74 (0.38), residues: 100 sheet: 0.20 (0.21), residues: 536 loop : -0.17 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 101 TYR 0.017 0.002 TYR C 701 PHE 0.013 0.002 PHE B 422 TRP 0.018 0.002 TRP E 509 HIS 0.005 0.001 HIS D 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (19280) covalent geometry : angle 0.56591 / 0.30 (26253) SS BOND : bond 0.00597 / 0.30 ( 2) SS BOND : angle 1.00767 / 0.57 ( 4) hydrogen bonds : bond 0.03127 / 1.90 ( 240) hydrogen bonds : angle 6.20406 / 4.32 ( 495) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 187 time to evaluate : 0.818 Fit side-chains REVERT: A 485 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.7494 (ttt90) REVERT: A 579 GLN cc_start: 0.7734 (mt0) cc_final: 0.7262 (mt0) REVERT: B 485 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7952 (ttt180) REVERT: B 514 ARG cc_start: 0.7361 (mtm180) cc_final: 0.5731 (mtp85) REVERT: C 254 ASN cc_start: 0.8312 (m-40) cc_final: 0.7792 (t0) REVERT: C 312 ARG cc_start: 0.8142 (mtt180) cc_final: 0.7844 (ttm170) REVERT: C 406 ARG cc_start: 0.7894 (mtt180) cc_final: 0.6424 (mtm110) REVERT: C 418 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7354 (tp30) REVERT: C 641 LYS cc_start: 0.8688 (mtpm) cc_final: 0.8413 (mttt) REVERT: C 673 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: D 349 ASP cc_start: 0.8438 (m-30) cc_final: 0.8128 (m-30) REVERT: D 682 GLU cc_start: 0.8023 (tt0) cc_final: 0.7515 (tm-30) REVERT: E 485 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7936 (ttm170) REVERT: F 235 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8288 (mt) REVERT: F 333 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7659 (t) REVERT: F 387 GLN cc_start: 0.8416 (mt0) cc_final: 0.7091 (mm-40) REVERT: F 406 ARG cc_start: 0.8062 (mtt180) cc_final: 0.6261 (mtm110) REVERT: F 412 GLN cc_start: 0.8249 (pt0) cc_final: 0.7540 (pp30) outliers start: 49 outliers final: 35 residues processed: 225 average time/residue: 0.7270 time to fit residues: 181.8775 Evaluate side-chains 223 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 673 GLN Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain E residue 449 LYS Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 425 SER Chi-restraints excluded: chain F residue 532 ASP Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 128 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 201 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 105 optimal weight: 20.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 GLN F 304 ASN F 588 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.094249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.080357 restraints weight = 30368.038| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 1.52 r_work: 0.2762 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19282 Z= 0.111 Angle : 0.501 8.809 26257 Z= 0.261 Chirality : 0.041 0.135 2714 Planarity : 0.004 0.042 3493 Dihedral : 4.904 46.784 2578 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.46 % Allowed : 11.77 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.16), residues: 2341 helix: -3.37 (0.51), residues: 74 sheet: 0.44 (0.22), residues: 497 loop : -0.03 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 312 TYR 0.012 0.001 TYR B 443 PHE 0.011 0.001 PHE A 629 TRP 0.013 0.001 TRP E 509 HIS 0.004 0.001 HIS D 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (19280) covalent geometry : angle 0.50098 / 0.26 (26253) SS BOND : bond 0.00472 / 0.23 ( 2) SS BOND : angle 0.78188 / 0.45 ( 4) hydrogen bonds : bond 0.02602 / 1.60 ( 240) hydrogen bonds : angle 5.71868 / 3.98 ( 495) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.801 Fit side-chains REVERT: A 485 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7408 (ttt90) REVERT: A 579 GLN cc_start: 0.7732 (mt0) cc_final: 0.7211 (mt0) REVERT: B 514 ARG cc_start: 0.7368 (mtm180) cc_final: 0.5801 (mtp85) REVERT: C 254 ASN cc_start: 0.8324 (m-40) cc_final: 0.7727 (t0) REVERT: C 312 ARG cc_start: 0.8113 (mtt180) cc_final: 0.7831 (ttm170) REVERT: C 406 ARG cc_start: 0.7846 (mtt180) cc_final: 0.6445 (mtm110) REVERT: C 641 LYS cc_start: 0.8677 (mtpm) cc_final: 0.8425 (mttt) REVERT: D 262 ASN cc_start: 0.7214 (t0) cc_final: 0.6927 (t0) REVERT: D 349 ASP cc_start: 0.8375 (m-30) cc_final: 0.8094 (m-30) REVERT: D 556 ASP cc_start: 0.8126 (p0) cc_final: 0.7916 (p0) REVERT: D 682 GLU cc_start: 0.8016 (tt0) cc_final: 0.7490 (tm-30) REVERT: F 333 THR cc_start: 0.8173 (OUTLIER) cc_final: 0.7684 (t) REVERT: F 387 GLN cc_start: 0.8400 (mt0) cc_final: 0.7118 (mm-40) REVERT: F 406 ARG cc_start: 0.8051 (mtt180) cc_final: 0.5570 (mtm110) REVERT: F 412 GLN cc_start: 0.8207 (pt0) cc_final: 0.7470 (pp30) REVERT: H 140 GLN cc_start: 0.8313 (pp30) cc_final: 0.7739 (pm20) REVERT: L 103 GLU cc_start: 0.8149 (pm20) cc_final: 0.7915 (pm20) outliers start: 30 outliers final: 23 residues processed: 217 average time/residue: 0.7399 time to fit residues: 178.4158 Evaluate side-chains 208 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 532 ASP Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 128 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 109 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 212 optimal weight: 20.0000 chunk 229 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 222 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 38 optimal weight: 0.0670 chunk 77 optimal weight: 10.0000 overall best weight: 4.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 GLN C 456 GLN F 304 ASN F 588 GLN F 673 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.092885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.079037 restraints weight = 30147.717| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.51 r_work: 0.2729 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19282 Z= 0.182 Angle : 0.547 9.227 26257 Z= 0.286 Chirality : 0.043 0.134 2714 Planarity : 0.004 0.044 3493 Dihedral : 5.150 47.863 2575 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.61 % Allowed : 11.52 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.16), residues: 2341 helix: -3.36 (0.45), residues: 86 sheet: 0.37 (0.21), residues: 520 loop : -0.11 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 550 TYR 0.016 0.002 TYR C 701 PHE 0.012 0.002 PHE B 422 TRP 0.015 0.002 TRP E 509 HIS 0.005 0.001 HIS D 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (19280) covalent geometry : angle 0.54727 / 0.29 (26253) SS BOND : bond 0.00573 / 0.28 ( 2) SS BOND : angle 0.89283 / 0.51 ( 4) hydrogen bonds : bond 0.02959 / 1.80 ( 240) hydrogen bonds : angle 6.00717 / 4.19 ( 495) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.803 Fit side-chains REVERT: A 485 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7463 (ttt90) REVERT: A 579 GLN cc_start: 0.7728 (mt0) cc_final: 0.7205 (mt0) REVERT: B 514 ARG cc_start: 0.7368 (mtm180) cc_final: 0.5744 (mtp85) REVERT: C 254 ASN cc_start: 0.8316 (m-40) cc_final: 0.7739 (t0) REVERT: C 312 ARG cc_start: 0.8124 (mtt180) cc_final: 0.7834 (ttm170) REVERT: C 406 ARG cc_start: 0.7865 (mtt180) cc_final: 0.6441 (mtm110) REVERT: C 641 LYS cc_start: 0.8689 (mtpm) cc_final: 0.8446 (mttt) REVERT: D 349 ASP cc_start: 0.8413 (m-30) cc_final: 0.8110 (m-30) REVERT: F 333 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7687 (t) REVERT: F 387 GLN cc_start: 0.8415 (mt0) cc_final: 0.7051 (mm-40) REVERT: F 406 ARG cc_start: 0.8068 (mtt180) cc_final: 0.5581 (mtm110) REVERT: F 412 GLN cc_start: 0.8217 (pt0) cc_final: 0.7515 (pp30) REVERT: L 103 GLU cc_start: 0.8149 (pm20) cc_final: 0.7914 (pm20) outliers start: 33 outliers final: 25 residues processed: 205 average time/residue: 0.7124 time to fit residues: 162.5366 Evaluate side-chains 205 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain E residue 449 LYS Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 532 ASP Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 128 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 197 optimal weight: 10.0000 chunk 226 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 206 optimal weight: 20.0000 chunk 125 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 GLN C 321 GLN C 456 GLN E 470 ASN E 588 GLN F 304 ASN F 588 GLN F 700 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.091386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.077474 restraints weight = 30594.108| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 1.52 r_work: 0.2705 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 19282 Z= 0.264 Angle : 0.606 9.247 26257 Z= 0.320 Chirality : 0.046 0.146 2714 Planarity : 0.005 0.048 3493 Dihedral : 5.518 49.086 2575 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.95 % Allowed : 11.23 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.16), residues: 2341 helix: -3.78 (0.37), residues: 98 sheet: 0.16 (0.21), residues: 536 loop : -0.22 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 550 TYR 0.019 0.002 TYR C 701 PHE 0.015 0.002 PHE B 422 TRP 0.019 0.002 TRP E 509 HIS 0.006 0.002 HIS D 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.26 (19280) covalent geometry : angle 0.60594 / 0.32 (26253) SS BOND : bond 0.00670 / 0.33 ( 2) SS BOND : angle 1.07205 / 0.60 ( 4) hydrogen bonds : bond 0.03364 / 2.03 ( 240) hydrogen bonds : angle 6.34816 / 4.43 ( 495) =============================================================================== Job complete usr+sys time: 5701.08 seconds wall clock time: 98 minutes 21.73 seconds (5901.73 seconds total)