Starting phenix.real_space_refine on Sun Aug 24 07:56:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7m_44316/08_2025/9b7m_44316.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7m_44316/08_2025/9b7m_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 { model { file = "/net/cci-nas-00/data/ceres_data/9b7m_44316/08_2025/9b7m_44316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7m_44316/08_2025/9b7m_44316.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b7m_44316/08_2025/9b7m_44316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7m_44316/08_2025/9b7m_44316.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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, 2 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 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: 4.00, per 1000 atoms: 0.21 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: 1.44 Conformation dependent library (CDL) restraints added in 806.0 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.45 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: 3.11 Time building geometry restraints manager: 1.83 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 2.510 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.670 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 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 aren 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 covalent geometry : bond 0.00529 (19280) covalent geometry : angle 0.94237 (26253) SS BOND : bond 0.00586 ( 2) SS BOND : angle 0.99926 ( 4) hydrogen bonds : bond 0.22903 ( 240) hydrogen bonds : angle 8.45917 ( 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 : 0.627 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: 0.7680 (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: 0.8034 (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: 0.6070 time to fit residues: 230.8978 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 : 0.753 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 588 GLN 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: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.093773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.079962 restraints weight = 30635.379| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 1.53 r_work: 0.2744 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19282 Z= 0.221 Angle : 0.628 8.779 26257 Z= 0.332 Chirality : 0.046 0.147 2714 Planarity : 0.005 0.049 3493 Dihedral : 6.133 53.129 2591 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.49 % Allowed : 8.06 % Favored : 89.45 % 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 aren not related in a simple way. whole: -0.35 (0.15), residues: 2341 helix: -3.27 (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 0.009 0.001 ARG C 730 TYR 0.020 0.002 TYR C 731 PHE 0.014 0.002 PHE F 535 TRP 0.017 0.002 TRP F 281 HIS 0.007 0.002 HIS D 624 Details of bonding type rmsd covalent geometry : bond 0.00515 (19280) covalent geometry : angle 0.62807 (26253) SS BOND : bond 0.00565 ( 2) SS BOND : angle 1.28307 ( 4) hydrogen bonds : bond 0.03575 ( 240) hydrogen bonds : angle 6.59303 ( 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: 51 poor density : 211 time to evaluate : 0.669 Fit side-chains REVERT: A 579 GLN cc_start: 0.7734 (mt0) cc_final: 0.7255 (mt0) REVERT: B 485 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7895 (ttt180) REVERT: B 514 ARG cc_start: 0.7608 (mtm180) cc_final: 0.5923 (mtp85) REVERT: C 254 ASN cc_start: 0.8243 (m-40) cc_final: 0.7812 (t0) REVERT: C 406 ARG cc_start: 0.7935 (mtt180) cc_final: 0.6574 (mtm110) REVERT: C 418 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7352 (tp30) REVERT: C 641 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8412 (mttt) REVERT: D 316 LYS cc_start: 0.8293 (mtpp) cc_final: 0.7564 (mtmt) REVERT: D 349 ASP cc_start: 0.8334 (m-30) cc_final: 0.7992 (m-30) REVERT: D 419 ASN cc_start: 0.7931 (t0) cc_final: 0.7702 (t0) REVERT: D 682 GLU cc_start: 0.7997 (tt0) cc_final: 0.7386 (tm-30) REVERT: E 485 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7611 (ttm170) REVERT: F 324 GLU cc_start: 0.7328 (pp20) cc_final: 0.7086 (pp20) REVERT: F 334 ILE cc_start: 0.8888 (mt) cc_final: 0.8658 (mp) REVERT: F 387 GLN cc_start: 0.8289 (mt0) cc_final: 0.7170 (mm-40) REVERT: F 406 ARG cc_start: 0.8054 (mtt180) cc_final: 0.6228 (mtm-85) REVERT: F 412 GLN cc_start: 0.8209 (pt0) cc_final: 0.7657 (pt0) REVERT: F 579 GLN cc_start: 0.8008 (mt0) cc_final: 0.7774 (mt0) REVERT: H 38 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8373 (ttt180) REVERT: H 140 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7772 (pp30) outliers start: 51 outliers final: 20 residues processed: 246 average time/residue: 0.6949 time to fit residues: 189.1574 Evaluate side-chains 215 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 485 ARG 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 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: 3.9990 chunk 9 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 chunk 212 optimal weight: 30.0000 chunk 166 optimal weight: 7.9990 chunk 221 optimal weight: 0.9990 chunk 210 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 165 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3086 r_free = 0.3086 target = 0.095919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.082152 restraints weight = 30590.983| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.51 r_work: 0.2791 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19282 Z= 0.108 Angle : 0.507 7.564 26257 Z= 0.263 Chirality : 0.042 0.139 2714 Planarity : 0.004 0.040 3493 Dihedral : 5.177 57.138 2584 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.71 % Allowed : 9.47 % Favored : 88.82 % 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 aren not related in a simple way. whole: -0.14 (0.16), residues: 2341 helix: -3.30 (0.46), residues: 88 sheet: 0.36 (0.20), residues: 573 loop : -0.02 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 533 TYR 0.012 0.001 TYR H 69 PHE 0.010 0.001 PHE F 535 TRP 0.013 0.001 TRP E 509 HIS 0.004 0.001 HIS D 255 Details of bonding type rmsd covalent geometry : bond 0.00243 (19280) covalent geometry : angle 0.50718 (26253) SS BOND : bond 0.00492 ( 2) SS BOND : angle 0.87434 ( 4) hydrogen bonds : bond 0.02670 ( 240) hydrogen bonds : angle 5.86587 ( 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 251 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 0.785 Fit side-chains REVERT: A 485 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.6950 (ttt90) REVERT: A 579 GLN cc_start: 0.7722 (mt0) cc_final: 0.7216 (mt0) REVERT: B 485 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7886 (ttt180) REVERT: B 514 ARG cc_start: 0.7583 (mtm180) cc_final: 0.5905 (mtp85) REVERT: C 254 ASN cc_start: 0.8249 (m-40) cc_final: 0.7734 (t0) REVERT: C 406 ARG cc_start: 0.7904 (mtt180) cc_final: 0.6524 (mtm110) REVERT: C 524 MET cc_start: 0.8966 (mtm) cc_final: 0.8739 (mtp) REVERT: C 641 LYS cc_start: 0.8677 (mtpm) cc_final: 0.8428 (mttt) REVERT: D 316 LYS cc_start: 0.8330 (mtpp) cc_final: 0.7460 (mppt) REVERT: D 349 ASP cc_start: 0.8335 (m-30) cc_final: 0.7950 (m-30) REVERT: D 419 ASN cc_start: 0.7981 (t0) cc_final: 0.7776 (t0) REVERT: D 682 GLU cc_start: 0.7953 (tt0) cc_final: 0.7368 (tm-30) REVERT: F 324 GLU cc_start: 0.7366 (pp20) cc_final: 0.7101 (pp20) REVERT: F 334 ILE cc_start: 0.8829 (mt) cc_final: 0.8618 (mp) REVERT: F 387 GLN cc_start: 0.8394 (mt0) cc_final: 0.7255 (mm-40) REVERT: F 406 ARG cc_start: 0.8054 (mtt180) cc_final: 0.6393 (mtm110) REVERT: F 412 GLN cc_start: 0.8158 (pt0) cc_final: 0.7598 (pt0) REVERT: F 579 GLN cc_start: 0.7953 (mt0) cc_final: 0.7741 (mt0) REVERT: H 38 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8287 (ttt180) outliers start: 35 outliers final: 16 residues processed: 243 average time/residue: 0.7678 time to fit residues: 206.5480 Evaluate side-chains 212 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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: 9.9990 chunk 3 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 225 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 chunk 33 optimal weight: 20.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN A 588 GLN D 624 HIS 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 = 0.3025 r_free = 0.3025 target = 0.092070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.078099 restraints weight = 30660.791| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 1.54 r_work: 0.2714 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 19282 Z= 0.240 Angle : 0.596 7.588 26257 Z= 0.315 Chirality : 0.045 0.140 2714 Planarity : 0.005 0.046 3493 Dihedral : 5.682 49.461 2578 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.64 % Allowed : 9.62 % Favored : 87.74 % 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 aren not related in a simple way. whole: -0.32 (0.16), residues: 2341 helix: -3.66 (0.42), residues: 86 sheet: 0.27 (0.21), residues: 534 loop : -0.14 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 550 TYR 0.018 0.002 TYR F 701 PHE 0.013 0.002 PHE B 422 TRP 0.019 0.002 TRP E 509 HIS 0.005 0.002 HIS D 255 Details of bonding type rmsd covalent geometry : bond 0.00562 (19280) covalent geometry : angle 0.59630 (26253) SS BOND : bond 0.00645 ( 2) SS BOND : angle 1.02309 ( 4) hydrogen bonds : bond 0.03304 ( 240) hydrogen bonds : angle 6.36041 ( 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 251 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 197 time to evaluate : 0.910 Fit side-chains REVERT: A 485 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7348 (ttt90) REVERT: A 579 GLN cc_start: 0.7742 (mt0) cc_final: 0.7278 (mt0) REVERT: B 485 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7940 (ttt180) REVERT: B 514 ARG cc_start: 0.7540 (mtm180) cc_final: 0.5815 (mtp85) REVERT: C 254 ASN cc_start: 0.8284 (m-40) cc_final: 0.7740 (t0) REVERT: C 406 ARG cc_start: 0.7927 (mtt180) cc_final: 0.6499 (mtm110) REVERT: C 418 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7377 (tp30) REVERT: C 641 LYS cc_start: 0.8709 (mtpm) cc_final: 0.8425 (mttt) REVERT: D 316 LYS cc_start: 0.8324 (mtpp) cc_final: 0.7497 (mppt) REVERT: D 349 ASP cc_start: 0.8449 (m-30) cc_final: 0.8089 (m-30) REVERT: D 682 GLU cc_start: 0.8005 (tt0) cc_final: 0.7545 (tm-30) REVERT: E 436 MET cc_start: 0.8903 (pmm) cc_final: 0.8608 (ptp) REVERT: E 485 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7822 (ttm170) REVERT: F 324 GLU cc_start: 0.7421 (pp20) cc_final: 0.7152 (pp20) REVERT: F 334 ILE cc_start: 0.8873 (mt) cc_final: 0.8649 (mp) REVERT: F 387 GLN cc_start: 0.8303 (mt0) cc_final: 0.7101 (mm-40) REVERT: F 406 ARG cc_start: 0.8107 (mtt180) cc_final: 0.6243 (mtm110) REVERT: F 412 GLN cc_start: 0.8216 (pt0) cc_final: 0.7619 (pt0) REVERT: H 38 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8414 (ttt180) REVERT: H 140 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7705 (pp30) outliers start: 54 outliers final: 32 residues processed: 241 average time/residue: 0.7095 time to fit residues: 189.0478 Evaluate side-chains 226 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 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 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: 8.9990 chunk 3 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 162 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 585 GLN D 428 HIS D 608 GLN F 304 ASN F 588 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.091833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.077849 restraints weight = 30471.976| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 1.53 r_work: 0.2713 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 19282 Z= 0.224 Angle : 0.576 8.261 26257 Z= 0.304 Chirality : 0.045 0.137 2714 Planarity : 0.005 0.047 3493 Dihedral : 5.620 49.431 2578 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.49 % Allowed : 9.86 % Favored : 87.65 % 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 aren not related in a simple way. whole: -0.42 (0.16), residues: 2341 helix: -3.84 (0.40), residues: 88 sheet: 0.22 (0.21), residues: 534 loop : -0.21 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 101 TYR 0.017 0.002 TYR C 701 PHE 0.013 0.002 PHE B 422 TRP 0.019 0.002 TRP E 509 HIS 0.005 0.001 HIS D 624 Details of bonding type rmsd covalent geometry : bond 0.00524 (19280) covalent geometry : angle 0.57639 (26253) SS BOND : bond 0.00622 ( 2) SS BOND : angle 1.04275 ( 4) hydrogen bonds : bond 0.03165 ( 240) hydrogen bonds : angle 6.30707 ( 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 241 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 190 time to evaluate : 0.761 Fit side-chains REVERT: A 485 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7424 (ttt90) REVERT: A 579 GLN cc_start: 0.7739 (mt0) cc_final: 0.7262 (mt0) REVERT: B 485 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7924 (ttt180) REVERT: B 514 ARG cc_start: 0.7400 (mtm180) cc_final: 0.5733 (mtp85) REVERT: C 254 ASN cc_start: 0.8298 (m-40) cc_final: 0.7805 (t0) REVERT: C 324 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6669 (mm-30) REVERT: C 406 ARG cc_start: 0.7939 (mtt180) cc_final: 0.6502 (mtm110) REVERT: C 418 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7381 (tp30) REVERT: C 641 LYS cc_start: 0.8700 (mtpm) cc_final: 0.8422 (mttt) REVERT: D 349 ASP cc_start: 0.8449 (m-30) cc_final: 0.8093 (m-30) REVERT: E 485 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7799 (ttm170) REVERT: F 334 ILE cc_start: 0.8868 (mt) cc_final: 0.8654 (mp) REVERT: F 387 GLN cc_start: 0.8296 (mt0) cc_final: 0.7068 (mm-40) REVERT: F 406 ARG cc_start: 0.8101 (mtt180) cc_final: 0.6252 (mtm110) REVERT: F 412 GLN cc_start: 0.8206 (pt0) cc_final: 0.7615 (pt0) REVERT: H 38 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8454 (ttt180) REVERT: H 140 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7621 (pp30) REVERT: L 103 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7607 (pm20) outliers start: 51 outliers final: 33 residues processed: 232 average time/residue: 0.6621 time to fit residues: 170.1839 Evaluate side-chains 221 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 180 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 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 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 78 SER 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: 9.9990 chunk 216 optimal weight: 6.9990 chunk 208 optimal weight: 0.9990 chunk 182 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 210 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3028 r_free = 0.3028 target = 0.092301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.078320 restraints weight = 30233.259| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 1.53 r_work: 0.2722 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2312 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= 0.175 Angle : 0.541 8.332 26257 Z= 0.284 Chirality : 0.043 0.134 2714 Planarity : 0.004 0.044 3493 Dihedral : 5.424 57.251 2578 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.44 % Allowed : 10.25 % Favored : 87.30 % 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 aren not related in a simple way. whole: -0.37 (0.16), residues: 2341 helix: -3.82 (0.41), residues: 88 sheet: 0.25 (0.21), residues: 534 loop : -0.17 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 312 TYR 0.015 0.002 TYR C 701 PHE 0.012 0.001 PHE B 422 TRP 0.017 0.002 TRP E 509 HIS 0.005 0.001 HIS D 255 Details of bonding type rmsd covalent geometry : bond 0.00406 (19280) covalent geometry : angle 0.54051 (26253) SS BOND : bond 0.00557 ( 2) SS BOND : angle 0.96259 ( 4) hydrogen bonds : bond 0.02901 ( 240) hydrogen bonds : angle 6.11933 ( 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 241 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 191 time to evaluate : 0.781 Fit side-chains REVERT: A 485 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7389 (ttt90) REVERT: A 579 GLN cc_start: 0.7753 (mt0) cc_final: 0.7270 (mt0) REVERT: B 485 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7939 (ttt180) REVERT: B 514 ARG cc_start: 0.7391 (mtm180) cc_final: 0.5717 (mtp85) REVERT: C 254 ASN cc_start: 0.8319 (m-40) cc_final: 0.7752 (t0) REVERT: C 406 ARG cc_start: 0.7901 (mtt180) cc_final: 0.6444 (mtm110) REVERT: C 418 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7338 (tp30) REVERT: C 641 LYS cc_start: 0.8673 (mtpm) cc_final: 0.8394 (mttt) REVERT: D 349 ASP cc_start: 0.8422 (m-30) cc_final: 0.8099 (m-30) REVERT: E 485 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7730 (ttm170) REVERT: F 334 ILE cc_start: 0.8872 (mt) cc_final: 0.8671 (mp) REVERT: F 387 GLN cc_start: 0.8406 (mt0) cc_final: 0.7084 (mm-40) REVERT: F 406 ARG cc_start: 0.8098 (mtt180) cc_final: 0.5596 (mtm110) REVERT: F 412 GLN cc_start: 0.8238 (pt0) cc_final: 0.7538 (pp30) REVERT: H 38 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8447 (ttt180) REVERT: H 140 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7709 (pp30) outliers start: 50 outliers final: 33 residues processed: 232 average time/residue: 0.6933 time to fit residues: 178.0858 Evaluate side-chains 219 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 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 22 GLN 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 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: 9.9990 chunk 148 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 220 optimal weight: 8.9990 chunk 166 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 231 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3039 r_free = 0.3039 target = 0.093007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.079022 restraints weight = 30367.336| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 1.53 r_work: 0.2738 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2376 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= 0.149 Angle : 0.522 8.495 26257 Z= 0.272 Chirality : 0.042 0.134 2714 Planarity : 0.004 0.043 3493 Dihedral : 5.215 52.905 2578 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.25 % Allowed : 10.60 % 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 aren not related in a simple way. whole: -0.19 (0.16), residues: 2341 helix: -3.43 (0.49), residues: 74 sheet: 0.32 (0.21), residues: 512 loop : -0.06 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 550 TYR 0.014 0.001 TYR C 701 PHE 0.011 0.001 PHE B 422 TRP 0.015 0.001 TRP E 509 HIS 0.005 0.001 HIS D 255 Details of bonding type rmsd covalent geometry : bond 0.00345 (19280) covalent geometry : angle 0.52153 (26253) SS BOND : bond 0.00501 ( 2) SS BOND : angle 0.91066 ( 4) hydrogen bonds : bond 0.02757 ( 240) hydrogen bonds : angle 5.94229 ( 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 239 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 0.780 Fit side-chains REVERT: A 485 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7459 (ttt90) REVERT: A 579 GLN cc_start: 0.7717 (mt0) cc_final: 0.7208 (mt0) REVERT: B 485 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7965 (ttt180) REVERT: B 514 ARG cc_start: 0.7361 (mtm180) cc_final: 0.5774 (mtp85) REVERT: C 254 ASN cc_start: 0.8335 (m-40) cc_final: 0.7742 (t0) REVERT: C 312 ARG cc_start: 0.8109 (mtt180) cc_final: 0.7822 (ttm170) REVERT: C 406 ARG cc_start: 0.7877 (mtt180) cc_final: 0.6512 (mtm110) REVERT: C 418 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7286 (tp30) REVERT: C 419 ASN cc_start: 0.8537 (t0) cc_final: 0.8213 (t0) REVERT: C 641 LYS cc_start: 0.8675 (mtpm) cc_final: 0.8407 (mttt) REVERT: D 349 ASP cc_start: 0.8400 (m-30) cc_final: 0.8103 (m-30) REVERT: E 485 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7637 (ttm170) REVERT: F 333 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7676 (t) REVERT: F 334 ILE cc_start: 0.8875 (mt) cc_final: 0.8670 (mp) REVERT: F 387 GLN cc_start: 0.8414 (mt0) cc_final: 0.7140 (mm-40) REVERT: F 406 ARG cc_start: 0.8068 (mtt180) cc_final: 0.5579 (mtm110) REVERT: F 412 GLN cc_start: 0.8247 (pt0) cc_final: 0.7534 (pp30) outliers start: 46 outliers final: 32 residues processed: 230 average time/residue: 0.7321 time to fit residues: 186.1619 Evaluate side-chains 223 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 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 22 GLN 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 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: 10.0000 chunk 131 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 229 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN F 304 ASN F 588 GLN F 700 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.091471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.077520 restraints weight = 30327.921| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 1.52 r_work: 0.2708 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2400 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= 0.238 Angle : 0.588 9.011 26257 Z= 0.310 Chirality : 0.045 0.136 2714 Planarity : 0.005 0.051 3493 Dihedral : 5.571 48.317 2578 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.44 % Allowed : 10.79 % 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 aren not related in a simple way. whole: -0.46 (0.16), residues: 2341 helix: -3.78 (0.37), residues: 100 sheet: 0.20 (0.21), residues: 534 loop : -0.22 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 101 TYR 0.018 0.002 TYR C 701 PHE 0.015 0.002 PHE B 422 TRP 0.018 0.002 TRP E 509 HIS 0.006 0.001 HIS D 255 Details of bonding type rmsd covalent geometry : bond 0.00557 (19280) covalent geometry : angle 0.58806 (26253) SS BOND : bond 0.00623 ( 2) SS BOND : angle 1.05924 ( 4) hydrogen bonds : bond 0.03220 ( 240) hydrogen bonds : angle 6.28606 ( 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 240 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 190 time to evaluate : 0.675 Fit side-chains REVERT: A 485 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.7519 (ttt90) REVERT: A 579 GLN cc_start: 0.7765 (mt0) cc_final: 0.7211 (mt0) REVERT: B 485 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7616 (ttp-170) REVERT: B 514 ARG cc_start: 0.7367 (mtm180) cc_final: 0.5773 (mtp85) REVERT: C 254 ASN cc_start: 0.8299 (m-40) cc_final: 0.7789 (t0) REVERT: C 312 ARG cc_start: 0.8126 (mtt180) cc_final: 0.7833 (ttm170) REVERT: C 406 ARG cc_start: 0.7911 (mtt180) cc_final: 0.6451 (mtm110) REVERT: C 418 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7364 (tp30) REVERT: C 641 LYS cc_start: 0.8689 (mtpm) cc_final: 0.8411 (mttt) REVERT: D 349 ASP cc_start: 0.8440 (m-30) cc_final: 0.8125 (m-30) REVERT: D 556 ASP cc_start: 0.8158 (p0) cc_final: 0.7903 (p0) REVERT: D 682 GLU cc_start: 0.8024 (tt0) cc_final: 0.7520 (tm-30) REVERT: E 485 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7806 (ttm170) REVERT: F 235 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8255 (mt) REVERT: F 333 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7643 (t) REVERT: F 334 ILE cc_start: 0.8883 (mt) cc_final: 0.8676 (mp) REVERT: F 387 GLN cc_start: 0.8448 (mt0) cc_final: 0.7091 (mm-40) REVERT: F 406 ARG cc_start: 0.8050 (mtt180) cc_final: 0.5527 (mtm110) REVERT: F 412 GLN cc_start: 0.8261 (pt0) cc_final: 0.7562 (pp30) REVERT: F 707 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8635 (ptmm) REVERT: L 103 GLU cc_start: 0.8184 (pm20) cc_final: 0.7895 (pm20) outliers start: 50 outliers final: 37 residues processed: 232 average time/residue: 0.6855 time to fit residues: 176.8447 Evaluate side-chains 228 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 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 561 THR 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 F residue 707 LYS Chi-restraints excluded: chain H residue 22 GLN 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: 8.9990 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3033 r_free = 0.3033 target = 0.092625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.078727 restraints weight = 30361.792| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 1.53 r_work: 0.2733 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 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 : 0.004 0.043 19282 Z= 0.157 Angle : 0.533 9.205 26257 Z= 0.279 Chirality : 0.042 0.133 2714 Planarity : 0.004 0.044 3493 Dihedral : 5.219 47.639 2578 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.10 % Allowed : 10.99 % 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 aren not related in a simple way. whole: -0.27 (0.16), residues: 2341 helix: -3.36 (0.45), residues: 86 sheet: 0.37 (0.22), residues: 496 loop : -0.13 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 101 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 covalent geometry : bond 0.00364 (19280) covalent geometry : angle 0.53297 (26253) SS BOND : bond 0.00545 ( 2) SS BOND : angle 0.86806 ( 4) hydrogen bonds : bond 0.02844 ( 240) hydrogen bonds : angle 5.98345 ( 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 229 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 186 time to evaluate : 0.658 Fit side-chains REVERT: A 485 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7449 (ttt90) REVERT: A 579 GLN cc_start: 0.7733 (mt0) cc_final: 0.7203 (mt0) REVERT: B 485 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.8000 (ttt180) REVERT: B 514 ARG cc_start: 0.7345 (mtm180) cc_final: 0.5783 (mtp85) REVERT: C 254 ASN cc_start: 0.8323 (m-40) cc_final: 0.7742 (t0) REVERT: C 312 ARG cc_start: 0.8114 (mtt180) cc_final: 0.7831 (ttm170) REVERT: C 406 ARG cc_start: 0.7870 (mtt180) cc_final: 0.6455 (mtm110) REVERT: C 418 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7290 (tp30) REVERT: C 419 ASN cc_start: 0.8536 (t0) cc_final: 0.8223 (t0) REVERT: C 641 LYS cc_start: 0.8666 (mtpm) cc_final: 0.8409 (mttt) REVERT: D 349 ASP cc_start: 0.8408 (m-30) cc_final: 0.8105 (m-30) REVERT: D 556 ASP cc_start: 0.8158 (p0) cc_final: 0.7895 (p0) REVERT: D 682 GLU cc_start: 0.8051 (tt0) cc_final: 0.7534 (tm-30) REVERT: E 485 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7644 (ttm170) REVERT: F 235 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8381 (mt) REVERT: F 333 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7623 (t) REVERT: F 334 ILE cc_start: 0.8850 (mt) cc_final: 0.8650 (mp) REVERT: F 387 GLN cc_start: 0.8419 (mt0) cc_final: 0.7082 (mm-40) REVERT: F 406 ARG cc_start: 0.8025 (mtt180) cc_final: 0.5519 (mtm110) REVERT: F 412 GLN cc_start: 0.8238 (pt0) cc_final: 0.7511 (pp30) REVERT: F 707 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8608 (ptmm) REVERT: H 25 GLU cc_start: 0.8753 (mp0) cc_final: 0.8037 (mp0) REVERT: H 140 GLN cc_start: 0.8282 (pp30) cc_final: 0.7735 (pm20) REVERT: L 103 GLU cc_start: 0.8158 (pm20) cc_final: 0.7896 (pm20) outliers start: 43 outliers final: 33 residues processed: 221 average time/residue: 0.7053 time to fit residues: 172.2675 Evaluate side-chains 221 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 485 ARG 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 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 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 F residue 707 LYS Chi-restraints excluded: chain H residue 22 GLN 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 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: 6.9990 chunk 207 optimal weight: 0.0570 chunk 114 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 212 optimal weight: 20.0000 chunk 229 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 222 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 overall best weight: 4.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN E 470 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 = 0.3030 r_free = 0.3030 target = 0.092445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.078591 restraints weight = 30153.524| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 1.52 r_work: 0.2719 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19282 Z= 0.183 Angle : 0.552 9.236 26257 Z= 0.289 Chirality : 0.043 0.134 2714 Planarity : 0.004 0.045 3493 Dihedral : 5.287 47.813 2577 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.20 % Allowed : 10.99 % 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 aren not related in a simple way. whole: -0.32 (0.16), residues: 2341 helix: -3.43 (0.43), residues: 86 sheet: 0.32 (0.21), residues: 518 loop : -0.17 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 312 TYR 0.016 0.002 TYR C 701 PHE 0.013 0.002 PHE B 422 TRP 0.016 0.002 TRP E 509 HIS 0.005 0.001 HIS D 255 Details of bonding type rmsd covalent geometry : bond 0.00425 (19280) covalent geometry : angle 0.55182 (26253) SS BOND : bond 0.00556 ( 2) SS BOND : angle 0.93969 ( 4) hydrogen bonds : bond 0.02978 ( 240) hydrogen bonds : angle 6.07009 ( 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 229 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 0.646 Fit side-chains REVERT: A 485 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7455 (ttt90) REVERT: A 579 GLN cc_start: 0.7741 (mt0) cc_final: 0.7269 (mt0) REVERT: B 485 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7980 (ttt180) REVERT: B 514 ARG cc_start: 0.7356 (mtm180) cc_final: 0.5785 (mtp85) REVERT: C 254 ASN cc_start: 0.8292 (m-40) cc_final: 0.7769 (t0) REVERT: C 312 ARG cc_start: 0.8119 (mtt180) cc_final: 0.7840 (ttm170) REVERT: C 406 ARG cc_start: 0.7882 (mtt180) cc_final: 0.6461 (mtm110) REVERT: C 418 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7302 (tp30) REVERT: C 641 LYS cc_start: 0.8670 (mtpm) cc_final: 0.8399 (mttt) REVERT: D 349 ASP cc_start: 0.8421 (m-30) cc_final: 0.8122 (m-30) REVERT: D 556 ASP cc_start: 0.8143 (p0) cc_final: 0.7886 (p0) REVERT: D 682 GLU cc_start: 0.8021 (tt0) cc_final: 0.7505 (tm-30) REVERT: E 485 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7749 (ttm170) REVERT: F 235 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8385 (mt) REVERT: F 333 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7668 (t) REVERT: F 334 ILE cc_start: 0.8885 (mt) cc_final: 0.8677 (mp) REVERT: F 387 GLN cc_start: 0.8428 (mt0) cc_final: 0.7053 (mm-40) REVERT: F 406 ARG cc_start: 0.8030 (mtt180) cc_final: 0.5522 (mtm110) REVERT: F 412 GLN cc_start: 0.8228 (pt0) cc_final: 0.7527 (pp30) REVERT: F 707 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8595 (ptmm) REVERT: L 103 GLU cc_start: 0.8102 (pm20) cc_final: 0.7840 (pm20) outliers start: 45 outliers final: 32 residues processed: 221 average time/residue: 0.7070 time to fit residues: 172.9642 Evaluate side-chains 222 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 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 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 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 F residue 707 LYS Chi-restraints excluded: chain H residue 22 GLN 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 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: 9.9990 chunk 226 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 163 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 206 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 96 optimal weight: 0.0970 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.092965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.078978 restraints weight = 30405.492| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 1.54 r_work: 0.2734 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19282 Z= 0.151 Angle : 0.530 9.278 26257 Z= 0.277 Chirality : 0.042 0.133 2714 Planarity : 0.004 0.044 3493 Dihedral : 5.111 47.636 2577 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.95 % Allowed : 11.08 % Favored : 86.96 % 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 aren not related in a simple way. whole: -0.25 (0.16), residues: 2341 helix: -3.37 (0.44), residues: 86 sheet: 0.36 (0.22), residues: 496 loop : -0.11 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 312 TYR 0.017 0.002 TYR C 399 PHE 0.012 0.001 PHE B 422 TRP 0.015 0.001 TRP D 509 HIS 0.005 0.001 HIS D 255 Details of bonding type rmsd covalent geometry : bond 0.00351 (19280) covalent geometry : angle 0.52966 (26253) SS BOND : bond 0.00514 ( 2) SS BOND : angle 0.85711 ( 4) hydrogen bonds : bond 0.02817 ( 240) hydrogen bonds : angle 5.91964 ( 495) =============================================================================== Job complete usr+sys time: 5630.42 seconds wall clock time: 97 minutes 7.00 seconds (5827.00 seconds total)