Starting phenix.real_space_refine on Mon May 19 07:43:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7m_44316/05_2025/9b7m_44316.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7m_44316/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b7m_44316/05_2025/9b7m_44316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7m_44316/05_2025/9b7m_44316.map" model { file = "/net/cci-nas-00/data/ceres_data/9b7m_44316/05_2025/9b7m_44316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7m_44316/05_2025/9b7m_44316.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.06, per 1000 atoms: 0.54 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: 4.04 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.98 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: 5.14 Time building geometry restraints manager: 4.81 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 37.980 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:10.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.430 ------------------------------------------------------------------------------- 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 : 12.34 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (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 TRP 0.023 0.002 TRP F 281 HIS 0.011 0.002 HIS C 527 PHE 0.018 0.002 PHE A 286 TYR 0.022 0.002 TYR C 701 ARG 0.022 0.001 ARG C 730 Details of bonding type rmsd hydrogen bonds : bond 0.22903 ( 240) hydrogen bonds : angle 8.45917 ( 495) SS BOND : bond 0.00586 ( 2) SS BOND : angle 0.99926 ( 4) covalent geometry : bond 0.00529 (19280) covalent geometry : angle 0.94237 (26253) *********************** 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 : 2.190 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: 1.4305 time to fit residues: 546.0506 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 : 2.076 ------------------------------------------------------------------------------- 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 195 optimal weight: 20.0000 chunk 175 optimal weight: 0.0970 chunk 97 optimal weight: 0.2980 chunk 60 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 181 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 210 optimal weight: 5.9990 overall best weight: 2.0782 ------------------------------------------------------------------------------- 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 624 HIS A 646 GLN A 651 ASN A 673 GLN ** 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 430 GLN C 497 ASN C 552 ASN C 646 GLN C 651 ASN 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 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 = 0.3110 r_free = 0.3110 target = 0.097530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.083765 restraints weight = 30371.611| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.54 r_work: 0.2821 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19282 Z= 0.115 Angle : 0.546 8.062 26257 Z= 0.284 Chirality : 0.043 0.151 2714 Planarity : 0.004 0.044 3493 Dihedral : 5.571 58.743 2591 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.81 % Allowed : 8.50 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 2341 helix: -2.89 (0.50), residues: 86 sheet: 0.37 (0.20), residues: 595 loop : -0.07 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 281 HIS 0.005 0.001 HIS E 584 PHE 0.012 0.001 PHE F 535 TYR 0.015 0.002 TYR B 484 ARG 0.007 0.001 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.03028 ( 240) hydrogen bonds : angle 6.20414 ( 495) SS BOND : bond 0.00494 ( 2) SS BOND : angle 1.10572 ( 4) covalent geometry : bond 0.00258 (19280) covalent geometry : angle 0.54590 (26253) *********************** 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 269 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 232 time to evaluate : 1.981 Fit side-chains REVERT: A 579 GLN cc_start: 0.7661 (mt0) cc_final: 0.7157 (mt0) REVERT: B 514 ARG cc_start: 0.7657 (mtm180) cc_final: 0.6007 (mtp85) REVERT: B 575 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8367 (mm-30) REVERT: C 254 ASN cc_start: 0.8198 (m-40) cc_final: 0.7718 (t0) REVERT: C 406 ARG cc_start: 0.7759 (mtt180) cc_final: 0.6575 (mtm110) REVERT: C 418 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7826 (pt0) REVERT: C 641 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8400 (mttt) REVERT: D 316 LYS cc_start: 0.8309 (mtpp) cc_final: 0.7567 (mtmt) REVERT: D 349 ASP cc_start: 0.8297 (m-30) cc_final: 0.7946 (m-30) REVERT: D 419 ASN cc_start: 0.7955 (t0) cc_final: 0.7722 (t0) REVERT: D 579 GLN cc_start: 0.8322 (mt0) cc_final: 0.8099 (mt0) REVERT: D 682 GLU cc_start: 0.7918 (tt0) cc_final: 0.7315 (tm-30) REVERT: E 515 ASN cc_start: 0.8033 (m-40) cc_final: 0.7610 (t0) REVERT: F 259 GLN cc_start: 0.8010 (tt0) cc_final: 0.6229 (pm20) REVERT: F 324 GLU cc_start: 0.7251 (pp20) cc_final: 0.7024 (pp20) REVERT: F 334 ILE cc_start: 0.8823 (mt) cc_final: 0.8575 (mp) REVERT: F 387 GLN cc_start: 0.8371 (mt0) cc_final: 0.7272 (mm-40) REVERT: F 406 ARG cc_start: 0.7935 (mtt180) cc_final: 0.6339 (mtm-85) REVERT: F 412 GLN cc_start: 0.8087 (pt0) cc_final: 0.7574 (pt0) REVERT: H 38 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8244 (ttt180) REVERT: L 41 VAL cc_start: 0.9127 (t) cc_final: 0.8850 (m) outliers start: 37 outliers final: 12 residues processed: 259 average time/residue: 1.4142 time to fit residues: 407.5466 Evaluate side-chains 219 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 204 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 660 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain 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 143 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 133 optimal weight: 30.0000 chunk 103 optimal weight: 0.0770 chunk 186 optimal weight: 10.0000 chunk 229 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 211 optimal weight: 0.0050 chunk 130 optimal weight: 10.0000 overall best weight: 3.0158 ------------------------------------------------------------------------------- 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 292 HIS C 709 ASN D 262 ASN D 292 HIS E 570 ASN F 304 ASN F 336 ASN F 588 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.095306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.081431 restraints weight = 30411.735| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 1.54 r_work: 0.2778 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1874 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= 0.134 Angle : 0.527 7.025 26257 Z= 0.274 Chirality : 0.042 0.136 2714 Planarity : 0.004 0.042 3493 Dihedral : 5.151 44.212 2579 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.20 % Allowed : 9.28 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.16), residues: 2341 helix: -3.17 (0.47), residues: 88 sheet: 0.49 (0.20), residues: 571 loop : 0.02 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 509 HIS 0.005 0.001 HIS D 255 PHE 0.011 0.001 PHE A 286 TYR 0.013 0.002 TYR H 69 ARG 0.007 0.001 ARG F 312 Details of bonding type rmsd hydrogen bonds : bond 0.02892 ( 240) hydrogen bonds : angle 5.98192 ( 495) SS BOND : bond 0.00603 ( 2) SS BOND : angle 0.97468 ( 4) covalent geometry : bond 0.00309 (19280) covalent geometry : angle 0.52647 (26253) *********************** 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 255 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 210 time to evaluate : 2.245 Fit side-chains REVERT: A 485 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.6300 (ttp-170) REVERT: A 579 GLN cc_start: 0.7723 (mt0) cc_final: 0.7221 (mt0) REVERT: B 514 ARG cc_start: 0.7574 (mtm180) cc_final: 0.5916 (mtp85) REVERT: C 254 ASN cc_start: 0.8230 (m-40) cc_final: 0.7714 (t0) REVERT: C 406 ARG cc_start: 0.7803 (mtt180) cc_final: 0.6537 (mtm110) REVERT: C 418 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7872 (pt0) REVERT: C 524 MET cc_start: 0.8991 (mtm) cc_final: 0.8765 (mtp) REVERT: C 641 LYS cc_start: 0.8703 (mtpm) cc_final: 0.8415 (mttt) REVERT: D 316 LYS cc_start: 0.8317 (mtpp) cc_final: 0.7601 (mtmt) REVERT: D 349 ASP cc_start: 0.8300 (m-30) cc_final: 0.7923 (m-30) REVERT: D 419 ASN cc_start: 0.7933 (t0) cc_final: 0.7693 (t0) REVERT: D 682 GLU cc_start: 0.7957 (tt0) cc_final: 0.7387 (tm-30) REVERT: E 485 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7718 (ttm170) REVERT: E 515 ASN cc_start: 0.8024 (m-40) cc_final: 0.7589 (t0) REVERT: F 324 GLU cc_start: 0.7311 (pp20) cc_final: 0.7053 (pp20) REVERT: F 334 ILE cc_start: 0.8854 (mt) cc_final: 0.8639 (mp) REVERT: F 387 GLN cc_start: 0.8306 (mt0) cc_final: 0.7164 (mm-40) REVERT: F 406 ARG cc_start: 0.8009 (mtt180) cc_final: 0.6392 (mtm110) REVERT: F 412 GLN cc_start: 0.8155 (pt0) cc_final: 0.7608 (pt0) REVERT: H 38 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8297 (ttt180) REVERT: L 41 VAL cc_start: 0.9137 (t) cc_final: 0.8865 (m) outliers start: 45 outliers final: 23 residues processed: 242 average time/residue: 1.4079 time to fit residues: 380.1095 Evaluate side-chains 226 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 711 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain E residue 531 GLU 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 532 ASP 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 121 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 45 CYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 103 optimal weight: 0.6980 chunk 186 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 227 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 156 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 221 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN A 608 GLN D 262 ASN F 304 ASN F 336 ASN F 343 GLN F 588 GLN F 651 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.093620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.079726 restraints weight = 30300.993| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.53 r_work: 0.2746 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19282 Z= 0.173 Angle : 0.546 7.666 26257 Z= 0.286 Chirality : 0.043 0.134 2714 Planarity : 0.004 0.042 3493 Dihedral : 5.283 46.510 2579 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.15 % Allowed : 9.77 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.16), residues: 2341 helix: -3.51 (0.43), residues: 88 sheet: 0.47 (0.21), residues: 512 loop : -0.01 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 509 HIS 0.005 0.001 HIS D 255 PHE 0.011 0.002 PHE F 535 TYR 0.015 0.002 TYR F 701 ARG 0.009 0.001 ARG F 312 Details of bonding type rmsd hydrogen bonds : bond 0.02949 ( 240) hydrogen bonds : angle 6.05750 ( 495) SS BOND : bond 0.00507 ( 2) SS BOND : angle 1.01786 ( 4) covalent geometry : bond 0.00403 (19280) covalent geometry : angle 0.54604 (26253) *********************** 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 250 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 206 time to evaluate : 1.954 Fit side-chains REVERT: A 485 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.6387 (ttp-170) REVERT: A 579 GLN cc_start: 0.7708 (mt0) cc_final: 0.7212 (mt0) REVERT: B 514 ARG cc_start: 0.7625 (mtm180) cc_final: 0.5940 (mtp85) REVERT: C 254 ASN cc_start: 0.8206 (m-40) cc_final: 0.7680 (t0) REVERT: C 406 ARG cc_start: 0.7880 (mtt180) cc_final: 0.6448 (mtm110) REVERT: C 418 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7904 (pt0) REVERT: C 641 LYS cc_start: 0.8688 (mtpm) cc_final: 0.8397 (mttt) REVERT: D 316 LYS cc_start: 0.8293 (mtpp) cc_final: 0.7462 (mppt) REVERT: D 349 ASP cc_start: 0.8403 (m-30) cc_final: 0.8024 (m-30) REVERT: D 682 GLU cc_start: 0.7978 (tt0) cc_final: 0.7390 (tm-30) REVERT: E 485 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7780 (ttm170) REVERT: F 324 GLU cc_start: 0.7370 (pp20) cc_final: 0.7124 (pp20) REVERT: F 334 ILE cc_start: 0.8861 (mt) cc_final: 0.8656 (mp) REVERT: F 387 GLN cc_start: 0.8261 (mt0) cc_final: 0.7051 (mm-40) REVERT: F 406 ARG cc_start: 0.8066 (mtt180) cc_final: 0.6276 (mtm110) REVERT: F 412 GLN cc_start: 0.8177 (pt0) cc_final: 0.7611 (pt0) REVERT: H 38 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8365 (ttt180) REVERT: H 140 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7630 (pp30) outliers start: 44 outliers final: 28 residues processed: 237 average time/residue: 1.4539 time to fit residues: 382.2182 Evaluate side-chains 226 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain E residue 531 GLU 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 532 ASP Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 38 ARG 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 45 CYS 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 218 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 chunk 134 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 206 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 167 optimal weight: 6.9990 chunk 214 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN D 262 ASN D 292 HIS E 515 ASN 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 = 0.3048 r_free = 0.3048 target = 0.093490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.079441 restraints weight = 30344.021| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.54 r_work: 0.2739 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2170 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= 0.161 Angle : 0.531 8.238 26257 Z= 0.278 Chirality : 0.043 0.135 2714 Planarity : 0.004 0.043 3493 Dihedral : 5.184 46.916 2577 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.49 % Allowed : 10.01 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.16), residues: 2341 helix: -3.55 (0.43), residues: 86 sheet: 0.43 (0.21), residues: 533 loop : -0.05 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 509 HIS 0.005 0.001 HIS D 255 PHE 0.011 0.001 PHE F 535 TYR 0.014 0.002 TYR F 701 ARG 0.008 0.001 ARG F 312 Details of bonding type rmsd hydrogen bonds : bond 0.02837 ( 240) hydrogen bonds : angle 5.96658 ( 495) SS BOND : bond 0.00459 ( 2) SS BOND : angle 1.02788 ( 4) covalent geometry : bond 0.00373 (19280) covalent geometry : angle 0.53093 (26253) *********************** 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 247 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 2.063 Fit side-chains REVERT: A 485 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.6498 (ttp-170) REVERT: A 579 GLN cc_start: 0.7695 (mt0) cc_final: 0.7182 (mt0) REVERT: B 514 ARG cc_start: 0.7544 (mtm180) cc_final: 0.5868 (mtp85) REVERT: C 254 ASN cc_start: 0.8276 (m-40) cc_final: 0.7712 (t0) REVERT: C 406 ARG cc_start: 0.7877 (mtt180) cc_final: 0.6449 (mtm110) REVERT: C 418 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7906 (pt0) REVERT: C 641 LYS cc_start: 0.8684 (mtpm) cc_final: 0.8397 (mttt) REVERT: D 316 LYS cc_start: 0.8299 (mtpp) cc_final: 0.7479 (mppt) REVERT: D 349 ASP cc_start: 0.8406 (m-30) cc_final: 0.8055 (m-30) REVERT: E 436 MET cc_start: 0.8824 (pmm) cc_final: 0.8583 (ptp) REVERT: E 485 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7703 (ttm170) REVERT: F 324 GLU cc_start: 0.7373 (pp20) cc_final: 0.7111 (pp20) REVERT: F 334 ILE cc_start: 0.8859 (mt) cc_final: 0.8654 (mp) REVERT: F 387 GLN cc_start: 0.8390 (mt0) cc_final: 0.7192 (mm-40) REVERT: F 406 ARG cc_start: 0.8106 (mtt180) cc_final: 0.6283 (mtm110) REVERT: F 412 GLN cc_start: 0.8204 (pt0) cc_final: 0.7606 (pt0) REVERT: F 449 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8204 (mtpt) REVERT: H 38 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8419 (ttt180) outliers start: 51 outliers final: 36 residues processed: 235 average time/residue: 1.4653 time to fit residues: 382.8347 Evaluate side-chains 231 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 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 485 ARG Chi-restraints excluded: chain E residue 531 GLU 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 449 LYS 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 49 SER Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 128 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 10 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 210 optimal weight: 0.6980 chunk 162 optimal weight: 9.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN D 262 ASN F 304 ASN F 588 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.092009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.078062 restraints weight = 30574.024| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 1.53 r_work: 0.2716 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 19282 Z= 0.230 Angle : 0.581 8.564 26257 Z= 0.307 Chirality : 0.045 0.137 2714 Planarity : 0.005 0.045 3493 Dihedral : 5.546 51.885 2577 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.08 % Allowed : 9.38 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.16), residues: 2341 helix: -3.75 (0.41), residues: 86 sheet: 0.30 (0.21), residues: 534 loop : -0.16 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 509 HIS 0.005 0.001 HIS D 255 PHE 0.014 0.002 PHE B 422 TYR 0.017 0.002 TYR F 701 ARG 0.007 0.001 ARG E 533 Details of bonding type rmsd hydrogen bonds : bond 0.03138 ( 240) hydrogen bonds : angle 6.23921 ( 495) SS BOND : bond 0.00610 ( 2) SS BOND : angle 1.20267 ( 4) covalent geometry : bond 0.00537 (19280) covalent geometry : angle 0.58058 (26253) *********************** 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 256 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 193 time to evaluate : 2.011 Fit side-chains REVERT: A 485 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.6571 (ttp-170) REVERT: A 579 GLN cc_start: 0.7696 (mt0) cc_final: 0.7240 (mt0) REVERT: B 514 ARG cc_start: 0.7370 (mtm180) cc_final: 0.5679 (mtp85) REVERT: C 254 ASN cc_start: 0.8282 (m-40) cc_final: 0.7778 (t0) REVERT: C 324 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6714 (mm-30) REVERT: C 406 ARG cc_start: 0.7889 (mtt180) cc_final: 0.6453 (mtm110) REVERT: C 418 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7937 (pt0) REVERT: C 485 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8658 (ttt180) REVERT: C 641 LYS cc_start: 0.8691 (mtpm) cc_final: 0.8400 (mttt) REVERT: D 349 ASP cc_start: 0.8445 (m-30) cc_final: 0.8103 (m-30) REVERT: E 485 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7877 (ttm170) REVERT: F 324 GLU cc_start: 0.7437 (pp20) cc_final: 0.7227 (pp20) REVERT: F 387 GLN cc_start: 0.8274 (mt0) cc_final: 0.7047 (mm-40) REVERT: F 406 ARG cc_start: 0.8124 (mtt180) cc_final: 0.6295 (mtm110) REVERT: F 412 GLN cc_start: 0.8209 (pt0) cc_final: 0.7612 (pt0) REVERT: F 449 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8219 (mtpt) REVERT: H 38 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8462 (ttt180) REVERT: H 140 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7596 (pp30) REVERT: L 91 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8495 (p) REVERT: L 103 GLU cc_start: 0.8010 (pm20) cc_final: 0.7752 (pm20) outliers start: 63 outliers final: 37 residues processed: 243 average time/residue: 1.4503 time to fit residues: 391.9531 Evaluate side-chains 233 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 187 time to evaluate : 2.275 ------------------------------------------------------------------------------- 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 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 485 ARG 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 531 GLU 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 449 LYS 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 90 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 140 GLN Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 128 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 100 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 153 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 190 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 129 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 = 0.3044 r_free = 0.3044 target = 0.093301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.079391 restraints weight = 30183.263| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 1.52 r_work: 0.2731 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19282 Z= 0.162 Angle : 0.531 8.490 26257 Z= 0.279 Chirality : 0.043 0.135 2714 Planarity : 0.004 0.047 3493 Dihedral : 5.323 52.167 2577 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.44 % Allowed : 10.21 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 2341 helix: -3.71 (0.43), residues: 86 sheet: 0.32 (0.21), residues: 533 loop : -0.11 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 509 HIS 0.005 0.001 HIS D 255 PHE 0.011 0.001 PHE A 629 TYR 0.014 0.002 TYR C 701 ARG 0.009 0.001 ARG F 312 Details of bonding type rmsd hydrogen bonds : bond 0.02824 ( 240) hydrogen bonds : angle 5.97403 ( 495) SS BOND : bond 0.00455 ( 2) SS BOND : angle 0.93121 ( 4) covalent geometry : bond 0.00376 (19280) covalent geometry : angle 0.53090 (26253) *********************** 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 242 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 192 time to evaluate : 1.995 Fit side-chains REVERT: A 485 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.6545 (ttp-170) REVERT: A 579 GLN cc_start: 0.7717 (mt0) cc_final: 0.7188 (mt0) REVERT: B 514 ARG cc_start: 0.7357 (mtm180) cc_final: 0.5699 (mtp85) REVERT: C 254 ASN cc_start: 0.8290 (m-40) cc_final: 0.7711 (t0) REVERT: C 324 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6708 (mm-30) REVERT: C 406 ARG cc_start: 0.7865 (mtt180) cc_final: 0.6469 (mtm110) REVERT: C 418 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7915 (pt0) REVERT: C 485 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8668 (ttt180) REVERT: C 641 LYS cc_start: 0.8681 (mtpm) cc_final: 0.8404 (mttt) REVERT: D 349 ASP cc_start: 0.8411 (m-30) cc_final: 0.8117 (m-30) REVERT: E 485 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7772 (ttm170) REVERT: F 324 GLU cc_start: 0.7381 (pp20) cc_final: 0.7122 (pp20) REVERT: F 387 GLN cc_start: 0.8406 (mt0) cc_final: 0.7119 (mm-40) REVERT: F 406 ARG cc_start: 0.8095 (mtt180) cc_final: 0.5639 (mtm110) REVERT: F 412 GLN cc_start: 0.8227 (pt0) cc_final: 0.7627 (pt0) REVERT: F 449 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8212 (mtpt) REVERT: H 38 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8455 (ttt180) REVERT: L 103 GLU cc_start: 0.7911 (pm20) cc_final: 0.7624 (pm20) outliers start: 50 outliers final: 35 residues processed: 229 average time/residue: 1.5721 time to fit residues: 398.1707 Evaluate side-chains 226 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 1.990 ------------------------------------------------------------------------------- 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 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 485 ARG 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 531 GLU 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 449 LYS 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 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 42 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 75 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 150 optimal weight: 20.0000 chunk 200 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN A 673 GLN F 304 ASN F 588 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.093488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.079563 restraints weight = 30455.052| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.53 r_work: 0.2743 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19282 Z= 0.143 Angle : 0.516 8.779 26257 Z= 0.270 Chirality : 0.042 0.135 2714 Planarity : 0.004 0.043 3493 Dihedral : 5.186 56.013 2577 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.64 % Allowed : 10.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.16), residues: 2341 helix: -3.39 (0.49), residues: 74 sheet: 0.39 (0.21), residues: 511 loop : -0.03 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 509 HIS 0.005 0.001 HIS D 255 PHE 0.011 0.001 PHE A 629 TYR 0.014 0.001 TYR C 399 ARG 0.007 0.001 ARG C 550 Details of bonding type rmsd hydrogen bonds : bond 0.02723 ( 240) hydrogen bonds : angle 5.81842 ( 495) SS BOND : bond 0.00490 ( 2) SS BOND : angle 0.87335 ( 4) covalent geometry : bond 0.00330 (19280) covalent geometry : angle 0.51580 (26253) *********************** 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 247 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 193 time to evaluate : 2.105 Fit side-chains REVERT: A 485 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.6463 (ttp-170) REVERT: A 579 GLN cc_start: 0.7738 (mt0) cc_final: 0.7221 (mt0) REVERT: B 514 ARG cc_start: 0.7351 (mtm180) cc_final: 0.5769 (mtp85) REVERT: C 254 ASN cc_start: 0.8305 (m-40) cc_final: 0.7714 (t0) REVERT: C 406 ARG cc_start: 0.7847 (mtt180) cc_final: 0.6448 (mtm110) REVERT: C 418 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7896 (pt0) REVERT: C 485 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8654 (ttt180) REVERT: C 641 LYS cc_start: 0.8686 (mtpm) cc_final: 0.8408 (mttt) REVERT: D 349 ASP cc_start: 0.8406 (m-30) cc_final: 0.8112 (m-30) REVERT: E 485 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7701 (ttm170) REVERT: F 324 GLU cc_start: 0.7382 (pp20) cc_final: 0.7178 (pp20) REVERT: F 387 GLN cc_start: 0.8418 (mt0) cc_final: 0.7139 (mm-40) REVERT: F 406 ARG cc_start: 0.8074 (mtt180) cc_final: 0.5649 (mtm110) REVERT: F 412 GLN cc_start: 0.8237 (pt0) cc_final: 0.7524 (pp30) REVERT: F 449 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8220 (mtpt) REVERT: L 103 GLU cc_start: 0.7904 (pm20) cc_final: 0.7594 (pm20) outliers start: 54 outliers final: 38 residues processed: 232 average time/residue: 1.5661 time to fit residues: 404.0181 Evaluate side-chains 230 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 2.127 ------------------------------------------------------------------------------- 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 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 485 ARG 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 531 GLU 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 449 LYS Chi-restraints excluded: chain F residue 532 ASP Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 128 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 169 optimal weight: 6.9990 chunk 91 optimal weight: 0.0470 chunk 13 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 208 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 188 optimal weight: 9.9990 overall best weight: 5.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN C 321 GLN F 304 ASN F 588 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.092283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.078365 restraints weight = 30502.119| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 1.52 r_work: 0.2716 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 19282 Z= 0.219 Angle : 0.572 8.952 26257 Z= 0.302 Chirality : 0.044 0.135 2714 Planarity : 0.004 0.047 3493 Dihedral : 5.492 49.439 2577 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.54 % Allowed : 10.45 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.16), residues: 2341 helix: -3.70 (0.38), residues: 98 sheet: 0.27 (0.21), residues: 534 loop : -0.17 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 509 HIS 0.006 0.001 HIS D 255 PHE 0.013 0.002 PHE B 422 TYR 0.018 0.002 TYR C 399 ARG 0.008 0.001 ARG H 101 Details of bonding type rmsd hydrogen bonds : bond 0.03110 ( 240) hydrogen bonds : angle 6.10487 ( 495) SS BOND : bond 0.00644 ( 2) SS BOND : angle 1.02943 ( 4) covalent geometry : bond 0.00511 (19280) covalent geometry : angle 0.57207 (26253) *********************** 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 239 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 2.087 Fit side-chains REVERT: A 485 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.6618 (ttp-170) REVERT: A 579 GLN cc_start: 0.7729 (mt0) cc_final: 0.7260 (mt0) REVERT: B 514 ARG cc_start: 0.7373 (mtm180) cc_final: 0.5709 (mtp85) REVERT: C 254 ASN cc_start: 0.8294 (m-40) cc_final: 0.7778 (t0) REVERT: C 312 ARG cc_start: 0.8136 (mtt180) cc_final: 0.7850 (ttm170) REVERT: C 321 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7822 (mt0) REVERT: C 406 ARG cc_start: 0.7878 (mtt180) cc_final: 0.6475 (mtm110) REVERT: C 418 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7936 (pt0) REVERT: C 485 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8660 (ttt180) REVERT: C 641 LYS cc_start: 0.8684 (mtpm) cc_final: 0.8399 (mttt) REVERT: D 349 ASP cc_start: 0.8426 (m-30) cc_final: 0.8130 (m-30) REVERT: E 485 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7883 (ttm170) REVERT: F 387 GLN cc_start: 0.8423 (mt0) cc_final: 0.7099 (mm-40) REVERT: F 406 ARG cc_start: 0.8092 (mtt180) cc_final: 0.5643 (mtm110) REVERT: F 412 GLN cc_start: 0.8249 (pt0) cc_final: 0.7555 (pp30) REVERT: F 449 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8267 (mtpt) REVERT: L 103 GLU cc_start: 0.7891 (pm20) cc_final: 0.7568 (pm20) outliers start: 52 outliers final: 39 residues processed: 227 average time/residue: 1.4509 time to fit residues: 366.5598 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 : 2.039 ------------------------------------------------------------------------------- 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 C residue 235 LEU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 485 ARG 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 531 GLU 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 449 LYS Chi-restraints excluded: chain F residue 532 ASP Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 128 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 197 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 170 optimal weight: 20.0000 chunk 226 optimal weight: 4.9990 chunk 217 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN C 321 GLN F 304 ASN F 588 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.091667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.077663 restraints weight = 30353.531| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 1.52 r_work: 0.2711 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 19282 Z= 0.244 Angle : 0.591 9.315 26257 Z= 0.312 Chirality : 0.045 0.137 2714 Planarity : 0.005 0.048 3493 Dihedral : 5.586 50.346 2577 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.39 % Allowed : 10.45 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.16), residues: 2341 helix: -3.76 (0.37), residues: 98 sheet: 0.20 (0.21), residues: 534 loop : -0.23 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 509 HIS 0.006 0.002 HIS D 255 PHE 0.015 0.002 PHE B 422 TYR 0.019 0.002 TYR C 399 ARG 0.008 0.001 ARG H 101 Details of bonding type rmsd hydrogen bonds : bond 0.03226 ( 240) hydrogen bonds : angle 6.19701 ( 495) SS BOND : bond 0.00695 ( 2) SS BOND : angle 1.17579 ( 4) covalent geometry : bond 0.00570 (19280) covalent geometry : angle 0.59102 (26253) ********************** 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 235 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 186 time to evaluate : 2.133 Fit side-chains REVERT: A 485 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.6620 (ttp-170) REVERT: A 579 GLN cc_start: 0.7739 (mt0) cc_final: 0.7197 (mt0) REVERT: B 514 ARG cc_start: 0.7381 (mtm180) cc_final: 0.5746 (mtp85) REVERT: C 254 ASN cc_start: 0.8306 (m-40) cc_final: 0.7789 (t0) REVERT: C 312 ARG cc_start: 0.8139 (mtt180) cc_final: 0.7848 (ttm170) REVERT: C 321 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7821 (mt0) REVERT: C 406 ARG cc_start: 0.7861 (mtt180) cc_final: 0.6448 (mtm110) REVERT: C 485 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8655 (ttt180) REVERT: C 641 LYS cc_start: 0.8683 (mtpm) cc_final: 0.8442 (mttt) REVERT: D 349 ASP cc_start: 0.8455 (m-30) cc_final: 0.8141 (m-30) REVERT: E 485 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7905 (ttm170) REVERT: E 533 ARG cc_start: 0.7013 (ptt-90) cc_final: 0.6325 (pmt170) REVERT: F 235 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8355 (mt) REVERT: F 333 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.7692 (t) REVERT: F 387 GLN cc_start: 0.8439 (mt0) cc_final: 0.7108 (mm-40) REVERT: F 406 ARG cc_start: 0.8081 (mtt180) cc_final: 0.5636 (mtm110) REVERT: F 412 GLN cc_start: 0.8259 (pt0) cc_final: 0.7568 (pp30) REVERT: F 449 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8278 (mtpt) REVERT: H 140 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7593 (pp30) REVERT: L 103 GLU cc_start: 0.7877 (pm20) cc_final: 0.7577 (pm20) outliers start: 49 outliers final: 36 residues processed: 225 average time/residue: 1.4908 time to fit residues: 373.5638 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 : 2.252 ------------------------------------------------------------------------------- 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 C residue 235 LEU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 485 ARG 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 531 GLU 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 449 LYS Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 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 42 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 128 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 210 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 167 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN C 321 GLN E 588 GLN F 304 ASN F 588 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.091451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.077556 restraints weight = 30525.748| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 1.52 r_work: 0.2705 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 19282 Z= 0.244 Angle : 0.592 9.352 26257 Z= 0.313 Chirality : 0.045 0.138 2714 Planarity : 0.005 0.048 3493 Dihedral : 5.603 51.987 2577 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.49 % Allowed : 10.25 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.16), residues: 2341 helix: -3.80 (0.37), residues: 98 sheet: 0.14 (0.21), residues: 534 loop : -0.27 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 509 HIS 0.006 0.001 HIS D 255 PHE 0.015 0.002 PHE B 422 TYR 0.020 0.002 TYR C 399 ARG 0.008 0.001 ARG H 101 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 240) hydrogen bonds : angle 6.20777 ( 495) SS BOND : bond 0.00720 ( 2) SS BOND : angle 1.18229 ( 4) covalent geometry : bond 0.00571 (19280) covalent geometry : angle 0.59181 (26253) =============================================================================== Job complete usr+sys time: 11780.73 seconds wall clock time: 204 minutes 5.84 seconds (12245.84 seconds total)