Starting phenix.real_space_refine on Thu Sep 18 12:03:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7w_44326/09_2025/9b7w_44326.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7w_44326/09_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_44326/09_2025/9b7w_44326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7w_44326/09_2025/9b7w_44326.map" model { file = "/net/cci-nas-00/data/ceres_data/9b7w_44326/09_2025/9b7w_44326.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7w_44326/09_2025/9b7w_44326.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.34, per 1000 atoms: 0.20 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: 1.26 Conformation dependent library (CDL) restraints added in 786.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.39 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: 2.16 Time building geometry restraints manager: 1.78 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.960 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.290 ------------------------------------------------------------------------------- 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 : 16.48 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.016 0.002 ARG F 734 TYR 0.032 0.003 TYR C 443 PHE 0.038 0.003 PHE F 367 TRP 0.035 0.004 TRP C 281 HIS 0.016 0.003 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00899 (17443) covalent geometry : angle 1.02714 (23758) SS BOND : bond 0.00544 ( 2) SS BOND : angle 0.82768 ( 4) hydrogen bonds : bond 0.23783 ( 215) hydrogen bonds : angle 9.86666 ( 477) *********************** 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 : 0.491 Fit side-chains revert: symmetry clash REVERT: A 323 LYS cc_start: 0.6562 (mmtt) cc_final: 0.6253 (mptt) REVERT: A 552 ASN cc_start: 0.7790 (m-40) cc_final: 0.7261 (t0) REVERT: A 599 GLN cc_start: 0.8067 (tp40) cc_final: 0.7793 (tp40) REVERT: A 626 ASP cc_start: 0.7631 (m-30) cc_final: 0.7283 (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: 0.6803 (mt0) REVERT: C 406 ARG cc_start: 0.6474 (mtt180) cc_final: 0.5921 (mtm110) REVERT: C 419 ASN cc_start: 0.6742 (t0) cc_final: 0.6488 (m110) REVERT: C 626 ASP cc_start: 0.5436 (m-30) cc_final: 0.4799 (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: 0.6996 (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: 0.6643 (mt) REVERT: F 518 MET cc_start: 0.7636 (tpp) cc_final: 0.7200 (tpt) REVERT: F 736 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7783 (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: 0.1244 time to fit residues: 76.0743 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 : 0.450 ------------------------------------------------------------------------------- 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 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- 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 710 ASN D 646 GLN D 651 ASN E 452 ASN E 585 GLN E 608 GLN ** F 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 452 ASN F 646 GLN F 651 ASN F 673 GLN F 700 GLN F 704 ASN F 735 ASN H 101 GLN L 82 ASN L 101 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.135456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.116137 restraints weight = 26386.872| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.82 r_work: 0.3217 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17445 Z= 0.134 Angle : 0.610 10.879 23762 Z= 0.321 Chirality : 0.044 0.156 2471 Planarity : 0.004 0.049 3151 Dihedral : 6.645 79.906 2352 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.83 % Allowed : 6.67 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.16), residues: 2115 helix: -3.17 (0.44), residues: 82 sheet: -0.76 (0.19), residues: 597 loop : -0.69 (0.14), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 485 TYR 0.023 0.002 TYR D 484 PHE 0.016 0.002 PHE C 535 TRP 0.016 0.001 TRP C 306 HIS 0.006 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00303 (17443) covalent geometry : angle 0.60909 (23758) SS BOND : bond 0.01207 ( 2) SS BOND : angle 2.82627 ( 4) hydrogen bonds : bond 0.03209 ( 215) hydrogen bonds : angle 6.72522 ( 477) *********************** 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 337 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 303 time to evaluate : 0.658 Fit side-chains REVERT: A 323 LYS cc_start: 0.6228 (mmtt) cc_final: 0.5935 (mptt) REVERT: A 552 ASN cc_start: 0.7780 (m-40) cc_final: 0.7168 (t0) REVERT: A 599 GLN cc_start: 0.8131 (tp40) cc_final: 0.7860 (tp40) REVERT: B 567 LYS cc_start: 0.5665 (mmtt) cc_final: 0.4903 (mptt) REVERT: C 244 THR cc_start: 0.7396 (m) cc_final: 0.7194 (m) REVERT: C 406 ARG cc_start: 0.6420 (mtt180) cc_final: 0.5420 (mtm110) REVERT: C 419 ASN cc_start: 0.7003 (t0) cc_final: 0.6493 (m110) REVERT: C 529 GLU cc_start: 0.7668 (tp30) cc_final: 0.7386 (tp30) REVERT: C 626 ASP cc_start: 0.5742 (m-30) cc_final: 0.5245 (t70) REVERT: D 567 LYS cc_start: 0.7156 (pttm) cc_final: 0.6605 (tptp) REVERT: D 640 MET cc_start: 0.7916 (mmt) cc_final: 0.7468 (mmt) REVERT: E 607 TRP cc_start: 0.7533 (p90) cc_final: 0.7303 (p-90) REVERT: F 316 LYS cc_start: 0.7332 (mppt) cc_final: 0.6707 (mmtp) REVERT: F 332 LYS cc_start: 0.6371 (mtmm) cc_final: 0.6136 (mtmm) REVERT: F 461 LEU cc_start: 0.8601 (mp) cc_final: 0.8368 (mt) REVERT: H 31 VAL cc_start: 0.8988 (p) cc_final: 0.8775 (t) REVERT: H 32 GLN cc_start: 0.8353 (mm110) cc_final: 0.8011 (tp40) outliers start: 34 outliers final: 19 residues processed: 323 average time/residue: 0.1251 time to fit residues: 60.9505 Evaluate side-chains 258 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 239 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 559 MET Chi-restraints excluded: chain C residue 574 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 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 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 195 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 205 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 79 optimal weight: 0.0670 chunk 74 optimal weight: 8.9990 chunk 37 optimal weight: 0.0020 chunk 200 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 overall best weight: 2.2132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 646 GLN ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 HIS C 304 ASN C 343 GLN C 430 GLN C 497 ASN C 585 GLN E 585 GLN F 255 HIS ** F 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 735 ASN H 101 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.134757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115608 restraints weight = 26609.619| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.82 r_work: 0.3215 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17445 Z= 0.116 Angle : 0.539 9.486 23762 Z= 0.282 Chirality : 0.042 0.146 2471 Planarity : 0.004 0.042 3151 Dihedral : 5.536 54.704 2330 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.21 % Allowed : 8.72 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.16), residues: 2115 helix: -3.11 (0.44), residues: 94 sheet: -0.59 (0.19), residues: 568 loop : -0.46 (0.15), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 300 TYR 0.020 0.001 TYR D 484 PHE 0.015 0.001 PHE C 535 TRP 0.012 0.001 TRP C 281 HIS 0.005 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00267 (17443) covalent geometry : angle 0.53887 (23758) SS BOND : bond 0.00258 ( 2) SS BOND : angle 1.96115 ( 4) hydrogen bonds : bond 0.02766 ( 215) hydrogen bonds : angle 5.99453 ( 477) *********************** 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 303 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 262 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 323 LYS cc_start: 0.6024 (mmtt) cc_final: 0.5821 (mptt) REVERT: A 552 ASN cc_start: 0.7727 (m-40) cc_final: 0.7107 (t0) REVERT: A 599 GLN cc_start: 0.8163 (tp40) cc_final: 0.7863 (tp40) REVERT: A 647 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7365 (pt) REVERT: B 564 GLU cc_start: 0.5681 (tp30) cc_final: 0.5257 (mt-10) REVERT: C 244 THR cc_start: 0.7383 (m) cc_final: 0.7119 (m) REVERT: C 406 ARG cc_start: 0.6319 (mtt180) cc_final: 0.5380 (mtm110) REVERT: C 419 ASN cc_start: 0.7118 (t0) cc_final: 0.6501 (m110) REVERT: C 679 VAL cc_start: 0.7476 (t) cc_final: 0.7246 (m) REVERT: D 567 LYS cc_start: 0.7238 (pttm) cc_final: 0.6655 (tptp) REVERT: E 607 TRP cc_start: 0.7517 (p90) cc_final: 0.7232 (p-90) REVERT: F 237 ASP cc_start: 0.7335 (p0) cc_final: 0.7113 (p0) REVERT: F 316 LYS cc_start: 0.7265 (mppt) cc_final: 0.6694 (mmtp) REVERT: F 332 LYS cc_start: 0.6415 (mtmm) cc_final: 0.6194 (mtmm) REVERT: F 461 LEU cc_start: 0.8523 (mp) cc_final: 0.8323 (mt) REVERT: H 32 GLN cc_start: 0.8424 (mm110) cc_final: 0.8025 (tp40) outliers start: 41 outliers final: 30 residues processed: 287 average time/residue: 0.1240 time to fit residues: 54.5924 Evaluate side-chains 267 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 236 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 647 ILE 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 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 42 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 143 optimal weight: 30.0000 chunk 207 optimal weight: 20.0000 chunk 190 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 204 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 19 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 ASN C 700 GLN D 673 GLN E 585 GLN F 255 HIS F 292 HIS F 428 HIS ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.130581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.111306 restraints weight = 26870.905| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.82 r_work: 0.3164 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 17445 Z= 0.245 Angle : 0.621 9.451 23762 Z= 0.325 Chirality : 0.046 0.155 2471 Planarity : 0.005 0.043 3151 Dihedral : 5.893 57.068 2330 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.23 % Allowed : 10.06 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.16), residues: 2115 helix: -2.98 (0.46), residues: 82 sheet: -0.71 (0.20), residues: 576 loop : -0.73 (0.15), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 485 TYR 0.023 0.002 TYR D 484 PHE 0.032 0.002 PHE A 501 TRP 0.020 0.002 TRP C 281 HIS 0.010 0.002 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00579 (17443) covalent geometry : angle 0.62043 (23758) SS BOND : bond 0.00697 ( 2) SS BOND : angle 1.86288 ( 4) hydrogen bonds : bond 0.03208 ( 215) hydrogen bonds : angle 6.07522 ( 477) *********************** 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 299 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 239 time to evaluate : 0.627 Fit side-chains REVERT: A 323 LYS cc_start: 0.6299 (mmtt) cc_final: 0.5890 (mptt) REVERT: A 488 ARG cc_start: 0.6906 (ttp-170) cc_final: 0.6625 (ttp-170) REVERT: A 489 VAL cc_start: 0.6830 (p) cc_final: 0.6354 (t) REVERT: A 552 ASN cc_start: 0.7799 (m-40) cc_final: 0.7247 (t0) REVERT: A 599 GLN cc_start: 0.8204 (tp40) cc_final: 0.7930 (tp40) REVERT: C 244 THR cc_start: 0.7334 (m) cc_final: 0.7050 (m) REVERT: C 406 ARG cc_start: 0.6394 (mtt180) cc_final: 0.5407 (mtm110) REVERT: C 419 ASN cc_start: 0.7038 (t0) cc_final: 0.6456 (m110) REVERT: D 567 LYS cc_start: 0.7348 (pttm) cc_final: 0.7053 (ptmt) REVERT: D 613 TYR cc_start: 0.6227 (m-80) cc_final: 0.5802 (m-80) REVERT: D 640 MET cc_start: 0.8122 (mmt) cc_final: 0.7618 (mmt) REVERT: F 237 ASP cc_start: 0.7491 (p0) cc_final: 0.7191 (p0) REVERT: F 316 LYS cc_start: 0.7447 (mppt) cc_final: 0.6792 (mmtp) REVERT: F 461 LEU cc_start: 0.8633 (mp) cc_final: 0.8419 (mt) REVERT: H 32 GLN cc_start: 0.8483 (mm110) cc_final: 0.8162 (tp40) REVERT: H 106 ARG cc_start: 0.7637 (mtt180) cc_final: 0.7374 (ptp90) outliers start: 60 outliers final: 45 residues processed: 277 average time/residue: 0.1167 time to fit residues: 50.4368 Evaluate side-chains 267 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 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 341 THR 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 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 344 VAL Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 110 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 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 181 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 174 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 chunk 78 optimal weight: 0.9990 chunk 146 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 189 optimal weight: 20.0000 chunk 161 optimal weight: 9.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 GLN A 519 ASN ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN C 585 GLN E 585 GLN F 255 HIS ** 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 = 0.3559 r_free = 0.3559 target = 0.133141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113946 restraints weight = 26454.155| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.81 r_work: 0.3191 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17445 Z= 0.129 Angle : 0.524 9.398 23762 Z= 0.273 Chirality : 0.042 0.145 2471 Planarity : 0.004 0.045 3151 Dihedral : 5.485 59.747 2330 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.69 % Allowed : 11.46 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.17), residues: 2115 helix: -2.86 (0.49), residues: 82 sheet: -0.60 (0.21), residues: 553 loop : -0.60 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 550 TYR 0.021 0.001 TYR D 484 PHE 0.014 0.001 PHE C 535 TRP 0.012 0.001 TRP C 281 HIS 0.006 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00303 (17443) covalent geometry : angle 0.52403 (23758) SS BOND : bond 0.00523 ( 2) SS BOND : angle 1.48256 ( 4) hydrogen bonds : bond 0.02652 ( 215) hydrogen bonds : angle 5.65775 ( 477) *********************** 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 298 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 248 time to evaluate : 0.648 Fit side-chains REVERT: A 323 LYS cc_start: 0.6140 (mmtt) cc_final: 0.5922 (mptt) REVERT: A 384 ASP cc_start: 0.6995 (t70) cc_final: 0.6360 (m-30) REVERT: A 489 VAL cc_start: 0.6859 (p) cc_final: 0.6431 (t) REVERT: A 552 ASN cc_start: 0.7772 (m-40) cc_final: 0.7112 (t0) REVERT: A 599 GLN cc_start: 0.8174 (tp40) cc_final: 0.7886 (tp40) REVERT: C 406 ARG cc_start: 0.6390 (mtt180) cc_final: 0.5409 (mtm110) REVERT: C 412 GLN cc_start: 0.8082 (pt0) cc_final: 0.7064 (pm20) REVERT: C 419 ASN cc_start: 0.7052 (t0) cc_final: 0.6468 (m110) REVERT: C 691 ASN cc_start: 0.7468 (m-40) cc_final: 0.7168 (p0) REVERT: D 567 LYS cc_start: 0.7329 (pttm) cc_final: 0.6573 (tptp) REVERT: D 611 ASP cc_start: 0.7105 (t0) cc_final: 0.6009 (m-30) REVERT: D 613 TYR cc_start: 0.6210 (m-80) cc_final: 0.5767 (m-80) REVERT: D 640 MET cc_start: 0.8037 (mmt) cc_final: 0.7550 (mmt) REVERT: E 607 TRP cc_start: 0.7578 (p90) cc_final: 0.7253 (p-90) REVERT: F 237 ASP cc_start: 0.7461 (p0) cc_final: 0.7165 (p0) REVERT: F 316 LYS cc_start: 0.7356 (mppt) cc_final: 0.6741 (mmtp) REVERT: F 461 LEU cc_start: 0.8485 (mp) cc_final: 0.8261 (mt) REVERT: F 512 ASN cc_start: 0.7889 (t0) cc_final: 0.7246 (m-40) REVERT: H 32 GLN cc_start: 0.8461 (mm110) cc_final: 0.8146 (tp40) outliers start: 50 outliers final: 40 residues processed: 276 average time/residue: 0.1140 time to fit residues: 48.6537 Evaluate side-chains 272 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 574 THR 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 574 THR Chi-restraints excluded: chain C residue 679 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 430 GLN 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 344 VAL Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain H residue 24 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 32 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 204 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 141 optimal weight: 20.0000 chunk 208 optimal weight: 0.9990 chunk 179 optimal weight: 0.0050 chunk 107 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 overall best weight: 5.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN C 585 GLN E 585 GLN F 255 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.130607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.111801 restraints weight = 26589.976| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.79 r_work: 0.3165 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17445 Z= 0.195 Angle : 0.570 8.564 23762 Z= 0.298 Chirality : 0.044 0.152 2471 Planarity : 0.004 0.053 3151 Dihedral : 5.638 56.837 2330 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.18 % Allowed : 11.95 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.17), residues: 2115 helix: -3.04 (0.47), residues: 82 sheet: -0.66 (0.21), residues: 556 loop : -0.71 (0.15), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 296 TYR 0.019 0.002 TYR F 443 PHE 0.016 0.002 PHE C 535 TRP 0.016 0.002 TRP C 281 HIS 0.008 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00461 (17443) covalent geometry : angle 0.56990 (23758) SS BOND : bond 0.00595 ( 2) SS BOND : angle 1.56712 ( 4) hydrogen bonds : bond 0.02942 ( 215) hydrogen bonds : angle 5.77034 ( 477) *********************** 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 295 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 236 time to evaluate : 0.661 Fit side-chains REVERT: A 384 ASP cc_start: 0.7101 (t70) cc_final: 0.6494 (m-30) REVERT: A 489 VAL cc_start: 0.6935 (p) cc_final: 0.6488 (t) REVERT: A 552 ASN cc_start: 0.7793 (m-40) cc_final: 0.7212 (t0) REVERT: A 599 GLN cc_start: 0.8225 (tp40) cc_final: 0.7932 (tp40) REVERT: C 377 TYR cc_start: 0.7799 (t80) cc_final: 0.7427 (t80) REVERT: C 406 ARG cc_start: 0.6360 (mtt180) cc_final: 0.5376 (mtm110) REVERT: C 412 GLN cc_start: 0.8121 (pt0) cc_final: 0.7115 (pm20) REVERT: C 419 ASN cc_start: 0.7050 (t0) cc_final: 0.6441 (m110) REVERT: C 691 ASN cc_start: 0.7455 (m-40) cc_final: 0.7137 (p0) REVERT: D 567 LYS cc_start: 0.7368 (pttm) cc_final: 0.7033 (ptmt) REVERT: D 611 ASP cc_start: 0.7044 (t0) cc_final: 0.5785 (m-30) REVERT: D 613 TYR cc_start: 0.6150 (m-80) cc_final: 0.5768 (m-80) REVERT: D 640 MET cc_start: 0.8083 (mmt) cc_final: 0.7538 (mmt) REVERT: F 237 ASP cc_start: 0.7508 (p0) cc_final: 0.7148 (p0) REVERT: F 316 LYS cc_start: 0.7380 (mppt) cc_final: 0.6747 (mmtp) REVERT: F 461 LEU cc_start: 0.8566 (mp) cc_final: 0.8333 (mt) REVERT: F 512 ASN cc_start: 0.7966 (t0) cc_final: 0.7377 (m-40) REVERT: H 32 GLN cc_start: 0.8488 (mm110) cc_final: 0.8175 (tp40) outliers start: 59 outliers final: 49 residues processed: 273 average time/residue: 0.1211 time to fit residues: 51.4028 Evaluate side-chains 275 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 226 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 519 ASN Chi-restraints excluded: chain A residue 557 LYS 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 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 679 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 432 LEU 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 241 THR 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 622 ILE Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 729 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 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 8 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 135 optimal weight: 20.0000 chunk 205 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 C 452 ASN E 430 GLN E 585 GLN F 255 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.131011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.111783 restraints weight = 26541.712| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.80 r_work: 0.3158 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 17445 Z= 0.193 Angle : 0.568 8.371 23762 Z= 0.296 Chirality : 0.044 0.143 2471 Planarity : 0.004 0.047 3151 Dihedral : 5.625 59.446 2330 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.50 % Allowed : 11.89 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.17), residues: 2115 helix: -3.06 (0.47), residues: 82 sheet: -0.74 (0.21), residues: 548 loop : -0.77 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 300 TYR 0.018 0.002 TYR F 443 PHE 0.029 0.002 PHE A 501 TRP 0.017 0.002 TRP F 509 HIS 0.007 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00457 (17443) covalent geometry : angle 0.56760 (23758) SS BOND : bond 0.00560 ( 2) SS BOND : angle 1.47935 ( 4) hydrogen bonds : bond 0.02922 ( 215) hydrogen bonds : angle 5.76921 ( 477) *********************** 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 294 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 229 time to evaluate : 0.707 Fit side-chains REVERT: A 384 ASP cc_start: 0.7221 (t70) cc_final: 0.6586 (m-30) REVERT: A 489 VAL cc_start: 0.6904 (p) cc_final: 0.6451 (t) REVERT: A 552 ASN cc_start: 0.7766 (m-40) cc_final: 0.7116 (t0) REVERT: A 599 GLN cc_start: 0.8197 (tp40) cc_final: 0.7927 (tp40) REVERT: A 647 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7318 (pt) REVERT: C 406 ARG cc_start: 0.6361 (mtt180) cc_final: 0.5505 (mtm110) REVERT: C 412 GLN cc_start: 0.8182 (pt0) cc_final: 0.7160 (pm20) REVERT: C 419 ASN cc_start: 0.7087 (t0) cc_final: 0.6456 (m110) REVERT: C 691 ASN cc_start: 0.7331 (m-40) cc_final: 0.7031 (p0) REVERT: D 567 LYS cc_start: 0.7459 (pttm) cc_final: 0.7033 (ptmt) REVERT: D 611 ASP cc_start: 0.7036 (t0) cc_final: 0.5797 (m-30) REVERT: D 613 TYR cc_start: 0.6099 (m-80) cc_final: 0.5734 (m-80) REVERT: D 640 MET cc_start: 0.7996 (mmt) cc_final: 0.7444 (mmt) REVERT: F 461 LEU cc_start: 0.8553 (mp) cc_final: 0.8318 (mt) REVERT: F 512 ASN cc_start: 0.7847 (t0) cc_final: 0.7401 (m-40) REVERT: H 32 GLN cc_start: 0.8481 (mm110) cc_final: 0.8179 (tp40) outliers start: 65 outliers final: 55 residues processed: 270 average time/residue: 0.1275 time to fit residues: 53.6039 Evaluate side-chains 274 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 218 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 499 SER Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 574 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 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 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 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 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 729 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 63 optimal weight: 0.8980 chunk 17 optimal weight: 20.0000 chunk 175 optimal weight: 20.0000 chunk 150 optimal weight: 40.0000 chunk 54 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 144 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.112196 restraints weight = 26797.960| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.81 r_work: 0.3168 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17445 Z= 0.168 Angle : 0.548 8.315 23762 Z= 0.285 Chirality : 0.043 0.146 2471 Planarity : 0.004 0.042 3151 Dihedral : 5.494 57.242 2330 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.50 % Allowed : 12.22 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.17), residues: 2115 helix: -3.10 (0.47), residues: 82 sheet: -0.77 (0.21), residues: 548 loop : -0.75 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 300 TYR 0.021 0.002 TYR D 484 PHE 0.020 0.002 PHE A 501 TRP 0.025 0.002 TRP F 509 HIS 0.007 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00398 (17443) covalent geometry : angle 0.54772 (23758) SS BOND : bond 0.00530 ( 2) SS BOND : angle 1.41432 ( 4) hydrogen bonds : bond 0.02809 ( 215) hydrogen bonds : angle 5.67114 ( 477) *********************** 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 291 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 226 time to evaluate : 0.661 Fit side-chains REVERT: A 384 ASP cc_start: 0.7177 (t70) cc_final: 0.6573 (m-30) REVERT: A 552 ASN cc_start: 0.7772 (m-40) cc_final: 0.7115 (t0) REVERT: A 599 GLN cc_start: 0.8219 (tp40) cc_final: 0.7938 (tp40) REVERT: A 647 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7310 (pt) REVERT: C 406 ARG cc_start: 0.6376 (mtt180) cc_final: 0.5500 (mtm110) REVERT: C 412 GLN cc_start: 0.8197 (pt0) cc_final: 0.7196 (pm20) REVERT: C 419 ASN cc_start: 0.7071 (t0) cc_final: 0.6420 (m110) REVERT: C 691 ASN cc_start: 0.7283 (m-40) cc_final: 0.7024 (p0) REVERT: D 567 LYS cc_start: 0.7408 (pttm) cc_final: 0.6677 (tptp) REVERT: D 611 ASP cc_start: 0.7029 (t0) cc_final: 0.5814 (m-30) REVERT: D 613 TYR cc_start: 0.6105 (m-80) cc_final: 0.5723 (m-80) REVERT: D 640 MET cc_start: 0.8047 (mmt) cc_final: 0.7500 (mmt) REVERT: E 485 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.5532 (ttp-170) REVERT: F 461 LEU cc_start: 0.8546 (mp) cc_final: 0.8314 (mt) REVERT: F 512 ASN cc_start: 0.7827 (t0) cc_final: 0.7395 (m-40) REVERT: H 32 GLN cc_start: 0.8484 (mm110) cc_final: 0.8177 (tp40) outliers start: 65 outliers final: 59 residues processed: 267 average time/residue: 0.1238 time to fit residues: 50.8957 Evaluate side-chains 276 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 215 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 499 SER Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 647 ILE 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 301 LEU 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 626 ASP 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 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 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 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 729 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 157 optimal weight: 0.9980 chunk 191 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 41 optimal weight: 0.0770 chunk 80 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 95 optimal weight: 0.3980 chunk 12 optimal weight: 10.0000 chunk 193 optimal weight: 7.9990 overall best weight: 1.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN 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 = 0.3578 r_free = 0.3578 target = 0.134531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.115499 restraints weight = 26353.777| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.80 r_work: 0.3213 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17445 Z= 0.092 Angle : 0.489 7.874 23762 Z= 0.253 Chirality : 0.041 0.143 2471 Planarity : 0.004 0.036 3151 Dihedral : 5.035 57.770 2330 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.53 % Allowed : 13.02 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.17), residues: 2115 helix: -3.18 (0.50), residues: 70 sheet: -0.67 (0.22), residues: 513 loop : -0.53 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 550 TYR 0.014 0.001 TYR C 706 PHE 0.020 0.001 PHE A 501 TRP 0.021 0.001 TRP F 509 HIS 0.003 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00214 (17443) covalent geometry : angle 0.48906 (23758) SS BOND : bond 0.00393 ( 2) SS BOND : angle 1.05623 ( 4) hydrogen bonds : bond 0.02380 ( 215) hydrogen bonds : angle 5.27326 ( 477) *********************** 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 293 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 246 time to evaluate : 0.478 Fit side-chains REVERT: A 384 ASP cc_start: 0.7080 (t70) cc_final: 0.6514 (m-30) REVERT: A 552 ASN cc_start: 0.7662 (m-40) cc_final: 0.7310 (t0) REVERT: A 599 GLN cc_start: 0.8202 (tp40) cc_final: 0.7903 (tp40) REVERT: C 406 ARG cc_start: 0.6260 (mtt180) cc_final: 0.5437 (mtm110) REVERT: C 412 GLN cc_start: 0.8174 (pt0) cc_final: 0.7145 (pm20) REVERT: C 419 ASN cc_start: 0.7125 (t0) cc_final: 0.6412 (m110) REVERT: C 462 LYS cc_start: 0.6825 (mmtt) cc_final: 0.6110 (mmmt) REVERT: C 691 ASN cc_start: 0.7254 (m-40) cc_final: 0.7053 (p0) REVERT: D 567 LYS cc_start: 0.7341 (pttm) cc_final: 0.6591 (tptp) REVERT: D 613 TYR cc_start: 0.6025 (m-80) cc_final: 0.5649 (m-80) REVERT: D 640 MET cc_start: 0.8021 (mmt) cc_final: 0.7545 (mmt) REVERT: E 485 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.5627 (ttp-170) REVERT: F 237 ASP cc_start: 0.7537 (p0) cc_final: 0.7181 (p0) REVERT: F 461 LEU cc_start: 0.8475 (mp) cc_final: 0.8242 (mt) REVERT: F 512 ASN cc_start: 0.7696 (t0) cc_final: 0.7351 (m-40) REVERT: H 32 GLN cc_start: 0.8582 (mm110) cc_final: 0.8180 (tp40) REVERT: H 106 ARG cc_start: 0.8202 (ptp90) cc_final: 0.7969 (ptp-110) outliers start: 47 outliers final: 37 residues processed: 273 average time/residue: 0.1238 time to fit residues: 52.1795 Evaluate side-chains 267 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 229 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 519 ASN Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 537 LEU 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 580 VAL Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain E residue 420 VAL Chi-restraints excluded: chain E residue 430 GLN 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 344 VAL Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 140 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 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 6 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 chunk 140 optimal weight: 20.0000 chunk 146 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN C 452 ASN D 628 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 = 0.3542 r_free = 0.3542 target = 0.131889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112802 restraints weight = 26541.466| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.80 r_work: 0.3181 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3174 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= 0.162 Angle : 0.547 8.018 23762 Z= 0.283 Chirality : 0.043 0.144 2471 Planarity : 0.004 0.057 3151 Dihedral : 5.073 55.771 2327 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.48 % Allowed : 13.24 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.17), residues: 2115 helix: -2.99 (0.48), residues: 82 sheet: -0.63 (0.22), residues: 527 loop : -0.60 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 734 TYR 0.017 0.002 TYR F 443 PHE 0.017 0.002 PHE A 501 TRP 0.028 0.002 TRP F 509 HIS 0.007 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00385 (17443) covalent geometry : angle 0.54676 (23758) SS BOND : bond 0.00487 ( 2) SS BOND : angle 1.29018 ( 4) hydrogen bonds : bond 0.02745 ( 215) hydrogen bonds : angle 5.44618 ( 477) ********************** 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 276 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 230 time to evaluate : 0.695 Fit side-chains REVERT: A 384 ASP cc_start: 0.7172 (t70) cc_final: 0.6599 (m-30) REVERT: A 552 ASN cc_start: 0.7707 (m-40) cc_final: 0.7052 (t0) REVERT: A 599 GLN cc_start: 0.8201 (tp40) cc_final: 0.7918 (tp40) REVERT: C 406 ARG cc_start: 0.6313 (mtt180) cc_final: 0.5477 (mtm110) REVERT: C 412 GLN cc_start: 0.8233 (pt0) cc_final: 0.7220 (pm20) REVERT: C 419 ASN cc_start: 0.7057 (t0) cc_final: 0.6384 (m110) REVERT: C 698 GLU cc_start: 0.7601 (mm-30) cc_final: 0.6888 (mm-30) REVERT: D 550 ARG cc_start: 0.7566 (ttp80) cc_final: 0.7308 (ttp80) REVERT: D 567 LYS cc_start: 0.7379 (pttm) cc_final: 0.6624 (tptp) REVERT: D 613 TYR cc_start: 0.6051 (m-80) cc_final: 0.5707 (m-80) REVERT: D 640 MET cc_start: 0.8035 (mmt) cc_final: 0.7528 (mmt) REVERT: E 485 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.5633 (ttp-170) REVERT: F 237 ASP cc_start: 0.7548 (p0) cc_final: 0.7159 (p0) REVERT: F 461 LEU cc_start: 0.8520 (mp) cc_final: 0.8285 (mt) REVERT: F 512 ASN cc_start: 0.7766 (t0) cc_final: 0.7370 (m-40) REVERT: H 32 GLN cc_start: 0.8537 (mm110) cc_final: 0.8153 (tp40) outliers start: 46 outliers final: 40 residues processed: 255 average time/residue: 0.1146 time to fit residues: 45.2706 Evaluate side-chains 266 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 519 ASN Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 537 LEU 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 494 THR 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 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 344 VAL Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 140 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 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 147 optimal weight: 0.9990 chunk 174 optimal weight: 20.0000 chunk 187 optimal weight: 8.9990 chunk 149 optimal weight: 0.4980 chunk 26 optimal weight: 30.0000 chunk 23 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 chunk 157 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 chunk 140 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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 ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 585 GLN F 255 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.132945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.113960 restraints weight = 26507.296| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.79 r_work: 0.3187 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17445 Z= 0.131 Angle : 0.525 7.929 23762 Z= 0.271 Chirality : 0.042 0.139 2471 Planarity : 0.004 0.038 3151 Dihedral : 4.988 56.845 2327 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.53 % Allowed : 13.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.17), residues: 2115 helix: -3.20 (0.50), residues: 70 sheet: -0.58 (0.22), residues: 519 loop : -0.59 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 300 TYR 0.015 0.001 TYR D 484 PHE 0.017 0.001 PHE A 501 TRP 0.023 0.001 TRP F 509 HIS 0.005 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00309 (17443) covalent geometry : angle 0.52488 (23758) SS BOND : bond 0.00434 ( 2) SS BOND : angle 1.21366 ( 4) hydrogen bonds : bond 0.02610 ( 215) hydrogen bonds : angle 5.40047 ( 477) =============================================================================== Job complete usr+sys time: 3861.51 seconds wall clock time: 66 minutes 54.61 seconds (4014.61 seconds total)