Starting phenix.real_space_refine on Sun May 18 05:49:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7w_44326/05_2025/9b7w_44326.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7w_44326/05_2025/9b7w_44326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b7w_44326/05_2025/9b7w_44326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7w_44326/05_2025/9b7w_44326.map" model { file = "/net/cci-nas-00/data/ceres_data/9b7w_44326/05_2025/9b7w_44326.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7w_44326/05_2025/9b7w_44326.cif" } resolution = 3.36 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 10697 2.51 5 N 2924 2.21 5 O 3280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16963 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2699 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 317} Chain breaks: 3 Chain: "B" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 927 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain breaks: 1 Chain: "C" Number of atoms: 3963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3963 Classifications: {'peptide': 495} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 462} Chain breaks: 1 Chain: "D" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2699 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 317} Chain breaks: 3 Chain: "E" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 927 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain breaks: 1 Chain: "F" Number of atoms: 3963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3963 Classifications: {'peptide': 495} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 462} Chain breaks: 1 Chain: "H" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 996 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "L" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 789 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Time building chain proxies: 9.81, per 1000 atoms: 0.58 Number of scatterers: 16963 At special positions: 0 Unit cell: (142.45, 133.2, 102.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 3280 8.00 N 2924 7.00 C 10697 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 42 " - pdb=" SG CYS L 110 " distance=2.03 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: 3.93 Conformation dependent library (CDL) restraints added in 2.5 seconds 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3940 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 49 sheets defined 6.1% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... 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: 3.530A pdb=" N ILE A 566 " --> pdb=" O GLU A 563 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR A 568 " --> pdb=" O GLU A 565 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 569 " --> pdb=" O ILE A 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 569 removed outlier: 4.128A pdb=" N THR B 568 " --> pdb=" O GLU B 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.430A pdb=" N HIS C 292 " --> pdb=" O ARG C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 355 through 359 removed outlier: 3.605A pdb=" N SER C 358 " --> pdb=" O VAL C 355 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA C 359 " --> pdb=" O LEU C 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 355 through 359' Processing helix chain 'C' and resid 563 through 567 Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 396 through 400 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 Processing helix chain 'E' and resid 431 through 436 removed outlier: 3.509A pdb=" N LEU E 435 " --> pdb=" O LEU E 432 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N MET E 436 " --> pdb=" O ASP E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 569 removed outlier: 3.904A pdb=" N THR E 568 " --> pdb=" O GLU E 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 256 Processing helix chain 'F' and resid 262 through 266 Processing helix chain 'F' and resid 288 through 292 Processing helix chain 'F' and resid 294 through 304 removed outlier: 3.531A pdb=" N GLN F 299 " --> pdb=" O PRO F 295 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU F 301 " --> pdb=" O ASP F 297 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN F 304 " --> pdb=" O ARG F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 359 removed outlier: 3.916A pdb=" N SER F 358 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 4.176A 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 Processing helix chain 'F' and resid 431 through 435 removed outlier: 3.615A pdb=" N LEU F 435 " --> pdb=" O LEU F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 563 through 568 removed outlier: 3.515A pdb=" N LYS F 567 " --> pdb=" O GLU F 564 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR F 568 " --> pdb=" O GLU F 565 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 258 through 261 removed outlier: 4.587A pdb=" N PHE A 275 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 328 Processing sheet with id=AA3, first strand: chain 'A' and resid 403 through 405 removed outlier: 3.607A pdb=" N GLN A 646 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 483 through 484 removed outlier: 3.537A pdb=" N SER A 483 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 542 through 544 Processing sheet with id=AA6, first strand: chain 'A' and resid 553 through 554 removed outlier: 4.411A pdb=" N THR C 450 " --> pdb=" O THR C 460 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS C 462 " --> pdb=" O SER C 448 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 578 through 581 removed outlier: 3.994A pdb=" N GLY A 578 " --> pdb=" O VAL A 596 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 619 through 621 Processing sheet with id=AA9, first strand: chain 'A' and resid 627 through 629 removed outlier: 3.798A pdb=" N MET C 605 " --> pdb=" O PHE A 629 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE C 479 " --> pdb=" O VAL C 606 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 445 through 451 removed outlier: 6.961A pdb=" N LYS B 462 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR B 450 " --> pdb=" O THR B 460 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL B 465 " --> pdb=" O ASP C 551 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASP C 551 " --> pdb=" O VAL B 465 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 479 through 480 removed outlier: 6.130A pdb=" N ILE B 479 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N MET B 605 " --> pdb=" O PHE C 629 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY C 627 " --> pdb=" O TRP B 607 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 483 through 484 removed outlier: 3.774A pdb=" N SER B 483 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 579 through 581 Processing sheet with id=AB5, first strand: chain 'C' and resid 231 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=AB6, first strand: chain 'C' and resid 258 through 261 Processing sheet with id=AB7, first strand: chain 'C' and resid 427 through 428 removed outlier: 6.153A pdb=" N ALA C 427 " --> pdb=" O ARG C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 483 through 484 Processing sheet with id=AB9, first strand: chain 'C' and resid 488 through 490 Processing sheet with id=AC1, first strand: chain 'C' and resid 508 through 511 Processing sheet with id=AC2, first strand: chain 'C' and resid 542 through 544 Processing sheet with id=AC3, first strand: chain 'C' and resid 578 through 581 removed outlier: 4.063A pdb=" N GLY C 578 " --> pdb=" O VAL C 596 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 619 through 621 removed outlier: 6.086A pdb=" N ALA C 620 " --> pdb=" O MET C 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 258 through 261 removed outlier: 7.998A pdb=" N THR D 279 " --> pdb=" O TYR D 379 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N TYR D 379 " --> pdb=" O THR D 279 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N TRP D 281 " --> pdb=" O TYR D 377 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 313 through 328 removed outlier: 4.227A pdb=" N VAL D 322 " --> pdb=" O ASN D 337 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN D 328 " --> pdb=" O VAL D 331 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 331 " --> pdb=" O ASN D 328 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 403 through 405 removed outlier: 4.148A pdb=" N GLN D 646 " --> pdb=" O ASP D 347 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 383 through 384 Processing sheet with id=AC9, first strand: chain 'D' and resid 483 through 484 Processing sheet with id=AD1, first strand: chain 'D' and resid 514 through 517 removed outlier: 3.587A pdb=" N SER D 508 " --> pdb=" O GLN F 579 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY F 578 " --> pdb=" O VAL F 596 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 542 through 544 Processing sheet with id=AD3, first strand: chain 'D' and resid 579 through 581 Processing sheet with id=AD4, first strand: chain 'D' and resid 619 through 621 removed outlier: 6.265A pdb=" N ALA D 620 " --> pdb=" O MET D 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 627 through 629 removed outlier: 3.803A pdb=" N MET F 605 " --> pdb=" O PHE D 629 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE F 479 " --> pdb=" O VAL F 606 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 445 through 451 removed outlier: 6.640A pdb=" N LYS E 462 " --> pdb=" O SER E 448 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR E 450 " --> pdb=" O THR E 460 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 479 through 480 removed outlier: 6.291A pdb=" N ILE E 479 " --> pdb=" O VAL E 606 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N MET E 605 " --> pdb=" O PHE F 629 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 483 through 484 Processing sheet with id=AD9, first strand: chain 'E' and resid 579 through 581 Processing sheet with id=AE1, first strand: chain 'F' and resid 233 through 235 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 238 through 249 current: chain 'F' and resid 331 through 336 Processing sheet with id=AE2, first strand: chain 'F' and resid 258 through 261 Processing sheet with id=AE3, first strand: chain 'F' and resid 427 through 428 removed outlier: 6.338A pdb=" N ALA F 427 " --> pdb=" O ARG F 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'F' and resid 445 through 447 Processing sheet with id=AE5, first strand: chain 'F' and resid 483 through 484 Processing sheet with id=AE6, first strand: chain 'F' and resid 488 through 490 Processing sheet with id=AE7, first strand: chain 'F' and resid 508 through 511 Processing sheet with id=AE8, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AE9, first strand: chain 'F' and resid 619 through 621 Processing sheet with id=AF1, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AF2, first strand: chain 'H' and resid 53 through 58 removed outlier: 6.549A pdb=" N ARG H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N TRP H 66 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP H 78 " --> pdb=" O TYR H 69 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 77 through 79 current: chain 'H' and resid 132 through 135 Processing sheet with id=AF3, first strand: chain 'L' and resid 29 through 32 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 29 through 32 current: chain 'L' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 67 through 71 current: chain 'L' and resid 119 through 120 No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'L' and resid 38 through 43 215 hydrogen bonds defined for protein. 477 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: 5.09 Time building geometry restraints manager: 4.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3857 1.33 - 1.45: 4271 1.45 - 1.57: 9208 1.57 - 1.69: 0 1.69 - 1.81: 107 Bond restraints: 17443 Sorted by residual: bond pdb=" C GLU C 723 " pdb=" O GLU C 723 " ideal model delta sigma weight residual 1.249 1.222 0.027 8.50e-03 1.38e+04 9.82e+00 bond pdb=" C GLN B 459 " pdb=" O GLN B 459 " ideal model delta sigma weight residual 1.234 1.207 0.028 1.20e-02 6.94e+03 5.28e+00 bond pdb=" C THR B 460 " pdb=" O THR B 460 " ideal model delta sigma weight residual 1.234 1.204 0.029 1.30e-02 5.92e+03 5.15e+00 bond pdb=" C GLN C 351 " pdb=" N LEU C 352 " ideal model delta sigma weight residual 1.328 1.295 0.032 1.45e-02 4.76e+03 5.00e+00 bond pdb=" CB GLN F 299 " pdb=" CG GLN F 299 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.84e+00 ... (remaining 17438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 22875 2.35 - 4.71: 776 4.71 - 7.06: 81 7.06 - 9.42: 16 9.42 - 11.77: 10 Bond angle restraints: 23758 Sorted by residual: angle pdb=" N LEU E 439 " pdb=" CA LEU E 439 " pdb=" C LEU E 439 " ideal model delta sigma weight residual 111.28 120.88 -9.60 1.09e+00 8.42e-01 7.75e+01 angle pdb=" N VAL H 67 " pdb=" CA VAL H 67 " pdb=" C VAL H 67 " ideal model delta sigma weight residual 110.53 117.78 -7.25 9.40e-01 1.13e+00 5.95e+01 angle pdb=" N GLY D 539 " pdb=" CA GLY D 539 " pdb=" C GLY D 539 " ideal model delta sigma weight residual 112.73 121.65 -8.92 1.20e+00 6.94e-01 5.53e+01 angle pdb=" N ILE E 440 " pdb=" CA ILE E 440 " pdb=" C ILE E 440 " ideal model delta sigma weight residual 109.20 118.64 -9.44 1.55e+00 4.16e-01 3.71e+01 angle pdb=" C LEU F 364 " pdb=" N PRO F 365 " pdb=" CA PRO F 365 " ideal model delta sigma weight residual 119.66 123.85 -4.19 7.30e-01 1.88e+00 3.30e+01 ... (remaining 23753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 9755 17.78 - 35.57: 352 35.57 - 53.35: 70 53.35 - 71.14: 11 71.14 - 88.92: 17 Dihedral angle restraints: 10205 sinusoidal: 4017 harmonic: 6188 Sorted by residual: dihedral pdb=" CA THR C 729 " pdb=" C THR C 729 " pdb=" N ARG C 730 " pdb=" CA ARG C 730 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA VAL H 83 " pdb=" C VAL H 83 " pdb=" N LYS H 84 " pdb=" CA LYS H 84 " ideal model delta harmonic sigma weight residual 180.00 -153.72 -26.28 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ASN A 383 " pdb=" C ASN A 383 " pdb=" N ASP A 384 " pdb=" CA ASP A 384 " ideal model delta harmonic sigma weight residual 180.00 154.59 25.41 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 10202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1941 0.072 - 0.143: 454 0.143 - 0.215: 59 0.215 - 0.287: 14 0.287 - 0.358: 3 Chirality restraints: 2471 Sorted by residual: chirality pdb=" CA CYS F 230 " pdb=" N CYS F 230 " pdb=" C CYS F 230 " pdb=" CB CYS F 230 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA LEU E 439 " pdb=" N LEU E 439 " pdb=" C LEU E 439 " pdb=" CB LEU E 439 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA ASP F 231 " pdb=" N ASP F 231 " pdb=" C ASP F 231 " pdb=" CB ASP F 231 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 2468 not shown) Planarity restraints: 3151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN F 497 " 0.021 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C ASN F 497 " -0.069 2.00e-02 2.50e+03 pdb=" O ASN F 497 " 0.026 2.00e-02 2.50e+03 pdb=" N ASN F 498 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 643 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO C 644 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 644 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 644 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 367 " 0.017 2.00e-02 2.50e+03 1.63e-02 4.64e+00 pdb=" CG PHE F 367 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE F 367 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE F 367 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE F 367 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 367 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE F 367 " 0.001 2.00e-02 2.50e+03 ... (remaining 3148 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 6 2.08 - 2.78: 4336 2.78 - 3.49: 22385 3.49 - 4.19: 42481 4.19 - 4.90: 73974 Nonbonded interactions: 143182 Sorted by model distance: nonbonded pdb=" NZ LYS C 332 " pdb=" OD2 ASP D 657 " model vdw 1.375 3.120 nonbonded pdb=" OD1 ASP D 384 " pdb=" CG1 VAL D 389 " model vdw 1.504 3.460 nonbonded pdb=" O CYS F 230 " pdb=" O THR F 242 " model vdw 1.733 3.040 nonbonded pdb=" OH TYR C 350 " pdb=" O PRO C 643 " model vdw 2.070 3.040 nonbonded pdb=" OH TYR F 415 " pdb=" O HIS F 642 " model vdw 2.077 3.040 ... (remaining 143177 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' 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: 0.410 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: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 37.540 Find NCS groups from input model: 0.450 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 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 : 0.009 0.068 17445 Z= 0.414 Angle : 1.027 11.771 23762 Z= 0.619 Chirality : 0.063 0.358 2471 Planarity : 0.006 0.057 3151 Dihedral : 11.009 88.923 6259 Min Nonbonded Distance : 1.375 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.35 % Allowed : 1.94 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.15), residues: 2115 helix: -3.05 (0.55), residues: 58 sheet: -1.27 (0.18), residues: 593 loop : -1.40 (0.13), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP C 281 HIS 0.016 0.003 HIS F 290 PHE 0.038 0.003 PHE F 367 TYR 0.032 0.003 TYR C 443 ARG 0.016 0.002 ARG F 734 Details of bonding type rmsd hydrogen bonds : bond 0.23783 ( 215) hydrogen bonds : angle 9.86666 ( 477) SS BOND : bond 0.00544 ( 2) SS BOND : angle 0.82768 ( 4) covalent geometry : bond 0.00899 (17443) covalent geometry : angle 1.02714 (23758) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 389 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 LYS cc_start: 0.6562 (mmtt) cc_final: 0.6254 (mptt) REVERT: A 552 ASN cc_start: 0.7790 (m-40) cc_final: 0.7262 (t0) REVERT: A 599 GLN cc_start: 0.8067 (tp40) cc_final: 0.7792 (tp40) REVERT: A 626 ASP cc_start: 0.7631 (m-30) cc_final: 0.7282 (m-30) REVERT: B 452 ASN cc_start: 0.7808 (t0) cc_final: 0.7523 (t0) REVERT: C 343 GLN cc_start: 0.7201 (mt0) cc_final: 0.6797 (mt0) REVERT: C 406 ARG cc_start: 0.6474 (mtt180) cc_final: 0.5919 (mtm110) REVERT: C 419 ASN cc_start: 0.6742 (t0) cc_final: 0.6487 (m110) REVERT: C 626 ASP cc_start: 0.5436 (m-30) cc_final: 0.4800 (t70) REVERT: D 332 LYS cc_start: 0.6914 (ptmt) cc_final: 0.6630 (ptpt) REVERT: D 567 LYS cc_start: 0.7271 (pttm) cc_final: 0.6995 (tptp) REVERT: E 586 SER cc_start: 0.8230 (p) cc_final: 0.7906 (m) REVERT: F 444 LEU cc_start: 0.7193 (mt) cc_final: 0.6644 (mt) REVERT: F 518 MET cc_start: 0.7636 (tpp) cc_final: 0.7199 (tpt) REVERT: F 736 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7781 (tp) REVERT: H 32 GLN cc_start: 0.7928 (mm110) cc_final: 0.7642 (tp40) outliers start: 25 outliers final: 15 residues processed: 408 average time/residue: 0.2969 time to fit residues: 179.3999 Evaluate side-chains 250 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 234 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain E residue 430 GLN Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 440 ILE Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 710 ASN Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 119 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 164 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 HIS A 651 ASN B 430 GLN ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 GLN C 233 GLN C 430 GLN ** C 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 GLN C 651 ASN C 673 GLN C 700 GLN C 710 ASN D 624 HIS D 646 GLN D 651 ASN E 452 ASN E 585 GLN E 608 GLN F 321 GLN ** F 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 452 ASN F 646 GLN F 651 ASN ** F 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 700 GLN F 704 ASN F 735 ASN H 101 GLN ** L 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.133415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.114206 restraints weight = 26498.230| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.81 r_work: 0.3202 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17445 Z= 0.169 Angle : 0.638 11.004 23762 Z= 0.338 Chirality : 0.045 0.157 2471 Planarity : 0.005 0.052 3151 Dihedral : 6.864 80.921 2352 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.05 % Allowed : 6.78 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.16), residues: 2115 helix: -3.27 (0.44), residues: 82 sheet: -0.88 (0.19), residues: 593 loop : -0.81 (0.14), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 281 HIS 0.008 0.001 HIS F 290 PHE 0.017 0.002 PHE C 535 TYR 0.025 0.002 TYR D 484 ARG 0.006 0.001 ARG F 734 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 215) hydrogen bonds : angle 6.91829 ( 477) SS BOND : bond 0.00609 ( 2) SS BOND : angle 2.71034 ( 4) covalent geometry : bond 0.00391 (17443) covalent geometry : angle 0.63719 (23758) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 287 time to evaluate : 1.990 Fit side-chains REVERT: A 323 LYS cc_start: 0.6266 (mmtt) cc_final: 0.5872 (mptt) REVERT: A 552 ASN cc_start: 0.7756 (m-40) cc_final: 0.7151 (t0) REVERT: A 599 GLN cc_start: 0.8187 (tp40) cc_final: 0.7941 (tp40) REVERT: B 567 LYS cc_start: 0.5731 (mmtt) cc_final: 0.4945 (mptt) REVERT: C 244 THR cc_start: 0.7417 (m) cc_final: 0.7200 (m) REVERT: C 406 ARG cc_start: 0.6435 (mtt180) cc_final: 0.5439 (mtm110) REVERT: C 419 ASN cc_start: 0.7019 (t0) cc_final: 0.6485 (m110) REVERT: C 436 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7288 (ptp) REVERT: C 529 GLU cc_start: 0.7749 (tp30) cc_final: 0.7434 (tp30) REVERT: C 626 ASP cc_start: 0.5804 (m-30) cc_final: 0.5269 (t70) REVERT: D 567 LYS cc_start: 0.7183 (pttm) cc_final: 0.6618 (tptp) REVERT: D 640 MET cc_start: 0.8023 (mmt) cc_final: 0.7516 (mmt) REVERT: F 332 LYS cc_start: 0.6405 (mtmm) cc_final: 0.6178 (mtmm) REVERT: F 461 LEU cc_start: 0.8658 (mp) cc_final: 0.8420 (mt) REVERT: H 32 GLN cc_start: 0.8359 (mm110) cc_final: 0.7988 (tp40) outliers start: 38 outliers final: 22 residues processed: 310 average time/residue: 0.2968 time to fit residues: 137.5910 Evaluate side-chains 255 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 232 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 430 GLN Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 559 MET Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 88 optimal weight: 6.9990 chunk 108 optimal weight: 0.5980 chunk 205 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 156 optimal weight: 0.4980 chunk 36 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 31 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 155 optimal weight: 30.0000 chunk 70 optimal weight: 10.0000 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN C 430 GLN C 585 GLN E 585 GLN ** F 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 673 GLN ** L 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.132915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113590 restraints weight = 26487.951| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.81 r_work: 0.3199 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17445 Z= 0.155 Angle : 0.572 9.857 23762 Z= 0.300 Chirality : 0.043 0.145 2471 Planarity : 0.004 0.059 3151 Dihedral : 5.846 53.613 2331 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.58 % Allowed : 8.61 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.16), residues: 2115 helix: -2.91 (0.48), residues: 82 sheet: -0.75 (0.19), residues: 577 loop : -0.64 (0.14), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 281 HIS 0.008 0.001 HIS F 290 PHE 0.016 0.002 PHE C 535 TYR 0.022 0.002 TYR D 484 ARG 0.006 0.001 ARG C 734 Details of bonding type rmsd hydrogen bonds : bond 0.03041 ( 215) hydrogen bonds : angle 6.23359 ( 477) SS BOND : bond 0.00571 ( 2) SS BOND : angle 1.94143 ( 4) covalent geometry : bond 0.00362 (17443) covalent geometry : angle 0.57173 (23758) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 249 time to evaluate : 1.774 Fit side-chains REVERT: A 323 LYS cc_start: 0.6311 (mmtt) cc_final: 0.5965 (mptt) REVERT: A 552 ASN cc_start: 0.7730 (m-40) cc_final: 0.7100 (t0) REVERT: A 557 LYS cc_start: 0.7156 (mmtm) cc_final: 0.6909 (mmtp) REVERT: A 599 GLN cc_start: 0.8226 (tp40) cc_final: 0.7938 (tp40) REVERT: B 564 GLU cc_start: 0.5710 (tp30) cc_final: 0.5363 (mt-10) REVERT: C 244 THR cc_start: 0.7402 (m) cc_final: 0.7182 (m) REVERT: C 406 ARG cc_start: 0.6336 (mtt180) cc_final: 0.5365 (mtm110) REVERT: C 419 ASN cc_start: 0.7078 (t0) cc_final: 0.6492 (m110) REVERT: C 626 ASP cc_start: 0.5688 (m-30) cc_final: 0.5243 (t70) REVERT: D 567 LYS cc_start: 0.7239 (pttm) cc_final: 0.6688 (tptp) REVERT: E 607 TRP cc_start: 0.7566 (p90) cc_final: 0.7234 (p-90) REVERT: F 237 ASP cc_start: 0.7351 (p0) cc_final: 0.7130 (p0) REVERT: F 316 LYS cc_start: 0.7423 (mppt) cc_final: 0.6763 (mmtp) REVERT: H 32 GLN cc_start: 0.8443 (mm110) cc_final: 0.8123 (tp40) REVERT: L 80 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8302 (m) outliers start: 48 outliers final: 34 residues processed: 277 average time/residue: 0.2705 time to fit residues: 115.2850 Evaluate side-chains 263 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 228 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 559 MET Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain E residue 440 ILE Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 7 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 20 optimal weight: 30.0000 chunk 176 optimal weight: 3.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 HIS D 673 GLN E 585 GLN F 255 HIS F 292 HIS F 321 GLN ** F 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.111304 restraints weight = 26632.782| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.80 r_work: 0.3147 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 17445 Z= 0.239 Angle : 0.627 9.637 23762 Z= 0.329 Chirality : 0.046 0.157 2471 Planarity : 0.005 0.044 3151 Dihedral : 6.034 58.280 2330 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.55 % Allowed : 9.90 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.16), residues: 2115 helix: -3.10 (0.45), residues: 82 sheet: -0.83 (0.20), residues: 550 loop : -0.86 (0.14), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 281 HIS 0.009 0.002 HIS F 290 PHE 0.028 0.002 PHE A 501 TYR 0.024 0.002 TYR D 484 ARG 0.005 0.001 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 215) hydrogen bonds : angle 6.17618 ( 477) SS BOND : bond 0.00680 ( 2) SS BOND : angle 1.87533 ( 4) covalent geometry : bond 0.00563 (17443) covalent geometry : angle 0.62631 (23758) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 230 time to evaluate : 1.851 Fit side-chains REVERT: A 323 LYS cc_start: 0.6280 (mmtt) cc_final: 0.5860 (mptt) REVERT: A 552 ASN cc_start: 0.7733 (m-40) cc_final: 0.7195 (t0) REVERT: A 557 LYS cc_start: 0.7039 (mmtm) cc_final: 0.6810 (mmtp) REVERT: A 599 GLN cc_start: 0.8229 (tp40) cc_final: 0.7963 (tp40) REVERT: C 244 THR cc_start: 0.7363 (m) cc_final: 0.7102 (m) REVERT: C 406 ARG cc_start: 0.6502 (mtt180) cc_final: 0.5469 (mtm110) REVERT: C 419 ASN cc_start: 0.7082 (t0) cc_final: 0.6438 (m110) REVERT: C 626 ASP cc_start: 0.5824 (m-30) cc_final: 0.5279 (t70) REVERT: C 679 VAL cc_start: 0.7435 (t) cc_final: 0.7215 (m) REVERT: C 691 ASN cc_start: 0.7351 (m-40) cc_final: 0.7130 (p0) REVERT: D 567 LYS cc_start: 0.7404 (pttm) cc_final: 0.7061 (ptmt) REVERT: D 613 TYR cc_start: 0.6342 (m-80) cc_final: 0.5999 (m-80) REVERT: D 640 MET cc_start: 0.8054 (mmt) cc_final: 0.7809 (mmt) REVERT: F 316 LYS cc_start: 0.7496 (mppt) cc_final: 0.6820 (mmtp) REVERT: H 32 GLN cc_start: 0.8463 (mm110) cc_final: 0.8139 (tp40) outliers start: 66 outliers final: 50 residues processed: 272 average time/residue: 0.2616 time to fit residues: 110.7263 Evaluate side-chains 267 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 217 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 559 MET Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 690 GLU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain E residue 440 ILE Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain F residue 733 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 112 optimal weight: 8.9990 chunk 186 optimal weight: 0.0980 chunk 83 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 60 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 GLN C 452 ASN C 585 GLN E 585 GLN F 255 HIS ** F 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.130248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110849 restraints weight = 26802.914| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.82 r_work: 0.3157 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17445 Z= 0.195 Angle : 0.580 9.226 23762 Z= 0.303 Chirality : 0.044 0.155 2471 Planarity : 0.004 0.042 3151 Dihedral : 5.815 59.847 2330 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.12 % Allowed : 11.09 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.16), residues: 2115 helix: -3.12 (0.45), residues: 82 sheet: -0.84 (0.20), residues: 550 loop : -0.82 (0.15), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 281 HIS 0.018 0.001 HIS D 630 PHE 0.016 0.002 PHE C 535 TYR 0.022 0.002 TYR D 484 ARG 0.004 0.001 ARG F 734 Details of bonding type rmsd hydrogen bonds : bond 0.02963 ( 215) hydrogen bonds : angle 5.97131 ( 477) SS BOND : bond 0.00559 ( 2) SS BOND : angle 1.56381 ( 4) covalent geometry : bond 0.00463 (17443) covalent geometry : angle 0.57956 (23758) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 233 time to evaluate : 1.933 Fit side-chains REVERT: A 552 ASN cc_start: 0.7753 (m-40) cc_final: 0.7185 (t0) REVERT: A 599 GLN cc_start: 0.8206 (tp40) cc_final: 0.7933 (tp40) REVERT: C 244 THR cc_start: 0.7336 (m) cc_final: 0.7071 (m) REVERT: C 377 TYR cc_start: 0.7878 (t80) cc_final: 0.7614 (t80) REVERT: C 406 ARG cc_start: 0.6518 (mtt180) cc_final: 0.5489 (mtm110) REVERT: C 412 GLN cc_start: 0.8110 (pt0) cc_final: 0.7102 (pm20) REVERT: C 419 ASN cc_start: 0.7085 (t0) cc_final: 0.6449 (m110) REVERT: C 626 ASP cc_start: 0.5740 (m-30) cc_final: 0.5397 (t70) REVERT: C 679 VAL cc_start: 0.7377 (t) cc_final: 0.7165 (m) REVERT: C 691 ASN cc_start: 0.7408 (m-40) cc_final: 0.7108 (p0) REVERT: D 567 LYS cc_start: 0.7372 (pttm) cc_final: 0.6617 (tptp) REVERT: D 613 TYR cc_start: 0.6247 (m-80) cc_final: 0.5904 (m-80) REVERT: D 640 MET cc_start: 0.8059 (mmt) cc_final: 0.7572 (mmt) REVERT: F 316 LYS cc_start: 0.7404 (mppt) cc_final: 0.6776 (mmtp) REVERT: F 512 ASN cc_start: 0.7992 (t0) cc_final: 0.7443 (m-40) REVERT: H 32 GLN cc_start: 0.8448 (mm110) cc_final: 0.8126 (tp40) REVERT: H 106 ARG cc_start: 0.7721 (ptp-170) cc_final: 0.7390 (ptp90) outliers start: 58 outliers final: 48 residues processed: 270 average time/residue: 0.2717 time to fit residues: 113.6524 Evaluate side-chains 268 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 559 MET Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain E residue 440 ILE Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain F residue 733 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 170 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 157 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 156 optimal weight: 50.0000 chunk 82 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 chunk 121 optimal weight: 20.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 585 GLN F 255 HIS ** F 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.130503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.111111 restraints weight = 26835.256| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.81 r_work: 0.3161 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17445 Z= 0.187 Angle : 0.565 8.904 23762 Z= 0.295 Chirality : 0.044 0.156 2471 Planarity : 0.004 0.043 3151 Dihedral : 5.694 57.302 2330 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.82 % Allowed : 11.09 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.17), residues: 2115 helix: -2.96 (0.50), residues: 70 sheet: -0.86 (0.20), residues: 558 loop : -0.79 (0.15), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 281 HIS 0.007 0.001 HIS F 290 PHE 0.025 0.002 PHE A 501 TYR 0.018 0.002 TYR F 443 ARG 0.004 0.001 ARG F 296 Details of bonding type rmsd hydrogen bonds : bond 0.02932 ( 215) hydrogen bonds : angle 5.84457 ( 477) SS BOND : bond 0.00558 ( 2) SS BOND : angle 1.45669 ( 4) covalent geometry : bond 0.00443 (17443) covalent geometry : angle 0.56512 (23758) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 230 time to evaluate : 1.963 Fit side-chains revert: symmetry clash REVERT: A 384 ASP cc_start: 0.6887 (t70) cc_final: 0.6312 (m-30) REVERT: A 552 ASN cc_start: 0.7752 (m-40) cc_final: 0.7138 (t0) REVERT: A 599 GLN cc_start: 0.8206 (tp40) cc_final: 0.7934 (tp40) REVERT: C 244 THR cc_start: 0.7249 (m) cc_final: 0.7013 (m) REVERT: C 406 ARG cc_start: 0.6471 (mtt180) cc_final: 0.5487 (mtm110) REVERT: C 412 GLN cc_start: 0.8201 (pt0) cc_final: 0.7144 (pm20) REVERT: C 419 ASN cc_start: 0.7076 (t0) cc_final: 0.6411 (m110) REVERT: C 626 ASP cc_start: 0.5683 (m-30) cc_final: 0.5338 (t70) REVERT: C 691 ASN cc_start: 0.7348 (m-40) cc_final: 0.7023 (p0) REVERT: D 567 LYS cc_start: 0.7402 (pttm) cc_final: 0.7040 (ptmt) REVERT: D 611 ASP cc_start: 0.7290 (t0) cc_final: 0.5945 (m-30) REVERT: D 613 TYR cc_start: 0.6181 (m-80) cc_final: 0.5822 (m-80) REVERT: D 640 MET cc_start: 0.8120 (mmt) cc_final: 0.7614 (mmt) REVERT: F 512 ASN cc_start: 0.7962 (t0) cc_final: 0.7480 (m-40) REVERT: H 32 GLN cc_start: 0.8449 (mm110) cc_final: 0.8148 (tp40) outliers start: 71 outliers final: 61 residues processed: 275 average time/residue: 0.2703 time to fit residues: 115.4839 Evaluate side-chains 280 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 219 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 559 MET Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 690 GLU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain E residue 420 VAL Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 440 ILE Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain F residue 733 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 87 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 165 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 ASN C 585 GLN D 254 ASN F 255 HIS ** F 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.129866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.110691 restraints weight = 26630.027| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.79 r_work: 0.3138 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 17445 Z= 0.239 Angle : 0.607 9.009 23762 Z= 0.318 Chirality : 0.045 0.145 2471 Planarity : 0.005 0.042 3151 Dihedral : 5.827 56.574 2330 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.25 % Allowed : 11.52 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.17), residues: 2115 helix: -3.14 (0.47), residues: 70 sheet: -0.98 (0.21), residues: 550 loop : -0.89 (0.15), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 509 HIS 0.007 0.001 HIS F 290 PHE 0.016 0.002 PHE C 535 TYR 0.020 0.002 TYR F 443 ARG 0.008 0.001 ARG F 300 Details of bonding type rmsd hydrogen bonds : bond 0.03153 ( 215) hydrogen bonds : angle 5.97034 ( 477) SS BOND : bond 0.00593 ( 2) SS BOND : angle 1.47449 ( 4) covalent geometry : bond 0.00568 (17443) covalent geometry : angle 0.60698 (23758) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 217 time to evaluate : 1.821 Fit side-chains REVERT: A 384 ASP cc_start: 0.6845 (t70) cc_final: 0.6199 (m-30) REVERT: A 552 ASN cc_start: 0.7687 (m-40) cc_final: 0.7167 (t0) REVERT: A 599 GLN cc_start: 0.8179 (tp40) cc_final: 0.7896 (tp40) REVERT: C 406 ARG cc_start: 0.6493 (mtt180) cc_final: 0.5520 (mtm110) REVERT: C 412 GLN cc_start: 0.8158 (pt0) cc_final: 0.7153 (pm20) REVERT: C 419 ASN cc_start: 0.7106 (t0) cc_final: 0.6422 (m110) REVERT: C 457 ASN cc_start: 0.7668 (m-40) cc_final: 0.7375 (m110) REVERT: C 626 ASP cc_start: 0.5700 (m-30) cc_final: 0.5315 (t70) REVERT: C 691 ASN cc_start: 0.7290 (m-40) cc_final: 0.6992 (p0) REVERT: D 567 LYS cc_start: 0.7490 (pttm) cc_final: 0.7075 (ptmt) REVERT: D 611 ASP cc_start: 0.7304 (t0) cc_final: 0.5950 (m-30) REVERT: D 613 TYR cc_start: 0.6187 (m-80) cc_final: 0.5859 (m-80) REVERT: D 640 MET cc_start: 0.8056 (mmt) cc_final: 0.7508 (mmt) REVERT: E 485 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.5580 (ttp-170) REVERT: F 316 LYS cc_start: 0.7486 (mppt) cc_final: 0.6921 (mmtp) REVERT: F 512 ASN cc_start: 0.8006 (t0) cc_final: 0.7505 (m-40) REVERT: H 32 GLN cc_start: 0.8439 (mm110) cc_final: 0.8111 (tp40) outliers start: 79 outliers final: 66 residues processed: 269 average time/residue: 0.2695 time to fit residues: 111.9814 Evaluate side-chains 281 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 214 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 559 MET Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 690 GLU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain E residue 420 VAL Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 440 ILE Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain F residue 733 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 147 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 180 optimal weight: 8.9990 chunk 203 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 585 GLN E 430 GLN E 585 GLN F 255 HIS ** F 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.130091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.111196 restraints weight = 26619.155| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.77 r_work: 0.3145 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17445 Z= 0.187 Angle : 0.566 8.835 23762 Z= 0.296 Chirality : 0.044 0.141 2471 Planarity : 0.004 0.041 3151 Dihedral : 5.653 55.683 2330 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.82 % Allowed : 12.11 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.17), residues: 2115 helix: -3.09 (0.48), residues: 70 sheet: -0.99 (0.21), residues: 544 loop : -0.83 (0.15), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 509 HIS 0.007 0.001 HIS F 290 PHE 0.020 0.002 PHE D 662 TYR 0.023 0.002 TYR D 484 ARG 0.006 0.001 ARG F 300 Details of bonding type rmsd hydrogen bonds : bond 0.02937 ( 215) hydrogen bonds : angle 5.84347 ( 477) SS BOND : bond 0.00529 ( 2) SS BOND : angle 1.36257 ( 4) covalent geometry : bond 0.00443 (17443) covalent geometry : angle 0.56613 (23758) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 225 time to evaluate : 1.897 Fit side-chains REVERT: A 384 ASP cc_start: 0.6805 (t70) cc_final: 0.6173 (m-30) REVERT: A 552 ASN cc_start: 0.7732 (m-40) cc_final: 0.7188 (t0) REVERT: A 599 GLN cc_start: 0.8179 (tp40) cc_final: 0.7886 (tp40) REVERT: C 258 LYS cc_start: 0.7286 (mtmt) cc_final: 0.7059 (mmtp) REVERT: C 406 ARG cc_start: 0.6466 (mtt180) cc_final: 0.5509 (mtm110) REVERT: C 412 GLN cc_start: 0.8195 (pt0) cc_final: 0.7158 (pm20) REVERT: C 419 ASN cc_start: 0.7087 (t0) cc_final: 0.6409 (m110) REVERT: C 457 ASN cc_start: 0.7659 (m-40) cc_final: 0.7373 (m110) REVERT: C 626 ASP cc_start: 0.5774 (m-30) cc_final: 0.5405 (t70) REVERT: C 691 ASN cc_start: 0.7294 (m-40) cc_final: 0.7000 (p0) REVERT: D 567 LYS cc_start: 0.7430 (pttm) cc_final: 0.6724 (tptp) REVERT: D 611 ASP cc_start: 0.7236 (t0) cc_final: 0.5801 (m-30) REVERT: D 613 TYR cc_start: 0.6159 (m-80) cc_final: 0.5810 (m-80) REVERT: D 640 MET cc_start: 0.8055 (mmt) cc_final: 0.7496 (mmt) REVERT: E 485 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.5573 (ttp-170) REVERT: F 316 LYS cc_start: 0.7360 (mppt) cc_final: 0.6809 (mmtp) REVERT: F 512 ASN cc_start: 0.7961 (t0) cc_final: 0.7482 (m-40) REVERT: H 32 GLN cc_start: 0.8438 (mm110) cc_final: 0.8107 (tp40) outliers start: 71 outliers final: 65 residues processed: 270 average time/residue: 0.2671 time to fit residues: 111.2475 Evaluate side-chains 279 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 213 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 559 MET Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 690 GLU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain E residue 420 VAL Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 440 ILE Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain F residue 733 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 15 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 129 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN E 585 GLN F 255 HIS ** F 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.130077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.111144 restraints weight = 26739.090| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.79 r_work: 0.3146 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17445 Z= 0.182 Angle : 0.566 8.816 23762 Z= 0.295 Chirality : 0.043 0.139 2471 Planarity : 0.004 0.041 3151 Dihedral : 5.604 55.482 2330 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.88 % Allowed : 12.38 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.17), residues: 2115 helix: -3.05 (0.49), residues: 70 sheet: -0.98 (0.21), residues: 544 loop : -0.82 (0.15), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 509 HIS 0.007 0.001 HIS F 290 PHE 0.020 0.002 PHE D 662 TYR 0.018 0.002 TYR F 443 ARG 0.004 0.001 ARG D 550 Details of bonding type rmsd hydrogen bonds : bond 0.02900 ( 215) hydrogen bonds : angle 5.79753 ( 477) SS BOND : bond 0.00525 ( 2) SS BOND : angle 1.34727 ( 4) covalent geometry : bond 0.00431 (17443) covalent geometry : angle 0.56570 (23758) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 224 time to evaluate : 1.911 Fit side-chains REVERT: A 384 ASP cc_start: 0.6849 (t70) cc_final: 0.6230 (m-30) REVERT: A 552 ASN cc_start: 0.7764 (m-40) cc_final: 0.7164 (t0) REVERT: A 599 GLN cc_start: 0.8169 (tp40) cc_final: 0.7890 (tp40) REVERT: C 258 LYS cc_start: 0.7259 (mtmt) cc_final: 0.7034 (mmtp) REVERT: C 406 ARG cc_start: 0.6461 (mtt180) cc_final: 0.5496 (mtm110) REVERT: C 412 GLN cc_start: 0.8190 (pt0) cc_final: 0.7147 (pm20) REVERT: C 419 ASN cc_start: 0.7098 (t0) cc_final: 0.6415 (m110) REVERT: C 457 ASN cc_start: 0.7659 (m-40) cc_final: 0.7370 (m110) REVERT: C 698 GLU cc_start: 0.7764 (mm-30) cc_final: 0.6931 (mm-30) REVERT: D 567 LYS cc_start: 0.7429 (pttm) cc_final: 0.6720 (tptp) REVERT: D 611 ASP cc_start: 0.7089 (t0) cc_final: 0.5737 (m-30) REVERT: D 613 TYR cc_start: 0.6111 (m-80) cc_final: 0.5763 (m-80) REVERT: D 640 MET cc_start: 0.8047 (mmt) cc_final: 0.7560 (mmt) REVERT: E 485 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.5512 (ttp-170) REVERT: F 512 ASN cc_start: 0.7968 (t0) cc_final: 0.7475 (m-40) REVERT: H 32 GLN cc_start: 0.8448 (mm110) cc_final: 0.8133 (tp40) outliers start: 72 outliers final: 68 residues processed: 271 average time/residue: 0.2717 time to fit residues: 113.4628 Evaluate side-chains 285 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 216 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 559 MET Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 690 GLU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain E residue 420 VAL Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 440 ILE Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain F residue 733 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 41 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 161 optimal weight: 9.9990 chunk 183 optimal weight: 20.0000 chunk 184 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN E 585 GLN F 255 HIS ** F 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.130123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.110831 restraints weight = 26764.962| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.81 r_work: 0.3153 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17445 Z= 0.187 Angle : 0.570 9.011 23762 Z= 0.296 Chirality : 0.044 0.142 2471 Planarity : 0.004 0.041 3151 Dihedral : 5.608 55.660 2330 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.77 % Allowed : 12.86 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.17), residues: 2115 helix: -3.06 (0.49), residues: 70 sheet: -1.02 (0.21), residues: 547 loop : -0.83 (0.15), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 509 HIS 0.007 0.001 HIS F 290 PHE 0.026 0.002 PHE A 501 TYR 0.018 0.002 TYR F 443 ARG 0.004 0.001 ARG D 550 Details of bonding type rmsd hydrogen bonds : bond 0.02906 ( 215) hydrogen bonds : angle 5.80393 ( 477) SS BOND : bond 0.00517 ( 2) SS BOND : angle 1.34243 ( 4) covalent geometry : bond 0.00444 (17443) covalent geometry : angle 0.56931 (23758) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 217 time to evaluate : 1.828 Fit side-chains REVERT: A 384 ASP cc_start: 0.6885 (t70) cc_final: 0.6262 (m-30) REVERT: A 552 ASN cc_start: 0.7768 (m-40) cc_final: 0.7165 (t0) REVERT: A 599 GLN cc_start: 0.8144 (tp40) cc_final: 0.7875 (tp40) REVERT: C 258 LYS cc_start: 0.7278 (mtmt) cc_final: 0.7057 (mmtp) REVERT: C 406 ARG cc_start: 0.6468 (mtt180) cc_final: 0.5505 (mtm110) REVERT: C 412 GLN cc_start: 0.8192 (pt0) cc_final: 0.7144 (pm20) REVERT: C 419 ASN cc_start: 0.7097 (t0) cc_final: 0.6420 (m110) REVERT: C 457 ASN cc_start: 0.7661 (m-40) cc_final: 0.7352 (m110) REVERT: C 698 GLU cc_start: 0.7757 (mm-30) cc_final: 0.6975 (mm-30) REVERT: D 567 LYS cc_start: 0.7446 (pttm) cc_final: 0.6726 (tptp) REVERT: D 611 ASP cc_start: 0.7166 (t0) cc_final: 0.5809 (m-30) REVERT: D 613 TYR cc_start: 0.6114 (m-80) cc_final: 0.5782 (m-80) REVERT: D 640 MET cc_start: 0.8067 (mmt) cc_final: 0.7538 (mmt) REVERT: E 485 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.5519 (ttp-170) REVERT: F 444 LEU cc_start: 0.7295 (mt) cc_final: 0.6581 (mp) REVERT: F 512 ASN cc_start: 0.7845 (t0) cc_final: 0.7491 (m-40) REVERT: H 32 GLN cc_start: 0.8458 (mm110) cc_final: 0.8150 (tp40) outliers start: 70 outliers final: 64 residues processed: 262 average time/residue: 0.2678 time to fit residues: 108.0586 Evaluate side-chains 275 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 210 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 690 GLU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain E residue 420 VAL Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 440 ILE Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain F residue 733 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 128 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 175 optimal weight: 1.9990 chunk 123 optimal weight: 20.0000 chunk 170 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 70 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 HIS C 497 ASN C 735 ASN E 585 GLN F 255 HIS ** F 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.132864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113859 restraints weight = 26454.877| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.78 r_work: 0.3184 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17445 Z= 0.105 Angle : 0.512 8.339 23762 Z= 0.264 Chirality : 0.042 0.139 2471 Planarity : 0.004 0.037 3151 Dihedral : 5.243 57.879 2330 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.26 % Allowed : 14.42 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.17), residues: 2115 helix: -3.00 (0.57), residues: 58 sheet: -0.86 (0.21), residues: 521 loop : -0.66 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 509 HIS 0.004 0.001 HIS F 290 PHE 0.026 0.001 PHE A 501 TYR 0.017 0.001 TYR D 484 ARG 0.005 0.000 ARG D 550 Details of bonding type rmsd hydrogen bonds : bond 0.02491 ( 215) hydrogen bonds : angle 5.46052 ( 477) SS BOND : bond 0.00403 ( 2) SS BOND : angle 1.09432 ( 4) covalent geometry : bond 0.00247 (17443) covalent geometry : angle 0.51143 (23758) =============================================================================== Job complete usr+sys time: 8207.76 seconds wall clock time: 142 minutes 56.31 seconds (8576.31 seconds total)