Starting phenix.real_space_refine on Wed Feb 4 16:10:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s3p_54546/02_2026/9s3p_54546.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s3p_54546/02_2026/9s3p_54546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9s3p_54546/02_2026/9s3p_54546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s3p_54546/02_2026/9s3p_54546.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9s3p_54546/02_2026/9s3p_54546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s3p_54546/02_2026/9s3p_54546.map" } resolution = 3.1 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 22 5.16 5 C 7390 2.51 5 N 1904 2.21 5 O 2174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11494 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1062 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 132} Chain: "B" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1116 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 137} Chain: "C" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1062 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 132} Chain: "D" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1116 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 137} Chain: "E" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1601 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 182} Chain: "F" Number of atoms: 2678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2678 Classifications: {'peptide': 327} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 311} Chain: "G" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2687 Classifications: {'peptide': 328} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 312} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.46, per 1000 atoms: 0.21 Number of scatterers: 11494 At special positions: 0 Unit cell: (115.108, 109.154, 130.985, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 22 16.00 O 2174 8.00 N 1904 7.00 C 7390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 631.9 milliseconds 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2700 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 49.8% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 removed outlier: 3.724A pdb=" N GLY A 18 " --> pdb=" O TRP A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 36 Processing helix chain 'A' and resid 37 through 43 removed outlier: 3.871A pdb=" N THR A 41 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'A' and resid 94 through 113 removed outlier: 3.663A pdb=" N PHE A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 137 Processing helix chain 'B' and resid 4 through 17 removed outlier: 3.672A pdb=" N LYS B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 36 through 46 removed outlier: 3.574A pdb=" N PHE B 41 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU B 43 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N SER B 44 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY B 46 " --> pdb=" O GLU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 56 removed outlier: 3.727A pdb=" N MET B 55 " --> pdb=" O PRO B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 77 Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 86 through 95 Processing helix chain 'B' and resid 99 through 119 removed outlier: 3.687A pdb=" N PHE B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 123 through 142 Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 20 through 36 Processing helix chain 'C' and resid 37 through 43 removed outlier: 3.687A pdb=" N THR C 41 " --> pdb=" O THR C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 72 Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 94 through 113 removed outlier: 3.505A pdb=" N PHE C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 137 Processing helix chain 'D' and resid 4 through 16 Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 36 through 43 removed outlier: 3.512A pdb=" N PHE D 41 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D 43 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 56 Processing helix chain 'D' and resid 57 through 77 removed outlier: 3.526A pdb=" N HIS D 77 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 85 Processing helix chain 'D' and resid 85 through 95 Processing helix chain 'D' and resid 99 through 119 removed outlier: 3.989A pdb=" N PHE D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 123 through 142 Processing helix chain 'D' and resid 143 through 146 Processing helix chain 'E' and resid 330 through 335 Processing helix chain 'E' and resid 364 through 370 Processing helix chain 'E' and resid 471 through 487 Proline residue: E 483 - end of helix Processing helix chain 'E' and resid 489 through 501 removed outlier: 3.597A pdb=" N GLN E 501 " --> pdb=" O LEU E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 521 removed outlier: 3.935A pdb=" N LYS E 513 " --> pdb=" O LYS E 509 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LYS E 514 " --> pdb=" O ALA E 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 340 removed outlier: 3.882A pdb=" N ILE F 340 " --> pdb=" O PRO F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 370 Processing helix chain 'F' and resid 392 through 394 No H-bonds generated for 'chain 'F' and resid 392 through 394' Processing helix chain 'F' and resid 465 through 469 removed outlier: 3.571A pdb=" N ASP F 468 " --> pdb=" O ASN F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 487 Proline residue: F 483 - end of helix Processing helix chain 'F' and resid 489 through 501 Processing helix chain 'F' and resid 505 through 507 No H-bonds generated for 'chain 'F' and resid 505 through 507' Processing helix chain 'F' and resid 508 through 534 Processing helix chain 'F' and resid 590 through 592 No H-bonds generated for 'chain 'F' and resid 590 through 592' Processing helix chain 'G' and resid 329 through 334 Processing helix chain 'G' and resid 364 through 370 Processing helix chain 'G' and resid 471 through 487 Proline residue: G 483 - end of helix Processing helix chain 'G' and resid 489 through 501 Processing helix chain 'G' and resid 505 through 529 removed outlier: 4.261A pdb=" N LYS G 514 " --> pdb=" O ALA G 510 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS G 515 " --> pdb=" O GLU G 511 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS G 528 " --> pdb=" O ALA G 524 " (cutoff:3.500A) Processing helix chain 'G' and resid 531 through 535 Processing helix chain 'G' and resid 564 through 568 removed outlier: 4.267A pdb=" N GLY G 567 " --> pdb=" O VAL G 564 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 349 through 352 removed outlier: 3.508A pdb=" N TYR E 423 " --> pdb=" O SER E 414 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER E 414 " --> pdb=" O TYR E 423 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ARG E 425 " --> pdb=" O LEU E 412 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LEU E 412 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 354 through 357 removed outlier: 5.245A pdb=" N HIS E 448 " --> pdb=" O TYR E 443 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N TYR E 443 " --> pdb=" O HIS E 448 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ASP E 450 " --> pdb=" O ILE E 441 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE E 441 " --> pdb=" O ASP E 450 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASP E 452 " --> pdb=" O SER E 439 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N SER E 439 " --> pdb=" O ASP E 452 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 349 through 352 removed outlier: 3.597A pdb=" N ARG F 350 " --> pdb=" O VAL F 377 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE F 426 " --> pdb=" O ILE F 386 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N TYR F 423 " --> pdb=" O VAL F 413 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 354 through 357 removed outlier: 4.378A pdb=" N TYR F 453 " --> pdb=" O ILE F 437 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE F 437 " --> pdb=" O TYR F 453 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LEU F 455 " --> pdb=" O VAL F 435 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL F 435 " --> pdb=" O LEU F 455 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL F 457 " --> pdb=" O ARG F 433 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N ARG F 433 " --> pdb=" O VAL F 457 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU F 442 " --> pdb=" O TRP F 396 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TRP F 396 " --> pdb=" O GLU F 442 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL F 401 " --> pdb=" O LEU F 408 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 549 through 550 removed outlier: 3.917A pdb=" N PHE F 573 " --> pdb=" O ALA F 550 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LYS F 587 " --> pdb=" O PRO F 572 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE F 620 " --> pdb=" O VAL F 584 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET F 586 " --> pdb=" O LEU F 618 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU F 618 " --> pdb=" O MET F 586 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ARG F 616 " --> pdb=" O THR F 588 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER F 608 " --> pdb=" O THR F 617 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE F 619 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N THR F 606 " --> pdb=" O ILE F 619 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 552 through 555 removed outlier: 3.698A pdb=" N ARG F 649 " --> pdb=" O PHE F 555 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL F 636 " --> pdb=" O TRP F 594 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TRP F 594 " --> pdb=" O VAL F 636 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 349 through 352 removed outlier: 7.826A pdb=" N VAL G 372 " --> pdb=" O LYS G 391 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LYS G 391 " --> pdb=" O VAL G 372 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY G 389 " --> pdb=" O PRO G 374 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR G 380 " --> pdb=" O GLY G 383 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE G 386 " --> pdb=" O PHE G 426 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE G 426 " --> pdb=" O ILE G 386 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR G 421 " --> pdb=" O TYR G 415 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR G 415 " --> pdb=" O TYR G 421 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N TYR G 423 " --> pdb=" O VAL G 413 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 354 through 357 removed outlier: 5.451A pdb=" N HIS G 448 " --> pdb=" O TYR G 443 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N TYR G 443 " --> pdb=" O HIS G 448 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ASP G 450 " --> pdb=" O ILE G 441 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE G 441 " --> pdb=" O ASP G 450 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASP G 452 " --> pdb=" O SER G 439 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N SER G 439 " --> pdb=" O ASP G 452 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N GLU G 442 " --> pdb=" O TRP G 396 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TRP G 396 " --> pdb=" O GLU G 442 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 549 through 550 removed outlier: 4.382A pdb=" N TYR G 574 " --> pdb=" O VAL G 585 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN G 581 " --> pdb=" O LEU G 578 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE G 620 " --> pdb=" O VAL G 584 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR G 617 " --> pdb=" O SER G 608 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N SER G 608 " --> pdb=" O THR G 617 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE G 619 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N THR G 606 " --> pdb=" O ILE G 619 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 553 through 556 removed outlier: 4.185A pdb=" N VAL G 599 " --> pdb=" O LYS G 602 " (cutoff:3.500A) 604 hydrogen bonds defined for protein. 1695 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: 2.31 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.39: 4864 1.39 - 1.56: 6878 1.56 - 1.72: 2 1.72 - 1.89: 38 1.89 - 2.06: 16 Bond restraints: 11798 Sorted by residual: bond pdb=" N VAL A 93 " pdb=" CA VAL A 93 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.22e-02 6.72e+03 1.11e+01 bond pdb=" C ASP D 94 " pdb=" O ASP D 94 " ideal model delta sigma weight residual 1.234 1.276 -0.042 1.30e-02 5.92e+03 1.02e+01 bond pdb=" N ASP D 94 " pdb=" CA ASP D 94 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.24e-02 6.50e+03 9.07e+00 bond pdb=" N VAL A 96 " pdb=" CA VAL A 96 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.45e+00 bond pdb=" N ASP A 94 " pdb=" CA ASP A 94 " ideal model delta sigma weight residual 1.452 1.490 -0.038 1.41e-02 5.03e+03 7.28e+00 ... (remaining 11793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 15738 1.98 - 3.96: 274 3.96 - 5.94: 45 5.94 - 7.92: 12 7.92 - 9.90: 6 Bond angle restraints: 16075 Sorted by residual: angle pdb=" C ASP A 94 " pdb=" N PRO A 95 " pdb=" CA PRO A 95 " ideal model delta sigma weight residual 119.05 123.68 -4.63 1.11e+00 8.12e-01 1.74e+01 angle pdb=" CB GLU G 403 " pdb=" CG GLU G 403 " pdb=" CD GLU G 403 " ideal model delta sigma weight residual 112.60 119.58 -6.98 1.70e+00 3.46e-01 1.69e+01 angle pdb=" C HIS A 87 " pdb=" N ALA A 88 " pdb=" CA ALA A 88 " ideal model delta sigma weight residual 120.72 114.17 6.55 1.67e+00 3.59e-01 1.54e+01 angle pdb=" N GLU D 90 " pdb=" CA GLU D 90 " pdb=" C GLU D 90 " ideal model delta sigma weight residual 111.28 107.52 3.76 1.09e+00 8.42e-01 1.19e+01 angle pdb=" CA GLU G 403 " pdb=" CB GLU G 403 " pdb=" CG GLU G 403 " ideal model delta sigma weight residual 114.10 120.99 -6.89 2.00e+00 2.50e-01 1.19e+01 ... (remaining 16070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5842 17.91 - 35.82: 759 35.82 - 53.73: 282 53.73 - 71.64: 66 71.64 - 89.55: 32 Dihedral angle restraints: 6981 sinusoidal: 2799 harmonic: 4182 Sorted by residual: dihedral pdb=" CD ARG C 141 " pdb=" NE ARG C 141 " pdb=" CZ ARG C 141 " pdb=" NH1 ARG C 141 " ideal model delta sinusoidal sigma weight residual 0.00 63.37 -63.37 1 1.00e+01 1.00e-02 5.30e+01 dihedral pdb=" CD ARG A 141 " pdb=" NE ARG A 141 " pdb=" CZ ARG A 141 " pdb=" NH1 ARG A 141 " ideal model delta sinusoidal sigma weight residual 0.00 -37.25 37.25 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" C1A HEM D 201 " pdb=" C2A HEM D 201 " pdb=" CAA HEM D 201 " pdb=" CBA HEM D 201 " ideal model delta sinusoidal sigma weight residual 0.00 89.55 -89.55 2 2.00e+01 2.50e-03 1.20e+01 ... (remaining 6978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1208 0.038 - 0.076: 375 0.076 - 0.114: 149 0.114 - 0.153: 13 0.153 - 0.191: 4 Chirality restraints: 1749 Sorted by residual: chirality pdb=" CA VAL A 96 " pdb=" N VAL A 96 " pdb=" C VAL A 96 " pdb=" CB VAL A 96 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.09e-01 chirality pdb=" CA ILE G 655 " pdb=" N ILE G 655 " pdb=" C ILE G 655 " pdb=" CB ILE G 655 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.58e-01 chirality pdb=" CA VAL A 93 " pdb=" N VAL A 93 " pdb=" C VAL A 93 " pdb=" CB VAL A 93 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.88e-01 ... (remaining 1746 not shown) Planarity restraints: 2049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 141 " -0.986 9.50e-02 1.11e+02 4.42e-01 1.18e+02 pdb=" NE ARG C 141 " 0.059 2.00e-02 2.50e+03 pdb=" CZ ARG C 141 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 141 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 141 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 141 " 0.662 9.50e-02 1.11e+02 2.97e-01 5.37e+01 pdb=" NE ARG A 141 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG A 141 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 141 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 141 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 92 " 0.269 9.50e-02 1.11e+02 1.21e-01 8.93e+00 pdb=" NE ARG A 92 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 92 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 92 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 92 " 0.009 2.00e-02 2.50e+03 ... (remaining 2046 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 5074 2.96 - 3.45: 11745 3.45 - 3.93: 19157 3.93 - 4.42: 21004 4.42 - 4.90: 34815 Nonbonded interactions: 91795 Sorted by model distance: nonbonded pdb=" O GLU G 403 " pdb=" OE1 GLU G 403 " model vdw 2.477 3.040 nonbonded pdb=" O VAL A 93 " pdb=" OH TYR A 140 " model vdw 2.495 3.040 nonbonded pdb=" N GLU E 491 " pdb=" OE1 GLU E 491 " model vdw 2.531 3.120 nonbonded pdb=" N ASP E 359 " pdb=" OD1 ASP E 359 " model vdw 2.532 3.120 nonbonded pdb=" N GLU E 400 " pdb=" OE1 GLU E 400 " model vdw 2.559 3.120 ... (remaining 91790 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 329 through 655) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.350 Find NCS groups from input model: 0.170 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:1.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 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 : 0.007 0.664 11802 Z= 0.191 Angle : 0.632 9.896 16075 Z= 0.336 Chirality : 0.043 0.191 1749 Planarity : 0.013 0.442 2049 Dihedral : 19.888 89.547 4281 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.49 % Favored : 97.44 % Rotamer: Outliers : 2.68 % Allowed : 34.61 % Favored : 62.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % 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 are not related in a simple way. whole: 1.82 (0.24), residues: 1404 helix: 2.81 (0.22), residues: 609 sheet: 0.34 (0.32), residues: 292 loop : -0.26 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 603 TYR 0.010 0.001 TYR G 508 PHE 0.025 0.001 PHE F 426 TRP 0.004 0.001 TRP G 594 HIS 0.003 0.000 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00333 (11798) covalent geometry : angle 0.63173 (16075) hydrogen bonds : bond 0.16565 ( 604) hydrogen bonds : angle 6.55838 ( 1695) Misc. bond : bond 0.34875 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 292 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8550 (m-30) cc_final: 0.8240 (m-30) REVERT: A 126 ASP cc_start: 0.8713 (t70) cc_final: 0.8510 (t0) REVERT: B 90 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8126 (tm-30) REVERT: B 120 LYS cc_start: 0.8324 (ttmm) cc_final: 0.8106 (mmtt) REVERT: C 16 LYS cc_start: 0.8598 (tppp) cc_final: 0.8062 (mmmm) REVERT: C 139 LYS cc_start: 0.8496 (tppp) cc_final: 0.8248 (tptp) REVERT: D 90 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7943 (pt0) REVERT: E 356 MET cc_start: 0.8679 (mmm) cc_final: 0.8429 (mmm) REVERT: E 421 TYR cc_start: 0.8409 (m-10) cc_final: 0.7913 (m-10) REVERT: E 429 SER cc_start: 0.7519 (t) cc_final: 0.7237 (m) REVERT: E 475 TYR cc_start: 0.7722 (t80) cc_final: 0.7399 (t80) REVERT: E 485 HIS cc_start: 0.6670 (m90) cc_final: 0.6458 (m-70) REVERT: E 488 LYS cc_start: 0.6815 (mtmt) cc_final: 0.6259 (ptmt) REVERT: E 504 LEU cc_start: 0.5511 (mt) cc_final: 0.5004 (tp) REVERT: E 515 LYS cc_start: 0.6978 (tppt) cc_final: 0.6654 (mtmt) REVERT: F 499 LYS cc_start: 0.8228 (mtpp) cc_final: 0.7876 (mtpt) REVERT: F 508 TYR cc_start: 0.5934 (OUTLIER) cc_final: 0.4987 (p90) REVERT: F 516 LEU cc_start: 0.7798 (tm) cc_final: 0.7578 (tp) REVERT: F 553 VAL cc_start: 0.8591 (m) cc_final: 0.8341 (p) REVERT: F 566 ASP cc_start: 0.7424 (t70) cc_final: 0.6924 (t0) REVERT: F 568 PHE cc_start: 0.6962 (t80) cc_final: 0.6592 (t80) REVERT: F 585 VAL cc_start: 0.7656 (m) cc_final: 0.7204 (p) REVERT: F 608 SER cc_start: 0.7041 (p) cc_final: 0.6809 (m) REVERT: F 639 ASN cc_start: 0.7861 (t0) cc_final: 0.7521 (t0) REVERT: F 645 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6489 (mm110) REVERT: G 488 LYS cc_start: 0.6990 (tppt) cc_final: 0.6690 (mmtp) REVERT: G 577 THR cc_start: 0.6012 (OUTLIER) cc_final: 0.5737 (p) outliers start: 33 outliers final: 9 residues processed: 317 average time/residue: 0.1285 time to fit residues: 54.7098 Evaluate side-chains 225 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 465 ASN Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 508 TYR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 645 GLN Chi-restraints excluded: chain G residue 454 THR Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 548 GLN Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain G residue 605 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 ASN D 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.144989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.114481 restraints weight = 17944.892| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.65 r_work: 0.3252 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.266 11802 Z= 0.130 Angle : 0.570 10.118 16075 Z= 0.281 Chirality : 0.042 0.164 1749 Planarity : 0.004 0.051 2049 Dihedral : 8.442 89.655 1578 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 6.09 % Allowed : 26.32 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % 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 are not related in a simple way. whole: 1.70 (0.24), residues: 1404 helix: 2.67 (0.22), residues: 622 sheet: 0.19 (0.32), residues: 291 loop : -0.28 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 363 TYR 0.012 0.001 TYR E 368 PHE 0.014 0.002 PHE G 365 TRP 0.005 0.001 TRP B 37 HIS 0.003 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00321 (11798) covalent geometry : angle 0.56978 (16075) hydrogen bonds : bond 0.03469 ( 604) hydrogen bonds : angle 5.16556 ( 1695) Misc. bond : bond 0.13736 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 209 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 60 LYS cc_start: 0.8526 (tttm) cc_final: 0.8150 (tttt) REVERT: A 139 LYS cc_start: 0.7867 (mptm) cc_final: 0.7476 (mttt) REVERT: B 61 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8017 (mttp) REVERT: B 90 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8235 (tm-30) REVERT: B 120 LYS cc_start: 0.8445 (ttmm) cc_final: 0.8114 (mmtt) REVERT: D 43 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7648 (tt0) REVERT: D 90 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8175 (pp20) REVERT: E 339 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7670 (tp) REVERT: E 348 ASN cc_start: 0.7651 (OUTLIER) cc_final: 0.7277 (m110) REVERT: E 407 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.7106 (ttmt) REVERT: E 429 SER cc_start: 0.7731 (t) cc_final: 0.7459 (m) REVERT: E 445 GLU cc_start: 0.5889 (OUTLIER) cc_final: 0.5309 (mt-10) REVERT: E 475 TYR cc_start: 0.7686 (t80) cc_final: 0.7433 (t80) REVERT: E 488 LYS cc_start: 0.6765 (mtmt) cc_final: 0.6135 (ptmt) REVERT: E 504 LEU cc_start: 0.5770 (OUTLIER) cc_final: 0.5245 (tp) REVERT: E 515 LYS cc_start: 0.7060 (tppt) cc_final: 0.6745 (mtmt) REVERT: F 377 VAL cc_start: 0.8628 (t) cc_final: 0.8274 (p) REVERT: F 477 LEU cc_start: 0.8091 (tm) cc_final: 0.7804 (tt) REVERT: F 516 LEU cc_start: 0.7991 (tm) cc_final: 0.7732 (tp) REVERT: F 600 GLU cc_start: 0.6517 (mm-30) cc_final: 0.6120 (mm-30) REVERT: F 639 ASN cc_start: 0.7724 (t0) cc_final: 0.7507 (t0) REVERT: F 645 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6728 (mm110) REVERT: G 341 ASP cc_start: 0.7947 (m-30) cc_final: 0.7365 (m-30) REVERT: G 356 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.7283 (mmm) REVERT: G 488 LYS cc_start: 0.6829 (tppt) cc_final: 0.6515 (mmtp) REVERT: G 511 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.6198 (tt0) REVERT: G 520 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.6565 (mtt-85) REVERT: G 586 MET cc_start: 0.3841 (tpt) cc_final: 0.3020 (tmm) REVERT: G 587 LYS cc_start: 0.6514 (OUTLIER) cc_final: 0.6159 (tmtt) REVERT: G 620 PHE cc_start: 0.7720 (p90) cc_final: 0.7437 (p90) REVERT: G 633 VAL cc_start: 0.7483 (t) cc_final: 0.7167 (m) outliers start: 75 outliers final: 34 residues processed: 266 average time/residue: 0.1065 time to fit residues: 39.3935 Evaluate side-chains 233 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 187 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 339 ILE Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 379 PHE Chi-restraints excluded: chain E residue 407 LYS Chi-restraints excluded: chain E residue 414 SER Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 465 ASN Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain F residue 357 LYS Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain F residue 508 TYR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 558 GLU Chi-restraints excluded: chain F residue 645 GLN Chi-restraints excluded: chain G residue 356 MET Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 464 ASN Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 511 GLU Chi-restraints excluded: chain G residue 520 ARG Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 548 GLN Chi-restraints excluded: chain G residue 587 LYS Chi-restraints excluded: chain G residue 605 THR Chi-restraints excluded: chain G residue 636 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 112 optimal weight: 8.9990 chunk 130 optimal weight: 0.4980 chunk 136 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 109 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 HIS F 526 GLN G 331 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.143256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.108602 restraints weight = 18023.063| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.71 r_work: 0.3205 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.168 11802 Z= 0.114 Angle : 0.536 9.047 16075 Z= 0.263 Chirality : 0.041 0.154 1749 Planarity : 0.004 0.051 2049 Dihedral : 8.107 88.171 1574 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 5.69 % Allowed : 25.59 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % 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 are not related in a simple way. whole: 1.62 (0.24), residues: 1404 helix: 2.62 (0.22), residues: 622 sheet: -0.03 (0.32), residues: 286 loop : -0.22 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 363 TYR 0.013 0.001 TYR F 495 PHE 0.013 0.001 PHE G 620 TRP 0.005 0.001 TRP E 396 HIS 0.003 0.001 HIS D 77 Details of bonding type rmsd covalent geometry : bond 0.00284 (11798) covalent geometry : angle 0.53602 (16075) hydrogen bonds : bond 0.03112 ( 604) hydrogen bonds : angle 4.74718 ( 1695) Misc. bond : bond 0.08912 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 193 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 139 LYS cc_start: 0.8077 (mptm) cc_final: 0.7618 (mttt) REVERT: B 66 LYS cc_start: 0.8993 (mtpp) cc_final: 0.8728 (mtmt) REVERT: B 95 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8605 (mmtp) REVERT: B 120 LYS cc_start: 0.8427 (ttmm) cc_final: 0.8006 (tptt) REVERT: C 16 LYS cc_start: 0.8504 (tppp) cc_final: 0.7990 (mmmm) REVERT: D 68 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8664 (tp) REVERT: D 77 HIS cc_start: 0.8043 (m170) cc_final: 0.7790 (m90) REVERT: D 90 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8391 (pp20) REVERT: D 144 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8000 (mptp) REVERT: E 339 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7467 (tp) REVERT: E 348 ASN cc_start: 0.7436 (OUTLIER) cc_final: 0.7123 (m110) REVERT: E 429 SER cc_start: 0.7657 (t) cc_final: 0.7371 (m) REVERT: E 445 GLU cc_start: 0.6026 (mp0) cc_final: 0.5508 (mt-10) REVERT: E 460 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7307 (tm-30) REVERT: E 475 TYR cc_start: 0.7656 (t80) cc_final: 0.7391 (t80) REVERT: E 488 LYS cc_start: 0.6683 (mtmt) cc_final: 0.5984 (ptmt) REVERT: E 498 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7468 (tp30) REVERT: E 504 LEU cc_start: 0.5764 (OUTLIER) cc_final: 0.5167 (pt) REVERT: F 377 VAL cc_start: 0.8688 (t) cc_final: 0.8315 (p) REVERT: F 477 LEU cc_start: 0.8143 (tm) cc_final: 0.7879 (tt) REVERT: F 516 LEU cc_start: 0.7896 (tm) cc_final: 0.7686 (tp) REVERT: F 600 GLU cc_start: 0.6406 (mm-30) cc_final: 0.5758 (mm-30) REVERT: F 639 ASN cc_start: 0.7773 (t0) cc_final: 0.7475 (t0) REVERT: F 645 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.6721 (mm110) REVERT: G 341 ASP cc_start: 0.7926 (m-30) cc_final: 0.7347 (m-30) REVERT: G 355 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7937 (mt0) REVERT: G 356 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.7085 (mmm) REVERT: G 362 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: G 424 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8179 (pt) REVERT: G 488 LYS cc_start: 0.6861 (tppt) cc_final: 0.6505 (mmtm) REVERT: G 492 ARG cc_start: 0.6815 (tpt90) cc_final: 0.6348 (tpt90) REVERT: G 520 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.6401 (mtt-85) REVERT: G 522 GLU cc_start: 0.4280 (mt-10) cc_final: 0.3938 (mt-10) REVERT: G 586 MET cc_start: 0.3935 (tpt) cc_final: 0.3508 (tmm) REVERT: G 587 LYS cc_start: 0.6564 (OUTLIER) cc_final: 0.6173 (tmtt) REVERT: G 620 PHE cc_start: 0.7826 (p90) cc_final: 0.7501 (p90) REVERT: G 633 VAL cc_start: 0.7700 (t) cc_final: 0.7277 (m) outliers start: 70 outliers final: 35 residues processed: 248 average time/residue: 0.1055 time to fit residues: 36.0560 Evaluate side-chains 229 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 180 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 339 ILE Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 379 PHE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 414 SER Chi-restraints excluded: chain E residue 465 ASN Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain F residue 357 LYS Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain F residue 480 LEU Chi-restraints excluded: chain F residue 508 TYR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 558 GLU Chi-restraints excluded: chain F residue 568 PHE Chi-restraints excluded: chain F residue 598 ILE Chi-restraints excluded: chain F residue 645 GLN Chi-restraints excluded: chain G residue 355 GLN Chi-restraints excluded: chain G residue 356 MET Chi-restraints excluded: chain G residue 362 GLU Chi-restraints excluded: chain G residue 373 GLU Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 436 LYS Chi-restraints excluded: chain G residue 464 ASN Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 520 ARG Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 548 GLN Chi-restraints excluded: chain G residue 551 HIS Chi-restraints excluded: chain G residue 584 VAL Chi-restraints excluded: chain G residue 587 LYS Chi-restraints excluded: chain G residue 605 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 69 optimal weight: 0.2980 chunk 130 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 HIS C 97 ASN F 653 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.141515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.111240 restraints weight = 17987.905| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.80 r_work: 0.3200 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 11802 Z= 0.133 Angle : 0.541 8.512 16075 Z= 0.267 Chirality : 0.042 0.145 1749 Planarity : 0.004 0.051 2049 Dihedral : 7.909 86.571 1574 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 6.26 % Allowed : 25.51 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % 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 are not related in a simple way. whole: 1.66 (0.24), residues: 1404 helix: 2.63 (0.22), residues: 608 sheet: -0.00 (0.32), residues: 279 loop : -0.07 (0.29), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 363 TYR 0.013 0.001 TYR F 512 PHE 0.017 0.002 PHE G 620 TRP 0.006 0.001 TRP A 14 HIS 0.004 0.001 HIS E 367 Details of bonding type rmsd covalent geometry : bond 0.00333 (11798) covalent geometry : angle 0.54124 (16075) hydrogen bonds : bond 0.03133 ( 604) hydrogen bonds : angle 4.62825 ( 1695) Misc. bond : bond 0.07039 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 180 time to evaluate : 0.294 Fit side-chains REVERT: A 16 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8091 (ttmm) REVERT: B 66 LYS cc_start: 0.9054 (mtpp) cc_final: 0.8811 (mtmt) REVERT: B 95 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8470 (mmtp) REVERT: B 120 LYS cc_start: 0.8480 (ttmm) cc_final: 0.8093 (tptt) REVERT: B 121 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7909 (mp0) REVERT: D 68 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8802 (tp) REVERT: D 77 HIS cc_start: 0.8107 (m170) cc_final: 0.7850 (m90) REVERT: D 90 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8370 (pp20) REVERT: D 95 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8277 (tttm) REVERT: D 144 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8155 (mptp) REVERT: E 348 ASN cc_start: 0.7658 (OUTLIER) cc_final: 0.7408 (m110) REVERT: E 421 TYR cc_start: 0.8502 (m-10) cc_final: 0.7914 (m-80) REVERT: E 429 SER cc_start: 0.7690 (t) cc_final: 0.7419 (m) REVERT: E 445 GLU cc_start: 0.6100 (OUTLIER) cc_final: 0.5663 (mt-10) REVERT: E 488 LYS cc_start: 0.6637 (mtmt) cc_final: 0.5909 (ptmt) REVERT: F 377 VAL cc_start: 0.8692 (t) cc_final: 0.8346 (p) REVERT: F 477 LEU cc_start: 0.8206 (tm) cc_final: 0.7926 (tt) REVERT: F 600 GLU cc_start: 0.6507 (mm-30) cc_final: 0.5462 (pp20) REVERT: F 645 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.6958 (mm-40) REVERT: G 335 LYS cc_start: 0.6761 (OUTLIER) cc_final: 0.6555 (mmtp) REVERT: G 341 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7722 (t0) REVERT: G 356 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.7225 (mmm) REVERT: G 424 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8281 (pt) REVERT: G 520 ARG cc_start: 0.6679 (OUTLIER) cc_final: 0.6464 (mtt-85) REVERT: G 522 GLU cc_start: 0.4318 (mt-10) cc_final: 0.3967 (mt-10) REVERT: G 537 VAL cc_start: 0.1193 (OUTLIER) cc_final: 0.0807 (m) REVERT: G 587 LYS cc_start: 0.6639 (OUTLIER) cc_final: 0.6220 (tmtt) REVERT: G 620 PHE cc_start: 0.7904 (p90) cc_final: 0.7612 (p90) REVERT: G 633 VAL cc_start: 0.7600 (t) cc_final: 0.7169 (m) outliers start: 77 outliers final: 44 residues processed: 238 average time/residue: 0.1064 time to fit residues: 34.9805 Evaluate side-chains 227 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 168 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 414 SER Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain E residue 465 ASN Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain F residue 357 LYS Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain F residue 480 LEU Chi-restraints excluded: chain F residue 490 LEU Chi-restraints excluded: chain F residue 508 TYR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 558 GLU Chi-restraints excluded: chain F residue 564 VAL Chi-restraints excluded: chain F residue 568 PHE Chi-restraints excluded: chain F residue 645 GLN Chi-restraints excluded: chain G residue 335 LYS Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain G residue 356 MET Chi-restraints excluded: chain G residue 373 GLU Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain G residue 386 ILE Chi-restraints excluded: chain G residue 388 LEU Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 436 LYS Chi-restraints excluded: chain G residue 464 ASN Chi-restraints excluded: chain G residue 520 ARG Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 551 HIS Chi-restraints excluded: chain G residue 584 VAL Chi-restraints excluded: chain G residue 587 LYS Chi-restraints excluded: chain G residue 605 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 109 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 HIS F 639 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.141404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.108392 restraints weight = 17914.237| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.78 r_work: 0.3185 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 11802 Z= 0.117 Angle : 0.529 8.173 16075 Z= 0.262 Chirality : 0.041 0.146 1749 Planarity : 0.004 0.051 2049 Dihedral : 7.437 86.889 1570 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 6.17 % Allowed : 25.59 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % 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 are not related in a simple way. whole: 1.66 (0.24), residues: 1404 helix: 2.63 (0.22), residues: 608 sheet: 0.04 (0.32), residues: 277 loop : -0.11 (0.29), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 363 TYR 0.018 0.001 TYR D 145 PHE 0.016 0.001 PHE G 620 TRP 0.007 0.001 TRP G 594 HIS 0.003 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00295 (11798) covalent geometry : angle 0.52919 (16075) hydrogen bonds : bond 0.02933 ( 604) hydrogen bonds : angle 4.52122 ( 1695) Misc. bond : bond 0.05856 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 179 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 139 LYS cc_start: 0.8226 (mptm) cc_final: 0.7814 (mttt) REVERT: B 66 LYS cc_start: 0.9023 (mtpp) cc_final: 0.8749 (mtmt) REVERT: B 95 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8514 (mmtp) REVERT: B 120 LYS cc_start: 0.8478 (ttmm) cc_final: 0.8032 (tptt) REVERT: B 121 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8019 (mp0) REVERT: D 43 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7600 (tt0) REVERT: D 68 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8797 (tp) REVERT: D 77 HIS cc_start: 0.8090 (m170) cc_final: 0.7848 (m90) REVERT: D 90 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8343 (pp20) REVERT: D 95 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8273 (tttm) REVERT: E 348 ASN cc_start: 0.7614 (OUTLIER) cc_final: 0.7387 (m110) REVERT: E 421 TYR cc_start: 0.8389 (m-10) cc_final: 0.7820 (m-80) REVERT: E 429 SER cc_start: 0.7688 (t) cc_final: 0.7418 (m) REVERT: E 445 GLU cc_start: 0.6149 (mp0) cc_final: 0.5618 (mt-10) REVERT: E 488 LYS cc_start: 0.6657 (mtmt) cc_final: 0.5839 (ptmt) REVERT: E 498 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7529 (tp30) REVERT: F 377 VAL cc_start: 0.8719 (t) cc_final: 0.8357 (p) REVERT: F 477 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7892 (tt) REVERT: F 553 VAL cc_start: 0.7928 (OUTLIER) cc_final: 0.7482 (p) REVERT: F 600 GLU cc_start: 0.6562 (mm-30) cc_final: 0.5426 (pp20) REVERT: F 645 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.6915 (mm-40) REVERT: G 335 LYS cc_start: 0.6687 (OUTLIER) cc_final: 0.6471 (mmtp) REVERT: G 341 ASP cc_start: 0.8025 (m-30) cc_final: 0.7792 (t0) REVERT: G 356 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.7081 (mmm) REVERT: G 424 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8237 (pt) REVERT: G 496 GLU cc_start: 0.6801 (mt-10) cc_final: 0.6540 (mt-10) REVERT: G 520 ARG cc_start: 0.6617 (OUTLIER) cc_final: 0.6415 (mtt-85) REVERT: G 522 GLU cc_start: 0.4314 (mt-10) cc_final: 0.3971 (mt-10) REVERT: G 537 VAL cc_start: 0.1125 (OUTLIER) cc_final: 0.0748 (m) REVERT: G 586 MET cc_start: 0.4432 (tmm) cc_final: 0.3408 (tmm) REVERT: G 620 PHE cc_start: 0.7896 (p90) cc_final: 0.7631 (p90) REVERT: G 633 VAL cc_start: 0.7736 (t) cc_final: 0.7302 (m) outliers start: 76 outliers final: 50 residues processed: 235 average time/residue: 0.1136 time to fit residues: 37.0568 Evaluate side-chains 231 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 168 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 414 SER Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 465 ASN Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain F residue 357 LYS Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 465 ASN Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 480 LEU Chi-restraints excluded: chain F residue 490 LEU Chi-restraints excluded: chain F residue 508 TYR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 558 GLU Chi-restraints excluded: chain F residue 564 VAL Chi-restraints excluded: chain F residue 568 PHE Chi-restraints excluded: chain F residue 575 THR Chi-restraints excluded: chain F residue 605 THR Chi-restraints excluded: chain F residue 645 GLN Chi-restraints excluded: chain G residue 335 LYS Chi-restraints excluded: chain G residue 356 MET Chi-restraints excluded: chain G residue 373 GLU Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain G residue 386 ILE Chi-restraints excluded: chain G residue 388 LEU Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 464 ASN Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 520 ARG Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 548 GLN Chi-restraints excluded: chain G residue 551 HIS Chi-restraints excluded: chain G residue 584 VAL Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 605 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 119 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 134 optimal weight: 7.9990 chunk 13 optimal weight: 0.0980 chunk 79 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 HIS F 639 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.140974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.108816 restraints weight = 18034.474| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.76 r_work: 0.3185 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 11802 Z= 0.118 Angle : 0.527 7.835 16075 Z= 0.260 Chirality : 0.042 0.147 1749 Planarity : 0.004 0.051 2049 Dihedral : 7.347 86.097 1570 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 5.93 % Allowed : 26.32 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % 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 are not related in a simple way. whole: 1.65 (0.24), residues: 1404 helix: 2.59 (0.22), residues: 608 sheet: 0.04 (0.32), residues: 275 loop : -0.05 (0.29), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 363 TYR 0.013 0.001 TYR D 145 PHE 0.016 0.001 PHE G 620 TRP 0.006 0.001 TRP G 594 HIS 0.003 0.001 HIS E 367 Details of bonding type rmsd covalent geometry : bond 0.00300 (11798) covalent geometry : angle 0.52674 (16075) hydrogen bonds : bond 0.02917 ( 604) hydrogen bonds : angle 4.48509 ( 1695) Misc. bond : bond 0.05796 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 175 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 139 LYS cc_start: 0.8232 (mptm) cc_final: 0.7852 (mttt) REVERT: B 66 LYS cc_start: 0.9057 (mtpp) cc_final: 0.8796 (mtmt) REVERT: B 95 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8536 (mmtp) REVERT: B 120 LYS cc_start: 0.8364 (ttmm) cc_final: 0.7970 (tptt) REVERT: B 121 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8011 (mp0) REVERT: D 68 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8801 (tp) REVERT: D 77 HIS cc_start: 0.8132 (m170) cc_final: 0.7900 (m90) REVERT: D 95 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8263 (tttm) REVERT: D 144 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.7928 (mptp) REVERT: E 348 ASN cc_start: 0.7647 (OUTLIER) cc_final: 0.7366 (t0) REVERT: E 429 SER cc_start: 0.7682 (t) cc_final: 0.7425 (m) REVERT: E 445 GLU cc_start: 0.6081 (OUTLIER) cc_final: 0.5339 (mt-10) REVERT: E 460 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7673 (tm-30) REVERT: E 488 LYS cc_start: 0.6847 (mtmt) cc_final: 0.5995 (ptmm) REVERT: F 377 VAL cc_start: 0.8688 (t) cc_final: 0.8350 (p) REVERT: F 477 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7914 (tt) REVERT: F 600 GLU cc_start: 0.6605 (mm-30) cc_final: 0.5447 (pp20) REVERT: F 645 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7049 (mm-40) REVERT: G 335 LYS cc_start: 0.6730 (OUTLIER) cc_final: 0.6521 (mmtp) REVERT: G 341 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7792 (t0) REVERT: G 356 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.7162 (mmm) REVERT: G 424 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8274 (pt) REVERT: G 496 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6639 (mt-10) REVERT: G 520 ARG cc_start: 0.6704 (OUTLIER) cc_final: 0.6473 (mtt-85) REVERT: G 522 GLU cc_start: 0.4260 (mt-10) cc_final: 0.3932 (mt-10) REVERT: G 537 VAL cc_start: 0.1081 (OUTLIER) cc_final: 0.0747 (m) REVERT: G 586 MET cc_start: 0.4593 (tmm) cc_final: 0.3833 (tmm) REVERT: G 620 PHE cc_start: 0.7888 (p90) cc_final: 0.7612 (p90) REVERT: G 633 VAL cc_start: 0.7655 (t) cc_final: 0.7222 (m) outliers start: 73 outliers final: 48 residues processed: 230 average time/residue: 0.1092 time to fit residues: 34.9357 Evaluate side-chains 228 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 166 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 414 SER Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain E residue 465 ASN Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain F residue 357 LYS Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 465 ASN Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 490 LEU Chi-restraints excluded: chain F residue 508 TYR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 558 GLU Chi-restraints excluded: chain F residue 564 VAL Chi-restraints excluded: chain F residue 568 PHE Chi-restraints excluded: chain F residue 575 THR Chi-restraints excluded: chain F residue 605 THR Chi-restraints excluded: chain F residue 645 GLN Chi-restraints excluded: chain G residue 335 LYS Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain G residue 356 MET Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain G residue 386 ILE Chi-restraints excluded: chain G residue 388 LEU Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 464 ASN Chi-restraints excluded: chain G residue 479 LYS Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 520 ARG Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 548 GLN Chi-restraints excluded: chain G residue 551 HIS Chi-restraints excluded: chain G residue 584 VAL Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 605 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 65 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 96 optimal weight: 0.0970 chunk 43 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.141422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.109427 restraints weight = 17960.220| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.78 r_work: 0.3151 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 11802 Z= 0.109 Angle : 0.526 10.624 16075 Z= 0.259 Chirality : 0.041 0.147 1749 Planarity : 0.004 0.051 2049 Dihedral : 7.126 85.782 1567 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.93 % Allowed : 26.81 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % 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 are not related in a simple way. whole: 1.65 (0.24), residues: 1404 helix: 2.61 (0.22), residues: 608 sheet: 0.01 (0.32), residues: 276 loop : -0.08 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 363 TYR 0.013 0.001 TYR F 512 PHE 0.015 0.001 PHE G 620 TRP 0.005 0.001 TRP C 14 HIS 0.003 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00278 (11798) covalent geometry : angle 0.52574 (16075) hydrogen bonds : bond 0.02820 ( 604) hydrogen bonds : angle 4.41831 ( 1695) Misc. bond : bond 0.05518 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 177 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8531 (ttmm) cc_final: 0.8032 (ttmm) REVERT: A 139 LYS cc_start: 0.8239 (mptm) cc_final: 0.7846 (mttt) REVERT: B 66 LYS cc_start: 0.9013 (mtpp) cc_final: 0.8729 (mtmt) REVERT: B 95 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8558 (mmtp) REVERT: B 120 LYS cc_start: 0.8408 (ttmm) cc_final: 0.7969 (tptt) REVERT: B 121 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8041 (mp0) REVERT: D 43 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7630 (tt0) REVERT: D 68 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8645 (tp) REVERT: D 77 HIS cc_start: 0.8070 (m170) cc_final: 0.7854 (m90) REVERT: D 95 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8262 (tttm) REVERT: D 144 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.7837 (mptp) REVERT: E 348 ASN cc_start: 0.7621 (OUTLIER) cc_final: 0.7315 (t0) REVERT: E 429 SER cc_start: 0.7689 (t) cc_final: 0.7415 (m) REVERT: E 445 GLU cc_start: 0.6033 (OUTLIER) cc_final: 0.5272 (mt-10) REVERT: E 488 LYS cc_start: 0.6876 (mtmt) cc_final: 0.5957 (ptmm) REVERT: E 498 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7357 (tp30) REVERT: F 377 VAL cc_start: 0.8655 (t) cc_final: 0.8297 (p) REVERT: F 477 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7873 (tt) REVERT: F 600 GLU cc_start: 0.6599 (mm-30) cc_final: 0.5404 (pp20) REVERT: F 645 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7051 (mm-40) REVERT: G 335 LYS cc_start: 0.6654 (OUTLIER) cc_final: 0.6442 (mmtp) REVERT: G 341 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7795 (t0) REVERT: G 356 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.7213 (mmm) REVERT: G 424 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8211 (pt) REVERT: G 496 GLU cc_start: 0.6857 (mt-10) cc_final: 0.6646 (mt-10) REVERT: G 522 GLU cc_start: 0.4215 (mt-10) cc_final: 0.3898 (mt-10) REVERT: G 537 VAL cc_start: 0.1157 (OUTLIER) cc_final: 0.0820 (m) REVERT: G 586 MET cc_start: 0.4714 (tmm) cc_final: 0.3989 (tmm) REVERT: G 620 PHE cc_start: 0.7837 (p90) cc_final: 0.7599 (p90) REVERT: G 633 VAL cc_start: 0.7667 (t) cc_final: 0.7224 (m) outliers start: 73 outliers final: 50 residues processed: 232 average time/residue: 0.1121 time to fit residues: 36.0867 Evaluate side-chains 230 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 167 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 414 SER Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain E residue 465 ASN Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain F residue 357 LYS Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 463 THR Chi-restraints excluded: chain F residue 465 ASN Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 480 LEU Chi-restraints excluded: chain F residue 490 LEU Chi-restraints excluded: chain F residue 508 TYR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 558 GLU Chi-restraints excluded: chain F residue 564 VAL Chi-restraints excluded: chain F residue 568 PHE Chi-restraints excluded: chain F residue 575 THR Chi-restraints excluded: chain F residue 605 THR Chi-restraints excluded: chain F residue 645 GLN Chi-restraints excluded: chain G residue 335 LYS Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain G residue 343 GLU Chi-restraints excluded: chain G residue 356 MET Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain G residue 386 ILE Chi-restraints excluded: chain G residue 388 LEU Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 464 ASN Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 548 GLN Chi-restraints excluded: chain G residue 551 HIS Chi-restraints excluded: chain G residue 584 VAL Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 605 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 77 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 15 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 HIS F 639 ASN G 344 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.141582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.109429 restraints weight = 17960.779| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.86 r_work: 0.3164 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 11802 Z= 0.105 Angle : 0.530 9.661 16075 Z= 0.260 Chirality : 0.041 0.150 1749 Planarity : 0.004 0.051 2049 Dihedral : 7.048 85.168 1567 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.28 % Allowed : 27.13 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % 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 are not related in a simple way. whole: 1.67 (0.24), residues: 1404 helix: 2.62 (0.22), residues: 610 sheet: 0.04 (0.33), residues: 276 loop : -0.08 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 363 TYR 0.013 0.001 TYR F 512 PHE 0.014 0.001 PHE G 620 TRP 0.005 0.001 TRP C 14 HIS 0.003 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00266 (11798) covalent geometry : angle 0.52957 (16075) hydrogen bonds : bond 0.02750 ( 604) hydrogen bonds : angle 4.35773 ( 1695) Misc. bond : bond 0.05204 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 170 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8501 (ttmm) cc_final: 0.7988 (ttmm) REVERT: A 139 LYS cc_start: 0.8197 (mptm) cc_final: 0.7813 (mttt) REVERT: B 66 LYS cc_start: 0.8998 (mtpp) cc_final: 0.8716 (mtmt) REVERT: B 120 LYS cc_start: 0.8421 (ttmm) cc_final: 0.7965 (tptt) REVERT: B 121 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8034 (mp0) REVERT: C 16 LYS cc_start: 0.8494 (tppp) cc_final: 0.7960 (mmmm) REVERT: D 43 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7645 (tt0) REVERT: D 68 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8598 (tp) REVERT: D 77 HIS cc_start: 0.8098 (m170) cc_final: 0.7879 (m90) REVERT: D 95 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8255 (tttm) REVERT: D 144 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.7831 (mptp) REVERT: E 348 ASN cc_start: 0.7592 (OUTLIER) cc_final: 0.7295 (t0) REVERT: E 429 SER cc_start: 0.7660 (t) cc_final: 0.7386 (m) REVERT: E 445 GLU cc_start: 0.6067 (OUTLIER) cc_final: 0.5548 (mt-10) REVERT: E 488 LYS cc_start: 0.6787 (mtmt) cc_final: 0.5900 (ptmm) REVERT: E 498 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7375 (tp30) REVERT: F 377 VAL cc_start: 0.8666 (t) cc_final: 0.8312 (p) REVERT: F 477 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7869 (tt) REVERT: F 502 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7186 (pp20) REVERT: F 600 GLU cc_start: 0.6594 (mm-30) cc_final: 0.5390 (pp20) REVERT: F 645 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6846 (mm-40) REVERT: G 335 LYS cc_start: 0.6624 (OUTLIER) cc_final: 0.6419 (mmtp) REVERT: G 341 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7876 (t0) REVERT: G 356 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.7188 (mmm) REVERT: G 424 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8193 (pt) REVERT: G 522 GLU cc_start: 0.4205 (mt-10) cc_final: 0.3888 (mt-10) REVERT: G 537 VAL cc_start: 0.1153 (OUTLIER) cc_final: 0.0822 (m) REVERT: G 586 MET cc_start: 0.4674 (tmm) cc_final: 0.3972 (tmm) REVERT: G 620 PHE cc_start: 0.7833 (p90) cc_final: 0.7614 (p90) REVERT: G 633 VAL cc_start: 0.7666 (t) cc_final: 0.7229 (m) outliers start: 65 outliers final: 46 residues processed: 219 average time/residue: 0.1147 time to fit residues: 34.7540 Evaluate side-chains 225 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 166 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 414 SER Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain E residue 465 ASN Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain F residue 357 LYS Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 465 ASN Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 502 GLU Chi-restraints excluded: chain F residue 508 TYR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 558 GLU Chi-restraints excluded: chain F residue 564 VAL Chi-restraints excluded: chain F residue 568 PHE Chi-restraints excluded: chain F residue 575 THR Chi-restraints excluded: chain F residue 605 THR Chi-restraints excluded: chain F residue 645 GLN Chi-restraints excluded: chain G residue 335 LYS Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain G residue 343 GLU Chi-restraints excluded: chain G residue 356 MET Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain G residue 386 ILE Chi-restraints excluded: chain G residue 388 LEU Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 436 LYS Chi-restraints excluded: chain G residue 464 ASN Chi-restraints excluded: chain G residue 479 LYS Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 548 GLN Chi-restraints excluded: chain G residue 551 HIS Chi-restraints excluded: chain G residue 584 VAL Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 605 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 41 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 75 optimal weight: 0.0870 chunk 124 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 135 optimal weight: 0.0970 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.141898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.109301 restraints weight = 17870.991| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.80 r_work: 0.3208 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 11802 Z= 0.102 Angle : 0.526 8.475 16075 Z= 0.259 Chirality : 0.041 0.148 1749 Planarity : 0.004 0.051 2049 Dihedral : 6.988 84.601 1567 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.87 % Allowed : 27.46 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % 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 are not related in a simple way. whole: 1.64 (0.24), residues: 1404 helix: 2.57 (0.22), residues: 616 sheet: 0.06 (0.33), residues: 276 loop : -0.11 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 616 TYR 0.013 0.001 TYR F 512 PHE 0.014 0.001 PHE G 620 TRP 0.005 0.001 TRP F 594 HIS 0.003 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00260 (11798) covalent geometry : angle 0.52599 (16075) hydrogen bonds : bond 0.02701 ( 604) hydrogen bonds : angle 4.30985 ( 1695) Misc. bond : bond 0.05158 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 175 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8447 (ttmm) cc_final: 0.7993 (ttmm) REVERT: A 139 LYS cc_start: 0.8171 (mptm) cc_final: 0.7824 (mttt) REVERT: B 66 LYS cc_start: 0.9057 (mtpp) cc_final: 0.8811 (mtmt) REVERT: B 120 LYS cc_start: 0.8373 (ttmm) cc_final: 0.8009 (tptt) REVERT: C 16 LYS cc_start: 0.8482 (tppp) cc_final: 0.7954 (mmmm) REVERT: D 43 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7669 (tt0) REVERT: D 68 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8600 (tp) REVERT: D 77 HIS cc_start: 0.8110 (m170) cc_final: 0.7898 (m90) REVERT: D 95 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8271 (tttm) REVERT: D 144 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.7869 (mptp) REVERT: E 348 ASN cc_start: 0.7666 (OUTLIER) cc_final: 0.7381 (t0) REVERT: E 429 SER cc_start: 0.7612 (t) cc_final: 0.7384 (m) REVERT: E 445 GLU cc_start: 0.6115 (mp0) cc_final: 0.5655 (mt-10) REVERT: E 488 LYS cc_start: 0.6844 (mtmt) cc_final: 0.5951 (ptmm) REVERT: F 377 VAL cc_start: 0.8661 (t) cc_final: 0.8352 (p) REVERT: F 477 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7908 (tt) REVERT: F 600 GLU cc_start: 0.6587 (mm-30) cc_final: 0.5451 (pp20) REVERT: F 645 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.6942 (mm-40) REVERT: G 341 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7854 (t0) REVERT: G 356 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.7205 (mmm) REVERT: G 424 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8256 (pt) REVERT: G 522 GLU cc_start: 0.4254 (mt-10) cc_final: 0.3929 (mt-10) REVERT: G 537 VAL cc_start: 0.1143 (OUTLIER) cc_final: 0.0757 (m) REVERT: G 586 MET cc_start: 0.4930 (tmm) cc_final: 0.4247 (tmm) REVERT: G 633 VAL cc_start: 0.7641 (t) cc_final: 0.7189 (m) outliers start: 60 outliers final: 47 residues processed: 220 average time/residue: 0.1122 time to fit residues: 34.0846 Evaluate side-chains 224 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 167 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 414 SER Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 465 ASN Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain F residue 357 LYS Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 463 THR Chi-restraints excluded: chain F residue 465 ASN Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 508 TYR Chi-restraints excluded: chain F residue 558 GLU Chi-restraints excluded: chain F residue 564 VAL Chi-restraints excluded: chain F residue 568 PHE Chi-restraints excluded: chain F residue 605 THR Chi-restraints excluded: chain F residue 645 GLN Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain G residue 343 GLU Chi-restraints excluded: chain G residue 356 MET Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain G residue 386 ILE Chi-restraints excluded: chain G residue 388 LEU Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 436 LYS Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 464 ASN Chi-restraints excluded: chain G residue 479 LYS Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 548 GLN Chi-restraints excluded: chain G residue 551 HIS Chi-restraints excluded: chain G residue 584 VAL Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 605 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 HIS C 78 ASN F 639 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.138575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.106581 restraints weight = 17930.472| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.75 r_work: 0.3130 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 11802 Z= 0.173 Angle : 0.592 9.109 16075 Z= 0.296 Chirality : 0.044 0.172 1749 Planarity : 0.004 0.051 2049 Dihedral : 7.222 86.414 1565 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 5.12 % Allowed : 26.89 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % 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 are not related in a simple way. whole: 1.39 (0.24), residues: 1404 helix: 2.34 (0.21), residues: 614 sheet: -0.00 (0.33), residues: 276 loop : -0.24 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 616 TYR 0.016 0.001 TYR F 512 PHE 0.032 0.002 PHE G 620 TRP 0.007 0.001 TRP A 14 HIS 0.005 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00430 (11798) covalent geometry : angle 0.59192 (16075) hydrogen bonds : bond 0.03457 ( 604) hydrogen bonds : angle 4.53558 ( 1695) Misc. bond : bond 0.06639 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 169 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: B 66 LYS cc_start: 0.9053 (mtpp) cc_final: 0.8749 (mtmt) REVERT: B 95 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8558 (mmtp) REVERT: B 120 LYS cc_start: 0.8450 (ttmm) cc_final: 0.7956 (tptt) REVERT: B 121 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8024 (mp0) REVERT: B 139 ASN cc_start: 0.8694 (t0) cc_final: 0.8066 (m-40) REVERT: D 68 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8741 (tp) REVERT: D 95 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8233 (tttm) REVERT: E 429 SER cc_start: 0.7894 (t) cc_final: 0.7570 (m) REVERT: E 445 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.5301 (mt-10) REVERT: E 488 LYS cc_start: 0.6848 (mtmt) cc_final: 0.5925 (ptmm) REVERT: E 498 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7359 (tp30) REVERT: F 377 VAL cc_start: 0.8766 (t) cc_final: 0.8464 (p) REVERT: F 477 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7951 (tt) REVERT: F 502 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7213 (pp20) REVERT: F 593 TYR cc_start: 0.7482 (m-10) cc_final: 0.7220 (m-80) REVERT: F 600 GLU cc_start: 0.6611 (mm-30) cc_final: 0.5341 (pp20) REVERT: F 645 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7023 (mm-40) REVERT: G 356 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.7286 (mmm) REVERT: G 424 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8285 (pt) REVERT: G 522 GLU cc_start: 0.4118 (mt-10) cc_final: 0.3793 (mt-10) REVERT: G 537 VAL cc_start: 0.1274 (OUTLIER) cc_final: 0.0918 (m) REVERT: G 586 MET cc_start: 0.4987 (tmm) cc_final: 0.4493 (tmm) outliers start: 63 outliers final: 46 residues processed: 214 average time/residue: 0.1052 time to fit residues: 31.3632 Evaluate side-chains 222 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 166 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 414 SER Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain E residue 465 ASN Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain F residue 357 LYS Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 463 THR Chi-restraints excluded: chain F residue 465 ASN Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 502 GLU Chi-restraints excluded: chain F residue 508 TYR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 558 GLU Chi-restraints excluded: chain F residue 564 VAL Chi-restraints excluded: chain F residue 568 PHE Chi-restraints excluded: chain F residue 575 THR Chi-restraints excluded: chain F residue 645 GLN Chi-restraints excluded: chain G residue 343 GLU Chi-restraints excluded: chain G residue 356 MET Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain G residue 386 ILE Chi-restraints excluded: chain G residue 388 LEU Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 464 ASN Chi-restraints excluded: chain G residue 479 LYS Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 548 GLN Chi-restraints excluded: chain G residue 551 HIS Chi-restraints excluded: chain G residue 584 VAL Chi-restraints excluded: chain G residue 605 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 HIS C 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.140458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.108394 restraints weight = 17943.981| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.77 r_work: 0.3178 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 11802 Z= 0.117 Angle : 0.546 8.925 16075 Z= 0.273 Chirality : 0.042 0.147 1749 Planarity : 0.004 0.051 2049 Dihedral : 7.101 86.334 1565 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.47 % Allowed : 27.54 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % 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 are not related in a simple way. whole: 1.46 (0.24), residues: 1404 helix: 2.42 (0.21), residues: 614 sheet: 0.00 (0.33), residues: 276 loop : -0.23 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 616 TYR 0.014 0.001 TYR F 512 PHE 0.033 0.001 PHE G 620 TRP 0.008 0.001 TRP G 594 HIS 0.003 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00295 (11798) covalent geometry : angle 0.54645 (16075) hydrogen bonds : bond 0.02928 ( 604) hydrogen bonds : angle 4.41975 ( 1695) Misc. bond : bond 0.05581 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3193.34 seconds wall clock time: 55 minutes 18.83 seconds (3318.83 seconds total)