Starting phenix.real_space_refine on Mon Jun 16 04:36:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7m_44316/06_2025/9b7m_44316.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7m_44316/06_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_44316/06_2025/9b7m_44316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7m_44316/06_2025/9b7m_44316.map" model { file = "/net/cci-nas-00/data/ceres_data/9b7m_44316/06_2025/9b7m_44316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7m_44316/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.78, per 1000 atoms: 0.58 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: 4.53 Conformation dependent library (CDL) restraints added in 2.3 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: 2.06 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: 5.29 Time building geometry restraints manager: 5.37 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: 0.450 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: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 41.210 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.080 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:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.700 ------------------------------------------------------------------------------- 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 : 2.088 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: 1.4984 time to fit residues: 571.5836 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 : 2.327 ------------------------------------------------------------------------------- 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 = 0.083773 restraints weight = 30371.611| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.54 r_work: 0.2824 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- 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 : 2.253 Fit side-chains REVERT: A 579 GLN cc_start: 0.7660 (mt0) cc_final: 0.7156 (mt0) REVERT: B 514 ARG cc_start: 0.7654 (mtm180) cc_final: 0.6010 (mtp85) REVERT: B 575 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8366 (mm-30) REVERT: C 254 ASN cc_start: 0.8198 (m-40) cc_final: 0.7720 (t0) REVERT: C 406 ARG cc_start: 0.7757 (mtt180) cc_final: 0.6577 (mtm110) REVERT: C 418 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7818 (pt0) REVERT: C 641 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8398 (mttt) REVERT: D 316 LYS cc_start: 0.8311 (mtpp) cc_final: 0.7571 (mtmt) REVERT: D 349 ASP cc_start: 0.8293 (m-30) cc_final: 0.7943 (m-30) REVERT: D 419 ASN cc_start: 0.7955 (t0) cc_final: 0.7721 (t0) REVERT: D 579 GLN cc_start: 0.8322 (mt0) cc_final: 0.8098 (mt0) REVERT: D 682 GLU cc_start: 0.7917 (tt0) cc_final: 0.7315 (tm-30) REVERT: E 515 ASN cc_start: 0.8031 (m-40) cc_final: 0.7610 (t0) REVERT: F 259 GLN cc_start: 0.8009 (tt0) cc_final: 0.6230 (pm20) REVERT: F 324 GLU cc_start: 0.7246 (pp20) cc_final: 0.7020 (pp20) REVERT: F 334 ILE cc_start: 0.8823 (mt) cc_final: 0.8576 (mp) REVERT: F 387 GLN cc_start: 0.8368 (mt0) cc_final: 0.7276 (mm-40) REVERT: F 406 ARG cc_start: 0.7931 (mtt180) cc_final: 0.6339 (mtm-85) REVERT: F 412 GLN cc_start: 0.8078 (pt0) cc_final: 0.7569 (pt0) REVERT: H 38 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8241 (ttt180) REVERT: L 41 VAL cc_start: 0.9124 (t) cc_final: 0.8849 (m) outliers start: 37 outliers final: 12 residues processed: 259 average time/residue: 1.5295 time to fit residues: 439.9645 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 : 2.270 ------------------------------------------------------------------------------- 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: 7.9990 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: 3.2158 ------------------------------------------------------------------------------- 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 A 608 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.094741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.080836 restraints weight = 30415.765| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.54 r_work: 0.2766 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19282 Z= 0.141 Angle : 0.533 7.013 26257 Z= 0.278 Chirality : 0.043 0.136 2714 Planarity : 0.004 0.047 3493 Dihedral : 5.192 44.758 2579 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.25 % Allowed : 9.13 % Favored : 88.62 % 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: -0.07 (0.16), residues: 2341 helix: -3.20 (0.46), residues: 88 sheet: 0.47 (0.20), residues: 571 loop : 0.01 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 509 HIS 0.004 0.001 HIS D 255 PHE 0.011 0.002 PHE A 286 TYR 0.013 0.002 TYR B 443 ARG 0.007 0.001 ARG F 312 Details of bonding type rmsd hydrogen bonds : bond 0.02938 ( 240) hydrogen bonds : angle 6.00262 ( 495) SS BOND : bond 0.00790 ( 2) SS BOND : angle 1.08819 ( 4) covalent geometry : bond 0.00323 (19280) covalent geometry : angle 0.53281 (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 254 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 208 time to evaluate : 2.233 Fit side-chains REVERT: A 485 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.6312 (ttp-170) REVERT: A 579 GLN cc_start: 0.7726 (mt0) cc_final: 0.7219 (mt0) REVERT: B 514 ARG cc_start: 0.7567 (mtm180) cc_final: 0.5901 (mtp85) REVERT: C 254 ASN cc_start: 0.8201 (m-40) cc_final: 0.7677 (t0) REVERT: C 406 ARG cc_start: 0.7886 (mtt180) cc_final: 0.6585 (mtm110) REVERT: C 418 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7866 (pt0) REVERT: C 641 LYS cc_start: 0.8692 (mtpm) cc_final: 0.8405 (mttt) REVERT: D 316 LYS cc_start: 0.8309 (mtpp) cc_final: 0.7593 (mtmt) REVERT: D 349 ASP cc_start: 0.8323 (m-30) cc_final: 0.7960 (m-30) REVERT: D 419 ASN cc_start: 0.7935 (t0) cc_final: 0.7705 (t0) REVERT: D 682 GLU cc_start: 0.7959 (tt0) cc_final: 0.7385 (tm-30) REVERT: E 485 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7768 (ttm170) REVERT: E 515 ASN cc_start: 0.8026 (m-40) cc_final: 0.7584 (t0) REVERT: E 529 GLU cc_start: 0.6402 (pm20) cc_final: 0.6200 (pm20) REVERT: F 324 GLU cc_start: 0.7317 (pp20) cc_final: 0.7055 (pp20) REVERT: F 334 ILE cc_start: 0.8857 (mt) cc_final: 0.8644 (mp) REVERT: F 387 GLN cc_start: 0.8238 (mt0) cc_final: 0.7119 (mm-40) REVERT: F 406 ARG cc_start: 0.7998 (mtt180) cc_final: 0.6320 (mtm110) REVERT: F 412 GLN cc_start: 0.8172 (pt0) cc_final: 0.7623 (pt0) REVERT: H 38 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8280 (ttt180) REVERT: L 41 VAL cc_start: 0.9134 (t) cc_final: 0.8858 (m) outliers start: 46 outliers final: 23 residues processed: 241 average time/residue: 1.4814 time to fit residues: 397.1478 Evaluate side-chains 223 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 2.068 ------------------------------------------------------------------------------- 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 680 SER Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 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 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: 0.8980 chunk 186 optimal weight: 6.9990 chunk 20 optimal weight: 0.0970 chunk 227 optimal weight: 0.0670 chunk 192 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 174 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 86 optimal weight: 0.0470 overall best weight: 1.2216 ------------------------------------------------------------------------------- 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 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 = 0.3118 r_free = 0.3118 target = 0.097913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.084231 restraints weight = 30197.924| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.51 r_work: 0.2826 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19282 Z= 0.082 Angle : 0.469 7.492 26257 Z= 0.241 Chirality : 0.040 0.135 2714 Planarity : 0.003 0.039 3493 Dihedral : 4.531 40.948 2577 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.71 % Allowed : 10.45 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.10 (0.16), residues: 2341 helix: -3.09 (0.49), residues: 86 sheet: 0.60 (0.20), residues: 573 loop : 0.12 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 509 HIS 0.004 0.001 HIS D 255 PHE 0.008 0.001 PHE F 535 TYR 0.011 0.001 TYR H 69 ARG 0.008 0.000 ARG F 312 Details of bonding type rmsd hydrogen bonds : bond 0.02324 ( 240) hydrogen bonds : angle 5.48408 ( 495) SS BOND : bond 0.00364 ( 2) SS BOND : angle 0.77759 ( 4) covalent geometry : bond 0.00182 (19280) covalent geometry : angle 0.46943 (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 259 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 224 time to evaluate : 2.322 Fit side-chains REVERT: A 332 LYS cc_start: 0.7741 (ptmt) cc_final: 0.7415 (ptmm) REVERT: A 579 GLN cc_start: 0.7665 (mt0) cc_final: 0.7194 (mt0) REVERT: B 514 ARG cc_start: 0.7573 (mtm180) cc_final: 0.5892 (mtp85) REVERT: C 254 ASN cc_start: 0.8187 (m-40) cc_final: 0.7632 (t0) REVERT: C 406 ARG cc_start: 0.7822 (mtt180) cc_final: 0.6501 (mtm110) REVERT: C 641 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8433 (mttt) REVERT: D 316 LYS cc_start: 0.8294 (mtpp) cc_final: 0.7619 (mtmt) REVERT: D 349 ASP cc_start: 0.8297 (m-30) cc_final: 0.7947 (m-30) REVERT: D 682 GLU cc_start: 0.7938 (tt0) cc_final: 0.7346 (tm-30) REVERT: E 515 ASN cc_start: 0.7998 (m-40) cc_final: 0.7532 (t0) REVERT: F 324 GLU cc_start: 0.7364 (pp20) cc_final: 0.7131 (pp20) REVERT: F 387 GLN cc_start: 0.8395 (mt0) cc_final: 0.7229 (mm-40) REVERT: F 406 ARG cc_start: 0.7995 (mtt180) cc_final: 0.6320 (mtm110) REVERT: F 412 GLN cc_start: 0.8071 (pt0) cc_final: 0.7532 (pt0) REVERT: H 38 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8280 (ttt180) REVERT: L 41 VAL cc_start: 0.9150 (t) cc_final: 0.8893 (m) outliers start: 35 outliers final: 14 residues processed: 250 average time/residue: 1.4967 time to fit residues: 415.3465 Evaluate side-chains 214 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 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 569 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 532 ASP Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 33 VAL 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: 0.8980 chunk 197 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 206 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 214 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN D 292 HIS F 304 ASN F 579 GLN F 588 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.093529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.079665 restraints weight = 30514.986| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.53 r_work: 0.2743 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19282 Z= 0.186 Angle : 0.547 7.866 26257 Z= 0.287 Chirality : 0.043 0.137 2714 Planarity : 0.004 0.043 3493 Dihedral : 5.151 50.079 2576 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.10 % Allowed : 10.55 % 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: -0.09 (0.16), residues: 2341 helix: -3.48 (0.44), residues: 86 sheet: 0.49 (0.21), residues: 534 loop : -0.01 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 509 HIS 0.005 0.001 HIS D 255 PHE 0.012 0.002 PHE B 422 TYR 0.017 0.002 TYR C 277 ARG 0.006 0.001 ARG H 101 Details of bonding type rmsd hydrogen bonds : bond 0.02930 ( 240) hydrogen bonds : angle 5.95198 ( 495) SS BOND : bond 0.00485 ( 2) SS BOND : angle 1.03658 ( 4) covalent geometry : bond 0.00435 (19280) covalent geometry : angle 0.54698 (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 242 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 199 time to evaluate : 2.104 Fit side-chains REVERT: A 485 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7135 (ttt90) REVERT: A 579 GLN cc_start: 0.7697 (mt0) cc_final: 0.7220 (mt0) REVERT: B 514 ARG cc_start: 0.7564 (mtm180) cc_final: 0.5867 (mtp85) REVERT: C 254 ASN cc_start: 0.8212 (m-40) cc_final: 0.7650 (t0) REVERT: C 324 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6649 (mm-30) REVERT: C 406 ARG cc_start: 0.7888 (mtt180) cc_final: 0.6462 (mtm110) REVERT: C 418 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7886 (pt0) REVERT: C 641 LYS cc_start: 0.8698 (mtpm) cc_final: 0.8402 (mttt) REVERT: D 316 LYS cc_start: 0.8280 (mtpp) cc_final: 0.7470 (mppt) REVERT: D 349 ASP cc_start: 0.8408 (m-30) cc_final: 0.8044 (m-30) REVERT: D 682 GLU cc_start: 0.7973 (tt0) cc_final: 0.7494 (tm-30) REVERT: E 436 MET cc_start: 0.8789 (pmm) cc_final: 0.8514 (ptp) REVERT: E 485 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7661 (ttm170) REVERT: F 324 GLU cc_start: 0.7358 (pp20) cc_final: 0.7090 (pp20) REVERT: F 387 GLN cc_start: 0.8396 (mt0) cc_final: 0.7206 (mm-40) REVERT: F 406 ARG cc_start: 0.8074 (mtt180) cc_final: 0.6236 (mtm110) REVERT: F 412 GLN cc_start: 0.8182 (pt0) cc_final: 0.7598 (pt0) REVERT: H 38 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8377 (ttt180) REVERT: H 140 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7683 (pp30) REVERT: L 103 GLU cc_start: 0.8082 (pm20) cc_final: 0.7839 (pm20) outliers start: 43 outliers final: 32 residues processed: 232 average time/residue: 1.4828 time to fit residues: 382.8533 Evaluate side-chains 225 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 2.102 ------------------------------------------------------------------------------- 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 418 GLU Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 593 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 489 VAL Chi-restraints excluded: chain E residue 569 THR 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 90 SER Chi-restraints excluded: chain H residue 140 GLN Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 111 GLN 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: 6.9990 chunk 17 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 82 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 210 optimal weight: 1.9990 chunk 162 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN E 515 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 = 0.3043 r_free = 0.3043 target = 0.093153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.079288 restraints weight = 30542.216| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 1.53 r_work: 0.2726 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19282 Z= 0.186 Angle : 0.545 8.538 26257 Z= 0.286 Chirality : 0.043 0.136 2714 Planarity : 0.004 0.043 3493 Dihedral : 5.227 50.190 2576 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.73 % Allowed : 10.50 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.19 (0.16), residues: 2341 helix: -3.61 (0.43), residues: 86 sheet: 0.43 (0.21), residues: 533 loop : -0.07 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 509 HIS 0.005 0.001 HIS D 255 PHE 0.011 0.002 PHE B 422 TYR 0.016 0.002 TYR C 277 ARG 0.007 0.001 ARG E 533 Details of bonding type rmsd hydrogen bonds : bond 0.02922 ( 240) hydrogen bonds : angle 6.00476 ( 495) SS BOND : bond 0.00496 ( 2) SS BOND : angle 1.02082 ( 4) covalent geometry : bond 0.00434 (19280) covalent geometry : angle 0.54486 (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 249 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 193 time to evaluate : 2.210 Fit side-chains REVERT: A 485 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7255 (ttt90) REVERT: A 579 GLN cc_start: 0.7713 (mt0) cc_final: 0.7201 (mt0) REVERT: B 514 ARG cc_start: 0.7483 (mtm180) cc_final: 0.5760 (mtp85) REVERT: C 254 ASN cc_start: 0.8270 (m-40) cc_final: 0.7699 (t0) REVERT: C 324 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6703 (mm-30) REVERT: C 406 ARG cc_start: 0.7868 (mtt180) cc_final: 0.6435 (mtm110) REVERT: C 418 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7921 (pt0) REVERT: C 485 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8649 (ttt180) REVERT: C 641 LYS cc_start: 0.8681 (mtpm) cc_final: 0.8388 (mttt) REVERT: D 316 LYS cc_start: 0.8310 (mtpp) cc_final: 0.7688 (mtmt) REVERT: D 349 ASP cc_start: 0.8425 (m-30) cc_final: 0.8097 (m-30) REVERT: D 682 GLU cc_start: 0.8010 (tt0) cc_final: 0.7552 (tm-30) REVERT: E 436 MET cc_start: 0.8881 (pmm) cc_final: 0.8552 (ptp) REVERT: E 485 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7715 (ttm170) REVERT: F 324 GLU cc_start: 0.7356 (pp20) cc_final: 0.7105 (pp20) REVERT: F 387 GLN cc_start: 0.8401 (mt0) cc_final: 0.7182 (mm-40) REVERT: F 406 ARG cc_start: 0.8077 (mtt180) cc_final: 0.6241 (mtm110) REVERT: F 412 GLN cc_start: 0.8248 (pt0) cc_final: 0.7644 (pt0) REVERT: F 449 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8210 (mtpt) REVERT: H 38 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8418 (ttt180) REVERT: H 140 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7622 (pp30) REVERT: L 103 GLU cc_start: 0.7906 (pm20) cc_final: 0.7613 (pm20) outliers start: 56 outliers final: 37 residues processed: 234 average time/residue: 1.5682 time to fit residues: 406.1821 Evaluate side-chains 232 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 2.155 ------------------------------------------------------------------------------- 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 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 676 THR Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 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 593 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 489 VAL Chi-restraints excluded: chain E residue 569 THR 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 64 LEU 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 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: 9.9990 chunk 125 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 164 optimal weight: 0.0470 chunk 190 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 overall best weight: 4.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN F 304 ASN F 588 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.092871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.079036 restraints weight = 30212.271| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 1.49 r_work: 0.2726 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 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 0.051 19282 Z= 0.187 Angle : 0.547 8.746 26257 Z= 0.287 Chirality : 0.043 0.136 2714 Planarity : 0.004 0.044 3493 Dihedral : 5.282 49.741 2576 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.54 % Allowed : 10.55 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.24 (0.16), residues: 2341 helix: -3.71 (0.42), residues: 86 sheet: 0.36 (0.21), residues: 534 loop : -0.09 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 509 HIS 0.005 0.001 HIS D 255 PHE 0.011 0.002 PHE C 535 TYR 0.016 0.002 TYR F 701 ARG 0.007 0.001 ARG H 101 Details of bonding type rmsd hydrogen bonds : bond 0.02928 ( 240) hydrogen bonds : angle 5.99956 ( 495) SS BOND : bond 0.00602 ( 2) SS BOND : angle 0.94761 ( 4) covalent geometry : bond 0.00436 (19280) covalent geometry : angle 0.54693 (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 246 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 194 time to evaluate : 2.265 Fit side-chains REVERT: A 485 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7245 (ttt90) REVERT: A 579 GLN cc_start: 0.7705 (mt0) cc_final: 0.7178 (mt0) REVERT: B 514 ARG cc_start: 0.7343 (mtm180) cc_final: 0.5673 (mtp85) REVERT: C 254 ASN cc_start: 0.8270 (m-40) cc_final: 0.7681 (t0) REVERT: C 321 GLN cc_start: 0.8108 (mt0) cc_final: 0.7838 (mt0) REVERT: C 324 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6758 (mm-30) REVERT: C 406 ARG cc_start: 0.7868 (mtt180) cc_final: 0.6430 (mtm110) REVERT: C 418 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7905 (pt0) REVERT: C 485 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8638 (ttt180) REVERT: C 641 LYS cc_start: 0.8682 (mtpm) cc_final: 0.8392 (mttt) REVERT: D 316 LYS cc_start: 0.8324 (mtpp) cc_final: 0.7682 (mtmt) REVERT: D 349 ASP cc_start: 0.8424 (m-30) cc_final: 0.8121 (m-30) REVERT: D 682 GLU cc_start: 0.8013 (tt0) cc_final: 0.7549 (tm-30) REVERT: E 436 MET cc_start: 0.8913 (pmm) cc_final: 0.8534 (ptp) REVERT: E 485 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7706 (ttm170) REVERT: F 324 GLU cc_start: 0.7377 (pp20) cc_final: 0.7168 (pp20) REVERT: F 387 GLN cc_start: 0.8400 (mt0) cc_final: 0.7117 (mm-40) REVERT: F 406 ARG cc_start: 0.8077 (mtt180) cc_final: 0.5598 (mtm110) REVERT: F 412 GLN cc_start: 0.8220 (pt0) cc_final: 0.7619 (pt0) REVERT: F 449 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8216 (mtpt) REVERT: H 140 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7601 (pp30) REVERT: L 103 GLU cc_start: 0.7850 (pm20) cc_final: 0.7530 (pm20) outliers start: 52 outliers final: 39 residues processed: 235 average time/residue: 1.5075 time to fit residues: 393.2934 Evaluate side-chains 232 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 2.071 ------------------------------------------------------------------------------- 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 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 676 THR Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 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 489 VAL Chi-restraints excluded: chain E residue 569 THR 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 H residue 31 VAL Chi-restraints excluded: chain H residue 64 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 150 optimal weight: 20.0000 chunk 200 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN C 253 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 = 0.3052 r_free = 0.3052 target = 0.093778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.079847 restraints weight = 30243.260| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 1.53 r_work: 0.2749 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19282 Z= 0.138 Angle : 0.512 8.984 26257 Z= 0.267 Chirality : 0.042 0.135 2714 Planarity : 0.004 0.042 3493 Dihedral : 5.057 50.104 2576 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.00 % Allowed : 11.04 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.14 (0.16), residues: 2341 helix: -3.63 (0.44), residues: 86 sheet: 0.44 (0.21), residues: 511 loop : -0.02 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 509 HIS 0.005 0.001 HIS D 255 PHE 0.010 0.001 PHE A 629 TYR 0.014 0.001 TYR C 399 ARG 0.007 0.001 ARG H 101 Details of bonding type rmsd hydrogen bonds : bond 0.02678 ( 240) hydrogen bonds : angle 5.74681 ( 495) SS BOND : bond 0.00510 ( 2) SS BOND : angle 0.78771 ( 4) covalent geometry : bond 0.00320 (19280) covalent geometry : angle 0.51235 (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 231 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 2.116 Fit side-chains REVERT: A 485 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7243 (ttt90) REVERT: A 579 GLN cc_start: 0.7731 (mt0) cc_final: 0.7204 (mt0) REVERT: B 514 ARG cc_start: 0.7315 (mtm180) cc_final: 0.5745 (mtp85) REVERT: C 254 ASN cc_start: 0.8287 (m-40) cc_final: 0.7698 (t0) REVERT: C 312 ARG cc_start: 0.8129 (mtt180) cc_final: 0.7855 (ttm170) REVERT: C 406 ARG cc_start: 0.7821 (mtt180) cc_final: 0.6419 (mtm110) REVERT: C 418 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7868 (pt0) REVERT: C 485 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8634 (ttt180) REVERT: C 641 LYS cc_start: 0.8677 (mtpm) cc_final: 0.8398 (mttt) REVERT: D 262 ASN cc_start: 0.7151 (t0) cc_final: 0.6917 (t0) REVERT: D 316 LYS cc_start: 0.8329 (mtpp) cc_final: 0.7686 (mtmt) REVERT: D 349 ASP cc_start: 0.8411 (m-30) cc_final: 0.8117 (m-30) REVERT: D 682 GLU cc_start: 0.7999 (tt0) cc_final: 0.7516 (tm-30) REVERT: E 485 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7615 (ttm170) REVERT: F 324 GLU cc_start: 0.7407 (pp20) cc_final: 0.7126 (pp20) REVERT: F 387 GLN cc_start: 0.8397 (mt0) cc_final: 0.7140 (mm-40) REVERT: F 406 ARG cc_start: 0.8037 (mtt180) cc_final: 0.5590 (mtm110) REVERT: F 412 GLN cc_start: 0.8234 (pt0) cc_final: 0.7624 (pt0) REVERT: F 449 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8097 (mtpt) REVERT: L 103 GLU cc_start: 0.7834 (pm20) cc_final: 0.7508 (pm20) outliers start: 41 outliers final: 31 residues processed: 219 average time/residue: 1.6106 time to fit residues: 392.3440 Evaluate side-chains 222 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 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 676 THR Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain F residue 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 64 LEU Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 121 THR 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 44 THR 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: 5.9990 chunk 91 optimal weight: 0.5980 chunk 13 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 208 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 overall best weight: 4.9188 ------------------------------------------------------------------------------- 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 = 0.3032 r_free = 0.3032 target = 0.092538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.078591 restraints weight = 30553.012| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 1.53 r_work: 0.2721 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19282 Z= 0.190 Angle : 0.548 9.068 26257 Z= 0.288 Chirality : 0.043 0.135 2714 Planarity : 0.004 0.044 3493 Dihedral : 5.306 55.363 2576 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.34 % Allowed : 10.84 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.24 (0.16), residues: 2341 helix: -3.75 (0.42), residues: 86 sheet: 0.36 (0.21), residues: 534 loop : -0.09 (0.14), residues: 1721 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 B 422 TYR 0.017 0.002 TYR C 399 ARG 0.008 0.001 ARG H 101 Details of bonding type rmsd hydrogen bonds : bond 0.02971 ( 240) hydrogen bonds : angle 5.96786 ( 495) SS BOND : bond 0.00636 ( 2) SS BOND : angle 0.99455 ( 4) covalent geometry : bond 0.00443 (19280) covalent geometry : angle 0.54787 (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 237 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 189 time to evaluate : 2.259 Fit side-chains REVERT: A 485 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7300 (ttt90) REVERT: A 579 GLN cc_start: 0.7717 (mt0) cc_final: 0.7187 (mt0) REVERT: B 514 ARG cc_start: 0.7365 (mtm180) cc_final: 0.5700 (mtp85) REVERT: C 254 ASN cc_start: 0.8272 (m-40) cc_final: 0.7754 (t0) REVERT: C 312 ARG cc_start: 0.8133 (mtt180) cc_final: 0.7856 (ttm170) REVERT: C 321 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7764 (mt0) REVERT: C 406 ARG cc_start: 0.7856 (mtt180) cc_final: 0.6460 (mtm110) REVERT: C 418 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7928 (pt0) REVERT: C 485 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8644 (ttt180) REVERT: C 641 LYS cc_start: 0.8682 (mtpm) cc_final: 0.8395 (mttt) REVERT: D 262 ASN cc_start: 0.7259 (t0) cc_final: 0.7011 (t0) REVERT: D 349 ASP cc_start: 0.8446 (m-30) cc_final: 0.8149 (m-30) REVERT: D 682 GLU cc_start: 0.8027 (tt0) cc_final: 0.7521 (tm-30) REVERT: E 485 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7709 (ttm170) REVERT: F 324 GLU cc_start: 0.7376 (pp20) cc_final: 0.7141 (pp20) REVERT: F 387 GLN cc_start: 0.8423 (mt0) cc_final: 0.7105 (mm-40) REVERT: F 406 ARG cc_start: 0.8048 (mtt180) cc_final: 0.5595 (mtm110) REVERT: F 412 GLN cc_start: 0.8226 (pt0) cc_final: 0.7630 (pt0) REVERT: F 449 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8251 (mtpt) REVERT: L 103 GLU cc_start: 0.7822 (pm20) cc_final: 0.7475 (pm20) outliers start: 48 outliers final: 38 residues processed: 225 average time/residue: 1.5623 time to fit residues: 389.8518 Evaluate side-chains 229 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 2.029 ------------------------------------------------------------------------------- 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 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 676 THR Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 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 489 VAL Chi-restraints excluded: chain E residue 531 GLU Chi-restraints excluded: chain E residue 569 THR 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 H residue 31 VAL Chi-restraints excluded: chain H residue 64 LEU 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 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: 9.9990 chunk 143 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 226 optimal weight: 6.9990 chunk 217 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 C 321 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 = 0.3036 r_free = 0.3036 target = 0.092772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.078771 restraints weight = 30276.088| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 1.53 r_work: 0.2721 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19282 Z= 0.181 Angle : 0.545 9.247 26257 Z= 0.286 Chirality : 0.043 0.136 2714 Planarity : 0.004 0.044 3493 Dihedral : 5.311 59.692 2576 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.29 % Allowed : 10.84 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.26 (0.16), residues: 2341 helix: -3.76 (0.42), residues: 86 sheet: 0.34 (0.21), residues: 533 loop : -0.10 (0.14), residues: 1722 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 0.012 0.002 PHE B 422 TYR 0.018 0.002 TYR C 399 ARG 0.008 0.001 ARG C 550 Details of bonding type rmsd hydrogen bonds : bond 0.02950 ( 240) hydrogen bonds : angle 5.93493 ( 495) SS BOND : bond 0.00631 ( 2) SS BOND : angle 0.98319 ( 4) covalent geometry : bond 0.00422 (19280) covalent geometry : angle 0.54494 (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 231 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 184 time to evaluate : 2.147 Fit side-chains REVERT: A 485 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7309 (ttt90) REVERT: A 579 GLN cc_start: 0.7705 (mt0) cc_final: 0.7176 (mt0) REVERT: B 514 ARG cc_start: 0.7349 (mtm180) cc_final: 0.5684 (mtp85) REVERT: C 254 ASN cc_start: 0.8267 (m-40) cc_final: 0.7762 (t0) REVERT: C 312 ARG cc_start: 0.8137 (mtt180) cc_final: 0.7859 (ttm170) REVERT: C 321 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7655 (mt0) REVERT: C 406 ARG cc_start: 0.7850 (mtt180) cc_final: 0.6444 (mtm110) REVERT: C 418 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7921 (pt0) REVERT: C 485 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8636 (ttt180) REVERT: C 641 LYS cc_start: 0.8675 (mtpm) cc_final: 0.8386 (mttt) REVERT: D 262 ASN cc_start: 0.7269 (t0) cc_final: 0.7018 (t0) REVERT: D 349 ASP cc_start: 0.8431 (m-30) cc_final: 0.8138 (m-30) REVERT: D 524 MET cc_start: 0.7913 (mtp) cc_final: 0.7689 (mtm) REVERT: D 682 GLU cc_start: 0.8025 (tt0) cc_final: 0.7515 (tm-30) REVERT: E 485 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7695 (ttm170) REVERT: E 533 ARG cc_start: 0.6997 (ptt-90) cc_final: 0.6325 (pmt170) REVERT: F 324 GLU cc_start: 0.7368 (pp20) cc_final: 0.7129 (pp20) REVERT: F 387 GLN cc_start: 0.8407 (mt0) cc_final: 0.7070 (mm-40) REVERT: F 406 ARG cc_start: 0.8042 (mtt180) cc_final: 0.5587 (mtm110) REVERT: F 412 GLN cc_start: 0.8234 (pt0) cc_final: 0.7634 (pt0) REVERT: F 449 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8273 (mtpt) REVERT: L 103 GLU cc_start: 0.7819 (pm20) cc_final: 0.7472 (pm20) outliers start: 47 outliers final: 38 residues processed: 220 average time/residue: 1.5079 time to fit residues: 368.7218 Evaluate side-chains 229 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 2.117 ------------------------------------------------------------------------------- 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 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 676 THR Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 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 489 VAL Chi-restraints excluded: chain E residue 569 THR 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 H residue 31 VAL Chi-restraints excluded: chain H residue 64 LEU 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 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: 0.7980 chunk 74 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 103 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 158 optimal weight: 8.9990 chunk 187 optimal weight: 0.5980 chunk 211 optimal weight: 0.0020 overall best weight: 1.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN C 710 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 = 0.3079 r_free = 0.3079 target = 0.095509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.081716 restraints weight = 30350.143| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 1.50 r_work: 0.2776 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19282 Z= 0.098 Angle : 0.484 9.291 26257 Z= 0.250 Chirality : 0.041 0.134 2714 Planarity : 0.004 0.042 3493 Dihedral : 4.791 52.884 2576 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.61 % Allowed : 11.47 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.06 (0.16), residues: 2341 helix: -3.57 (0.46), residues: 86 sheet: 0.47 (0.22), residues: 511 loop : 0.04 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 509 HIS 0.004 0.001 HIS D 255 PHE 0.010 0.001 PHE A 629 TYR 0.012 0.001 TYR E 426 ARG 0.008 0.000 ARG D 312 Details of bonding type rmsd hydrogen bonds : bond 0.02463 ( 240) hydrogen bonds : angle 5.44456 ( 495) SS BOND : bond 0.00486 ( 2) SS BOND : angle 0.64107 ( 4) covalent geometry : bond 0.00224 (19280) covalent geometry : angle 0.48362 (26253) =============================================================================== Job complete usr+sys time: 12544.98 seconds wall clock time: 214 minutes 40.31 seconds (12880.31 seconds total)