Starting phenix.real_space_refine on Mon Apr 6 03:29:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9unw_64367/04_2026/9unw_64367.cif Found real_map, /net/cci-nas-00/data/ceres_data/9unw_64367/04_2026/9unw_64367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9unw_64367/04_2026/9unw_64367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9unw_64367/04_2026/9unw_64367.map" model { file = "/net/cci-nas-00/data/ceres_data/9unw_64367/04_2026/9unw_64367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9unw_64367/04_2026/9unw_64367.cif" } resolution = 3.55 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= 0.073 sd= 0.578 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 86 5.16 5 C 9537 2.51 5 N 2643 2.21 5 O 2952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15218 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1862 Classifications: {'peptide': 247} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 237} Chain breaks: 1 Chain: "G" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1771 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 6, 'TRANS': 235} Chain breaks: 1 Chain: "H" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1784 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 7, 'TRANS': 227} Chain breaks: 1 Chain: "I" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1799 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 232} Chain breaks: 1 Chain: "F" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1811 Classifications: {'peptide': 240} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 230} Chain breaks: 1 Chain: "A" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1800 Classifications: {'peptide': 243} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 234} Chain breaks: 1 Chain: "B" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1822 Classifications: {'peptide': 239} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 228} Chain breaks: 1 Chain: "E" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1823 Classifications: {'peptide': 237} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 228} Chain breaks: 1 Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Time building chain proxies: 3.39, per 1000 atoms: 0.22 Number of scatterers: 15218 At special positions: 0 Unit cell: (128.76, 147.03, 166.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 86 16.00 O 2952 8.00 N 2643 7.00 C 9537 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=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 496.9 milliseconds 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 18 sheets defined 70.8% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'C' and resid 14 through 34 removed outlier: 4.293A pdb=" N SER C 34 " --> pdb=" O ASN C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 64 Processing helix chain 'C' and resid 69 through 86 removed outlier: 3.553A pdb=" N GLN C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 109 Processing helix chain 'C' and resid 113 through 134 Processing helix chain 'C' and resid 413 through 429 Processing helix chain 'C' and resid 430 through 431 No H-bonds generated for 'chain 'C' and resid 430 through 431' Processing helix chain 'C' and resid 432 through 433 No H-bonds generated for 'chain 'C' and resid 432 through 433' Processing helix chain 'C' and resid 434 through 445 Processing helix chain 'C' and resid 446 through 456 Processing helix chain 'C' and resid 459 through 477 removed outlier: 3.609A pdb=" N ALA C 465 " --> pdb=" O THR C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 502 Processing helix chain 'C' and resid 506 through 526 Processing helix chain 'G' and resid 24 through 41 removed outlier: 4.383A pdb=" N SER G 41 " --> pdb=" O ASP G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 74 Processing helix chain 'G' and resid 78 through 96 removed outlier: 3.624A pdb=" N GLN G 91 " --> pdb=" O MET G 87 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU G 94 " --> pdb=" O VAL G 90 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY G 96 " --> pdb=" O ASP G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 119 removed outlier: 3.518A pdb=" N SER G 115 " --> pdb=" O ARG G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 143 Processing helix chain 'G' and resid 411 through 426 Processing helix chain 'G' and resid 431 through 455 removed outlier: 4.042A pdb=" N ALA G 435 " --> pdb=" O LYS G 431 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU G 446 " --> pdb=" O ALA G 442 " (cutoff:3.500A) Proline residue: G 447 - end of helix Processing helix chain 'G' and resid 457 through 471 Processing helix chain 'G' and resid 488 through 492 Processing helix chain 'G' and resid 496 through 516 Processing helix chain 'H' and resid 20 through 38 removed outlier: 3.518A pdb=" N ILE H 36 " --> pdb=" O THR H 32 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE H 37 " --> pdb=" O ILE H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 41 No H-bonds generated for 'chain 'H' and resid 39 through 41' Processing helix chain 'H' and resid 62 through 70 Processing helix chain 'H' and resid 74 through 89 Processing helix chain 'H' and resid 94 through 108 removed outlier: 3.749A pdb=" N VAL H 108 " --> pdb=" O GLU H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 113 removed outlier: 4.201A pdb=" N PHE H 112 " --> pdb=" O VAL H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 139 Processing helix chain 'H' and resid 414 through 427 Processing helix chain 'H' and resid 433 through 444 removed outlier: 3.513A pdb=" N LEU H 444 " --> pdb=" O VAL H 440 " (cutoff:3.500A) Processing helix chain 'H' and resid 445 through 455 Processing helix chain 'H' and resid 458 through 473 Processing helix chain 'H' and resid 489 through 493 Processing helix chain 'H' and resid 498 through 518 Processing helix chain 'I' and resid 29 through 50 removed outlier: 3.571A pdb=" N ILE I 48 " --> pdb=" O VAL I 44 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N THR I 50 " --> pdb=" O ASP I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 82 removed outlier: 3.964A pdb=" N GLN I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 102 removed outlier: 3.500A pdb=" N LEU I 91 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 125 Processing helix chain 'I' and resid 129 through 149 Processing helix chain 'I' and resid 426 through 441 removed outlier: 3.591A pdb=" N ARG I 441 " --> pdb=" O THR I 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 446 through 458 removed outlier: 3.505A pdb=" N CYS I 450 " --> pdb=" O MET I 446 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET I 458 " --> pdb=" O PHE I 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 459 through 470 Processing helix chain 'I' and resid 472 through 487 Processing helix chain 'I' and resid 504 through 508 Processing helix chain 'I' and resid 511 through 531 removed outlier: 4.040A pdb=" N SER I 515 " --> pdb=" O PRO I 511 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 50 removed outlier: 4.299A pdb=" N THR F 50 " --> pdb=" O ASN F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 81 Processing helix chain 'F' and resid 85 through 96 Processing helix chain 'F' and resid 97 through 100 removed outlier: 3.898A pdb=" N ASP F 100 " --> pdb=" O SER F 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 97 through 100' Processing helix chain 'F' and resid 105 through 125 removed outlier: 3.524A pdb=" N GLN F 122 " --> pdb=" O GLU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 150 Processing helix chain 'F' and resid 425 through 438 removed outlier: 3.711A pdb=" N ASP F 438 " --> pdb=" O SER F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 456 Processing helix chain 'F' and resid 456 through 466 Processing helix chain 'F' and resid 469 through 481 Processing helix chain 'F' and resid 500 through 505 Processing helix chain 'F' and resid 509 through 529 Processing helix chain 'A' and resid 16 through 35 removed outlier: 4.351A pdb=" N LEU A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 38 No H-bonds generated for 'chain 'A' and resid 36 through 38' Processing helix chain 'A' and resid 59 through 67 Processing helix chain 'A' and resid 71 through 86 Processing helix chain 'A' and resid 91 through 111 Processing helix chain 'A' and resid 115 through 135 removed outlier: 3.681A pdb=" N ILE A 119 " --> pdb=" O HIS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 426 Processing helix chain 'A' and resid 433 through 444 Processing helix chain 'A' and resid 445 through 455 Processing helix chain 'A' and resid 458 through 473 Processing helix chain 'A' and resid 497 through 517 Processing helix chain 'B' and resid 18 through 35 Processing helix chain 'B' and resid 36 through 40 Processing helix chain 'B' and resid 61 through 70 removed outlier: 3.937A pdb=" N ASP B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 88 removed outlier: 4.071A pdb=" N ALA B 88 " --> pdb=" O LYS B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 113 Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 117 through 139 Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 430 through 443 removed outlier: 3.830A pdb=" N GLU B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 453 Processing helix chain 'B' and resid 456 through 470 Processing helix chain 'B' and resid 495 through 515 Processing helix chain 'E' and resid 27 through 45 removed outlier: 4.201A pdb=" N THR E 45 " --> pdb=" O GLN E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 76 Processing helix chain 'E' and resid 80 through 94 Processing helix chain 'E' and resid 100 through 120 Processing helix chain 'E' and resid 124 through 143 Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 415 through 428 Processing helix chain 'E' and resid 433 through 456 removed outlier: 4.163A pdb=" N ALA E 437 " --> pdb=" O LEU E 433 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA E 447 " --> pdb=" O GLU E 443 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE E 448 " --> pdb=" O ALA E 444 " (cutoff:3.500A) Proline residue: E 449 - end of helix Processing helix chain 'E' and resid 459 through 473 Processing helix chain 'E' and resid 500 through 520 Processing helix chain 'D' and resid 25 through 48 Processing helix chain 'D' and resid 49 through 61 Processing helix chain 'D' and resid 63 through 80 removed outlier: 3.760A pdb=" N ALA D 69 " --> pdb=" O GLU D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 104 removed outlier: 3.643A pdb=" N THR D 103 " --> pdb=" O VAL D 99 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 52 through 55 removed outlier: 7.823A pdb=" N ASP C 42 " --> pdb=" O ASP H 521 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N VAL H 523 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N MET C 44 " --> pdb=" O VAL H 523 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 409 through 410 Processing sheet with id=AA3, first strand: chain 'C' and resid 486 through 488 Processing sheet with id=AA4, first strand: chain 'C' and resid 527 through 532 removed outlier: 7.127A pdb=" N MET I 60 " --> pdb=" O ASP C 528 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU C 530 " --> pdb=" O MET I 60 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLN I 62 " --> pdb=" O LEU C 530 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LYS C 532 " --> pdb=" O GLN I 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 62 through 64 removed outlier: 7.881A pdb=" N ASP G 49 " --> pdb=" O ASP I 533 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL I 535 " --> pdb=" O ASP G 49 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE G 51 " --> pdb=" O VAL I 535 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ASN I 537 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LEU G 53 " --> pdb=" O ASN I 537 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 407 through 408 Processing sheet with id=AA7, first strand: chain 'G' and resid 476 through 479 Processing sheet with id=AA8, first strand: chain 'G' and resid 517 through 522 removed outlier: 6.557A pdb=" N ASP F 58 " --> pdb=" O VAL G 517 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASN G 519 " --> pdb=" O ASP F 58 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 56 through 60 removed outlier: 7.290A pdb=" N MET H 47 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N MET A 522 " --> pdb=" O MET H 47 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N MET H 49 " --> pdb=" O MET A 522 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 479 through 480 Processing sheet with id=AB2, first strand: chain 'I' and resid 492 through 494 Processing sheet with id=AB3, first strand: chain 'F' and resid 530 through 534 removed outlier: 4.243A pdb=" N ILE F 530 " --> pdb=" O ASP B 46 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU B 48 " --> pdb=" O ILE F 530 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP F 532 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL B 50 " --> pdb=" O ASP F 532 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ARG F 534 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 54 through 57 removed outlier: 7.446A pdb=" N MET A 44 " --> pdb=" O GLN E 523 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ILE E 525 " --> pdb=" O MET A 44 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N MET A 46 " --> pdb=" O ILE E 525 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 408 through 409 Processing sheet with id=AB6, first strand: chain 'A' and resid 477 through 479 Processing sheet with id=AB7, first strand: chain 'B' and resid 475 through 477 Processing sheet with id=AB8, first strand: chain 'B' and resid 516 through 521 removed outlier: 6.367A pdb=" N ASN E 53 " --> pdb=" O VAL B 516 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU B 518 " --> pdb=" O ASN E 53 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 478 through 480 1081 hydrogen bonds defined for protein. 3198 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: 2.68 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 4134 1.32 - 1.46: 4577 1.46 - 1.60: 6509 1.60 - 1.75: 65 1.75 - 1.89: 90 Bond restraints: 15375 Sorted by residual: bond pdb=" CB HIS H 74 " pdb=" CG HIS H 74 " ideal model delta sigma weight residual 1.497 1.368 0.129 1.40e-02 5.10e+03 8.49e+01 bond pdb=" CB HIS A 71 " pdb=" CG HIS A 71 " ideal model delta sigma weight residual 1.497 1.377 0.120 1.40e-02 5.10e+03 7.36e+01 bond pdb=" CB LEU I 504 " pdb=" CG LEU I 504 " ideal model delta sigma weight residual 1.530 1.372 0.158 2.00e-02 2.50e+03 6.22e+01 bond pdb=" CB HIS F 147 " pdb=" CG HIS F 147 " ideal model delta sigma weight residual 1.497 1.392 0.105 1.40e-02 5.10e+03 5.59e+01 bond pdb=" CB PHE H 112 " pdb=" CG PHE H 112 " ideal model delta sigma weight residual 1.502 1.339 0.163 2.30e-02 1.89e+03 5.04e+01 ... (remaining 15370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 18961 2.07 - 4.14: 1516 4.14 - 6.21: 247 6.21 - 8.28: 51 8.28 - 10.35: 3 Bond angle restraints: 20778 Sorted by residual: angle pdb=" C GLY B 41 " pdb=" N PRO B 42 " pdb=" CA PRO B 42 " ideal model delta sigma weight residual 119.56 127.82 -8.26 1.01e+00 9.80e-01 6.69e+01 angle pdb=" N ILE F 491 " pdb=" CA ILE F 491 " pdb=" C ILE F 491 " ideal model delta sigma weight residual 113.71 106.13 7.58 9.50e-01 1.11e+00 6.37e+01 angle pdb=" C GLY G 44 " pdb=" N PRO G 45 " pdb=" CA PRO G 45 " ideal model delta sigma weight residual 119.56 127.27 -7.71 1.01e+00 9.80e-01 5.82e+01 angle pdb=" C GLY F 53 " pdb=" N PRO F 54 " pdb=" CA PRO F 54 " ideal model delta sigma weight residual 119.56 127.21 -7.65 1.01e+00 9.80e-01 5.74e+01 angle pdb=" C GLY H 42 " pdb=" N PRO H 43 " pdb=" CA PRO H 43 " ideal model delta sigma weight residual 119.87 127.75 -7.88 1.04e+00 9.25e-01 5.74e+01 ... (remaining 20773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 9209 17.40 - 34.80: 206 34.80 - 52.20: 59 52.20 - 69.60: 39 69.60 - 87.00: 14 Dihedral angle restraints: 9527 sinusoidal: 3732 harmonic: 5795 Sorted by residual: dihedral pdb=" CA MET H 429 " pdb=" C MET H 429 " pdb=" N THR H 430 " pdb=" CA THR H 430 " ideal model delta harmonic sigma weight residual -180.00 -139.74 -40.26 0 5.00e+00 4.00e-02 6.48e+01 dihedral pdb=" CA GLY E 479 " pdb=" C GLY E 479 " pdb=" N LEU E 480 " pdb=" CA LEU E 480 " ideal model delta harmonic sigma weight residual 180.00 -146.67 -33.33 0 5.00e+00 4.00e-02 4.44e+01 dihedral pdb=" CA ASP I 28 " pdb=" C ASP I 28 " pdb=" N LYS I 29 " pdb=" CA LYS I 29 " ideal model delta harmonic sigma weight residual -180.00 -147.12 -32.88 0 5.00e+00 4.00e-02 4.32e+01 ... (remaining 9524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 1671 0.117 - 0.235: 788 0.235 - 0.352: 57 0.352 - 0.470: 10 0.470 - 0.587: 2 Chirality restraints: 2528 Sorted by residual: chirality pdb=" CB VAL I 109 " pdb=" CA VAL I 109 " pdb=" CG1 VAL I 109 " pdb=" CG2 VAL I 109 " both_signs ideal model delta sigma weight residual False -2.63 -2.04 -0.59 2.00e-01 2.50e+01 8.62e+00 chirality pdb=" CB ILE H 83 " pdb=" CA ILE H 83 " pdb=" CG1 ILE H 83 " pdb=" CG2 ILE H 83 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.50 2.00e-01 2.50e+01 6.31e+00 chirality pdb=" CB ILE B 427 " pdb=" CA ILE B 427 " pdb=" CG1 ILE B 427 " pdb=" CG2 ILE B 427 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 5.03e+00 ... (remaining 2525 not shown) Planarity restraints: 2668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS F 483 " -0.063 2.00e-02 2.50e+03 1.34e-01 1.80e+02 pdb=" C LYS F 483 " 0.232 2.00e-02 2.50e+03 pdb=" O LYS F 483 " -0.091 2.00e-02 2.50e+03 pdb=" N GLU F 484 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 484 " 0.063 2.00e-02 2.50e+03 1.32e-01 1.75e+02 pdb=" C GLY A 484 " -0.229 2.00e-02 2.50e+03 pdb=" O GLY A 484 " 0.087 2.00e-02 2.50e+03 pdb=" N GLU A 485 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 442 " -0.063 2.00e-02 2.50e+03 1.30e-01 1.69e+02 pdb=" C GLN H 442 " 0.224 2.00e-02 2.50e+03 pdb=" O GLN H 442 " -0.085 2.00e-02 2.50e+03 pdb=" N ALA H 443 " -0.076 2.00e-02 2.50e+03 ... (remaining 2665 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3638 2.75 - 3.29: 16553 3.29 - 3.83: 25679 3.83 - 4.36: 30908 4.36 - 4.90: 49446 Nonbonded interactions: 126224 Sorted by model distance: nonbonded pdb=" N GLN A 17 " pdb=" OE1 GLN A 17 " model vdw 2.218 3.120 nonbonded pdb=" N GLU C 416 " pdb=" OE1 GLU C 416 " model vdw 2.254 3.120 nonbonded pdb=" N GLU F 426 " pdb=" OE1 GLU F 426 " model vdw 2.280 3.120 nonbonded pdb=" N GLN A 70 " pdb=" OE1 GLN A 70 " model vdw 2.283 3.120 nonbonded pdb=" O ASP H 521 " pdb=" OD1 ASP H 521 " model vdw 2.296 3.040 ... (remaining 126219 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.600 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.420 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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 : 0.030 0.220 15375 Z= 1.653 Angle : 1.294 10.355 20778 Z= 0.905 Chirality : 0.119 0.587 2528 Planarity : 0.013 0.134 2668 Dihedral : 10.714 86.998 5767 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.32 % Favored : 97.63 % Rotamer: Outliers : 0.12 % Allowed : 0.37 % Favored : 99.51 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: 0.71 (0.18), residues: 1986 helix: 0.77 (0.13), residues: 1391 sheet: 0.90 (0.54), residues: 88 loop : -0.17 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 111 TYR 0.056 0.010 TYR H 437 PHE 0.030 0.006 PHE C 504 TRP 0.029 0.008 TRP E 506 HIS 0.009 0.002 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.03007 (15375) covalent geometry : angle 1.29401 (20778) hydrogen bonds : bond 0.17745 ( 1081) hydrogen bonds : angle 6.18558 ( 3198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 557 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 60 THR cc_start: 0.8495 (m) cc_final: 0.8203 (p) REVERT: C 433 ARG cc_start: 0.4503 (mmt180) cc_final: 0.4038 (mmt180) REVERT: H 26 ASN cc_start: 0.9084 (m-40) cc_final: 0.8876 (m-40) REVERT: H 62 ASP cc_start: 0.7665 (t0) cc_final: 0.7329 (t0) REVERT: I 494 ASN cc_start: 0.8541 (t0) cc_final: 0.7911 (t0) REVERT: I 535 VAL cc_start: 0.9398 (t) cc_final: 0.9171 (p) REVERT: F 68 VAL cc_start: 0.9458 (t) cc_final: 0.9244 (m) REVERT: F 126 ARG cc_start: 0.8200 (mtt-85) cc_final: 0.6703 (tmt170) REVERT: F 444 GLU cc_start: 0.8018 (mp0) cc_final: 0.7793 (mp0) REVERT: B 426 THR cc_start: 0.8863 (m) cc_final: 0.8657 (p) REVERT: B 475 TYR cc_start: 0.8382 (m-80) cc_final: 0.7933 (m-10) REVERT: B 483 ASN cc_start: 0.8387 (t0) cc_final: 0.8167 (t0) REVERT: D 40 ARG cc_start: 0.8961 (mtt-85) cc_final: 0.8679 (mmm160) REVERT: D 71 GLU cc_start: 0.8910 (tt0) cc_final: 0.8592 (tt0) outliers start: 2 outliers final: 0 residues processed: 557 average time/residue: 0.1887 time to fit residues: 137.7083 Evaluate side-chains 376 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 GLN C 69 HIS H 73 GLN ** I 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 ASN A 95 ASN E 102 ASN E 140 HIS ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.064390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.055369 restraints weight = 53015.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.056964 restraints weight = 26182.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.057980 restraints weight = 16112.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.058706 restraints weight = 11527.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.059150 restraints weight = 9052.425| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 15375 Z= 0.180 Angle : 0.685 11.944 20778 Z= 0.363 Chirality : 0.042 0.175 2528 Planarity : 0.005 0.072 2668 Dihedral : 4.758 41.721 2120 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.08 % Allowed : 9.66 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.03 (0.18), residues: 1986 helix: 1.97 (0.13), residues: 1388 sheet: 1.85 (0.59), residues: 54 loop : -0.29 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 480 TYR 0.024 0.002 TYR C 426 PHE 0.013 0.002 PHE E 441 TRP 0.008 0.001 TRP H 478 HIS 0.006 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00381 (15375) covalent geometry : angle 0.68485 (20778) hydrogen bonds : bond 0.05915 ( 1081) hydrogen bonds : angle 4.24664 ( 3198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 487 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 433 ARG cc_start: 0.3415 (mmt180) cc_final: 0.2296 (mtp85) REVERT: G 520 ILE cc_start: 0.8870 (mt) cc_final: 0.8652 (mm) REVERT: H 26 ASN cc_start: 0.8902 (m-40) cc_final: 0.8613 (m-40) REVERT: H 69 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8293 (tm-30) REVERT: H 74 HIS cc_start: 0.6305 (t-90) cc_final: 0.6028 (m-70) REVERT: H 425 LYS cc_start: 0.8728 (mtpp) cc_final: 0.8522 (mtpp) REVERT: H 478 TRP cc_start: 0.8276 (m100) cc_final: 0.7734 (m100) REVERT: I 73 ASP cc_start: 0.7571 (t0) cc_final: 0.7295 (t0) REVERT: I 89 ARG cc_start: 0.7608 (ttm110) cc_final: 0.6868 (mtm-85) REVERT: I 90 MET cc_start: 0.8410 (mtp) cc_final: 0.8075 (mtp) REVERT: F 126 ARG cc_start: 0.7797 (mtt-85) cc_final: 0.6689 (tmt170) REVERT: F 480 ARG cc_start: 0.7526 (tpp80) cc_final: 0.6929 (tpp80) REVERT: F 501 MET cc_start: 0.2794 (mtt) cc_final: 0.2087 (ttt) REVERT: A 58 LYS cc_start: 0.4950 (pttt) cc_final: 0.4273 (tttt) REVERT: A 415 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7804 (mp0) REVERT: A 460 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8396 (mp10) REVERT: A 461 GLU cc_start: 0.6090 (mm-30) cc_final: 0.5253 (mm-30) REVERT: A 480 ASP cc_start: 0.8141 (t0) cc_final: 0.7858 (t0) REVERT: A 519 ASP cc_start: 0.6984 (t0) cc_final: 0.6501 (t0) REVERT: A 522 MET cc_start: 0.6891 (ttm) cc_final: 0.6624 (ttm) REVERT: B 465 ARG cc_start: 0.7043 (ttp-170) cc_final: 0.6346 (mtm110) REVERT: B 518 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7559 (tm-30) REVERT: E 31 ARG cc_start: 0.7432 (mtm-85) cc_final: 0.7069 (mtm-85) REVERT: E 138 LYS cc_start: 0.7040 (mttt) cc_final: 0.6581 (tppt) REVERT: E 472 GLN cc_start: 0.8040 (tp40) cc_final: 0.7551 (tp40) REVERT: E 506 TRP cc_start: 0.8542 (m100) cc_final: 0.8323 (m100) REVERT: E 524 ILE cc_start: 0.8805 (mt) cc_final: 0.8484 (mm) REVERT: D 40 ARG cc_start: 0.8091 (mtt-85) cc_final: 0.7579 (mmm160) REVERT: D 41 ASN cc_start: 0.8954 (t0) cc_final: 0.8745 (t0) outliers start: 34 outliers final: 16 residues processed: 498 average time/residue: 0.1624 time to fit residues: 109.3474 Evaluate side-chains 419 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 402 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain I residue 491 THR Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 486 ASN Chi-restraints excluded: chain F residue 508 GLU Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 499 CYS Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 116 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 0.0030 chunk 167 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 28 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 HIS H 111 HIS I 37 ASN A 95 ASN E 422 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.064619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.055717 restraints weight = 53790.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.057259 restraints weight = 27012.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.058262 restraints weight = 16784.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.058931 restraints weight = 12072.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.059403 restraints weight = 9578.651| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15375 Z= 0.147 Angle : 0.628 11.994 20778 Z= 0.330 Chirality : 0.040 0.163 2528 Planarity : 0.004 0.051 2668 Dihedral : 4.504 38.557 2120 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.08 % Allowed : 13.51 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.08 (0.19), residues: 1986 helix: 2.10 (0.14), residues: 1388 sheet: 1.14 (0.60), residues: 58 loop : -0.51 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 79 TYR 0.022 0.001 TYR C 426 PHE 0.013 0.002 PHE I 454 TRP 0.005 0.001 TRP E 506 HIS 0.004 0.001 HIS C 113 Details of bonding type rmsd covalent geometry : bond 0.00314 (15375) covalent geometry : angle 0.62800 (20778) hydrogen bonds : bond 0.05158 ( 1081) hydrogen bonds : angle 4.02478 ( 3198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 448 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 433 ARG cc_start: 0.3285 (mmt180) cc_final: 0.2136 (mtp85) REVERT: G 488 MET cc_start: 0.8491 (tpp) cc_final: 0.7627 (tpp) REVERT: H 74 HIS cc_start: 0.6375 (t-90) cc_final: 0.6162 (m-70) REVERT: H 478 TRP cc_start: 0.8041 (m100) cc_final: 0.7278 (m100) REVERT: I 147 ILE cc_start: 0.7804 (mm) cc_final: 0.7471 (mt) REVERT: I 510 GLN cc_start: 0.6614 (pm20) cc_final: 0.6339 (pm20) REVERT: F 48 MET cc_start: 0.8040 (tpp) cc_final: 0.7703 (tpp) REVERT: F 60 MET cc_start: 0.8470 (ttm) cc_final: 0.8158 (ttm) REVERT: F 126 ARG cc_start: 0.7749 (mtt-85) cc_final: 0.6755 (tmt170) REVERT: F 501 MET cc_start: 0.2996 (mtt) cc_final: 0.2299 (ttt) REVERT: F 508 GLU cc_start: 0.5646 (OUTLIER) cc_final: 0.4953 (pm20) REVERT: A 58 LYS cc_start: 0.4648 (pttt) cc_final: 0.4070 (tttt) REVERT: A 124 GLU cc_start: 0.7911 (tp30) cc_final: 0.7693 (tp30) REVERT: A 415 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7925 (mp0) REVERT: A 460 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8310 (mp10) REVERT: B 518 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7504 (tm-30) REVERT: E 31 ARG cc_start: 0.7528 (mtm-85) cc_final: 0.7217 (mtm-85) REVERT: E 472 GLN cc_start: 0.7962 (tp40) cc_final: 0.7601 (tp40) REVERT: D 40 ARG cc_start: 0.7542 (mtt-85) cc_final: 0.7330 (mmt180) REVERT: D 71 GLU cc_start: 0.7901 (tt0) cc_final: 0.7554 (tt0) REVERT: D 76 GLN cc_start: 0.8569 (pp30) cc_final: 0.8328 (pp30) outliers start: 34 outliers final: 15 residues processed: 465 average time/residue: 0.1664 time to fit residues: 103.8643 Evaluate side-chains 426 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 409 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain I residue 491 THR Chi-restraints excluded: chain I residue 515 SER Chi-restraints excluded: chain I residue 535 VAL Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain F residue 486 ASN Chi-restraints excluded: chain F residue 508 GLU Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 499 CYS Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 482 ILE Chi-restraints excluded: chain E residue 499 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 78 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 195 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 83 optimal weight: 0.1980 chunk 26 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 80 optimal weight: 0.0070 chunk 18 optimal weight: 0.3980 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 GLN C 82 GLN I 80 GLN A 95 ASN B 481 ASN ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.064621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.055735 restraints weight = 53863.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.057272 restraints weight = 27065.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.058238 restraints weight = 16869.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.058950 restraints weight = 12176.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.059372 restraints weight = 9653.595| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15375 Z= 0.142 Angle : 0.633 12.537 20778 Z= 0.331 Chirality : 0.040 0.187 2528 Planarity : 0.004 0.056 2668 Dihedral : 4.426 35.772 2120 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.38 % Allowed : 14.30 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.12 (0.19), residues: 1986 helix: 2.16 (0.14), residues: 1385 sheet: 0.77 (0.56), residues: 70 loop : -0.55 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 496 TYR 0.028 0.002 TYR B 423 PHE 0.018 0.002 PHE A 133 TRP 0.020 0.001 TRP H 435 HIS 0.005 0.001 HIS H 420 Details of bonding type rmsd covalent geometry : bond 0.00310 (15375) covalent geometry : angle 0.63251 (20778) hydrogen bonds : bond 0.04842 ( 1081) hydrogen bonds : angle 3.93640 ( 3198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 436 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 433 ARG cc_start: 0.3273 (mmt180) cc_final: 0.2167 (mtp85) REVERT: G 86 ASP cc_start: 0.8383 (p0) cc_final: 0.8143 (p0) REVERT: G 119 LYS cc_start: 0.8881 (mtmm) cc_final: 0.8426 (mtmm) REVERT: H 73 GLN cc_start: 0.8175 (pm20) cc_final: 0.7334 (pp30) REVERT: H 78 LYS cc_start: 0.8957 (tptp) cc_final: 0.8466 (tptp) REVERT: H 82 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7676 (mm-30) REVERT: H 127 ARG cc_start: 0.8439 (mtt-85) cc_final: 0.8233 (mtt-85) REVERT: H 472 GLN cc_start: 0.7780 (tm-30) cc_final: 0.7525 (pp30) REVERT: H 478 TRP cc_start: 0.8001 (m100) cc_final: 0.7207 (m100) REVERT: I 495 VAL cc_start: 0.9021 (m) cc_final: 0.8804 (t) REVERT: I 510 GLN cc_start: 0.6625 (pm20) cc_final: 0.6420 (pm20) REVERT: F 39 MET cc_start: 0.8468 (mmt) cc_final: 0.8214 (mmt) REVERT: F 48 MET cc_start: 0.8016 (tpp) cc_final: 0.7816 (tpp) REVERT: F 61 MET cc_start: 0.8384 (mtm) cc_final: 0.8052 (mtm) REVERT: F 126 ARG cc_start: 0.7791 (mtt-85) cc_final: 0.6872 (tmt170) REVERT: F 501 MET cc_start: 0.3132 (mtt) cc_final: 0.2531 (ttt) REVERT: F 508 GLU cc_start: 0.5611 (OUTLIER) cc_final: 0.4899 (pm20) REVERT: A 58 LYS cc_start: 0.4770 (pttt) cc_final: 0.4267 (tttt) REVERT: E 31 ARG cc_start: 0.7607 (mtm-85) cc_final: 0.7372 (mtm-85) REVERT: E 138 LYS cc_start: 0.7074 (mttt) cc_final: 0.6508 (tppt) REVERT: E 472 GLN cc_start: 0.7913 (tp40) cc_final: 0.7626 (tp40) outliers start: 39 outliers final: 25 residues processed: 458 average time/residue: 0.1653 time to fit residues: 101.5256 Evaluate side-chains 429 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 403 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 489 ASP Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 491 THR Chi-restraints excluded: chain I residue 515 SER Chi-restraints excluded: chain I residue 535 VAL Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 486 ASN Chi-restraints excluded: chain F residue 508 GLU Chi-restraints excluded: chain A residue 499 CYS Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 482 ILE Chi-restraints excluded: chain E residue 499 ASP Chi-restraints excluded: chain D residue 43 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 75 optimal weight: 2.9990 chunk 168 optimal weight: 0.0040 chunk 181 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 195 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 129 optimal weight: 0.0980 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 GLN C 82 GLN C 110 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 HIS B 86 GLN B 481 ASN ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN D 58 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.064219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.055281 restraints weight = 53891.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.056805 restraints weight = 27308.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.057777 restraints weight = 17053.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.058478 restraints weight = 12321.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.058904 restraints weight = 9796.555| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15375 Z= 0.149 Angle : 0.646 12.784 20778 Z= 0.339 Chirality : 0.040 0.154 2528 Planarity : 0.004 0.053 2668 Dihedral : 4.380 33.541 2120 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.00 % Allowed : 15.59 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.10 (0.19), residues: 1986 helix: 2.16 (0.14), residues: 1384 sheet: 0.36 (0.58), residues: 66 loop : -0.52 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 79 TYR 0.026 0.002 TYR B 423 PHE 0.020 0.001 PHE A 133 TRP 0.013 0.001 TRP H 435 HIS 0.005 0.001 HIS H 74 Details of bonding type rmsd covalent geometry : bond 0.00332 (15375) covalent geometry : angle 0.64583 (20778) hydrogen bonds : bond 0.04864 ( 1081) hydrogen bonds : angle 3.90302 ( 3198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 418 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ASP cc_start: 0.7683 (t0) cc_final: 0.7335 (t0) REVERT: C 123 LEU cc_start: 0.8779 (mt) cc_final: 0.8574 (tp) REVERT: C 433 ARG cc_start: 0.3251 (mmt180) cc_final: 0.2165 (mtp85) REVERT: G 119 LYS cc_start: 0.8907 (mtmm) cc_final: 0.8495 (mtmm) REVERT: H 73 GLN cc_start: 0.8250 (pm20) cc_final: 0.7259 (pp30) REVERT: H 78 LYS cc_start: 0.8989 (tptp) cc_final: 0.8498 (tptp) REVERT: H 82 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7747 (mm-30) REVERT: H 472 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7593 (pp30) REVERT: I 510 GLN cc_start: 0.6670 (pm20) cc_final: 0.6438 (pm20) REVERT: F 48 MET cc_start: 0.8037 (tpp) cc_final: 0.7816 (tpp) REVERT: F 126 ARG cc_start: 0.7828 (mtt-85) cc_final: 0.6907 (tmt170) REVERT: F 501 MET cc_start: 0.3315 (mtt) cc_final: 0.2711 (ttt) REVERT: F 508 GLU cc_start: 0.5399 (OUTLIER) cc_final: 0.4722 (pm20) REVERT: F 532 ASP cc_start: 0.6146 (t0) cc_final: 0.5667 (t0) REVERT: A 24 ILE cc_start: 0.8085 (mt) cc_final: 0.7603 (mt) REVERT: A 58 LYS cc_start: 0.4853 (pttt) cc_final: 0.4195 (tttt) REVERT: A 461 GLU cc_start: 0.6238 (mm-30) cc_final: 0.4131 (mm-30) REVERT: E 31 ARG cc_start: 0.7644 (mtm-85) cc_final: 0.7428 (mtm-85) REVERT: E 59 ARG cc_start: 0.7880 (tpp80) cc_final: 0.7520 (tpp80) REVERT: E 138 LYS cc_start: 0.7095 (mttt) cc_final: 0.6773 (ttmt) REVERT: E 472 GLN cc_start: 0.7910 (tp40) cc_final: 0.7653 (tp40) REVERT: D 68 LYS cc_start: 0.9035 (tptt) cc_final: 0.8774 (tptt) REVERT: D 75 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.7888 (tp) outliers start: 49 outliers final: 29 residues processed: 446 average time/residue: 0.1649 time to fit residues: 98.3351 Evaluate side-chains 417 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 386 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 491 THR Chi-restraints excluded: chain I residue 515 SER Chi-restraints excluded: chain I residue 535 VAL Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 486 ASN Chi-restraints excluded: chain F residue 508 GLU Chi-restraints excluded: chain A residue 499 CYS Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 482 ILE Chi-restraints excluded: chain E residue 499 ASP Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 101 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 120 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 170 optimal weight: 0.0470 chunk 186 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 GLN C 82 GLN C 110 GLN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 HIS B 86 GLN ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.064702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.055774 restraints weight = 53553.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.057255 restraints weight = 27119.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.058300 restraints weight = 17062.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.058940 restraints weight = 12252.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.059389 restraints weight = 9787.153| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15375 Z= 0.142 Angle : 0.671 12.386 20778 Z= 0.346 Chirality : 0.041 0.228 2528 Planarity : 0.004 0.056 2668 Dihedral : 4.367 32.546 2120 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.08 % Allowed : 17.11 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.11 (0.19), residues: 1986 helix: 2.17 (0.14), residues: 1381 sheet: 0.47 (0.60), residues: 66 loop : -0.51 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 40 TYR 0.021 0.001 TYR B 423 PHE 0.021 0.002 PHE A 133 TRP 0.012 0.001 TRP H 435 HIS 0.008 0.001 HIS H 74 Details of bonding type rmsd covalent geometry : bond 0.00315 (15375) covalent geometry : angle 0.67066 (20778) hydrogen bonds : bond 0.04590 ( 1081) hydrogen bonds : angle 3.87334 ( 3198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 405 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ASP cc_start: 0.7607 (t0) cc_final: 0.7254 (t0) REVERT: C 433 ARG cc_start: 0.3374 (mmt180) cc_final: 0.2308 (mtp85) REVERT: C 462 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.8017 (p0) REVERT: G 86 ASP cc_start: 0.8383 (p0) cc_final: 0.8148 (p0) REVERT: H 68 ARG cc_start: 0.8213 (ttm110) cc_final: 0.8000 (ttm110) REVERT: H 74 HIS cc_start: 0.6348 (t70) cc_final: 0.6077 (m-70) REVERT: H 78 LYS cc_start: 0.8983 (tptp) cc_final: 0.8361 (tptp) REVERT: H 82 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7728 (mm-30) REVERT: H 132 ASP cc_start: 0.8053 (m-30) cc_final: 0.7838 (m-30) REVERT: I 495 VAL cc_start: 0.9116 (m) cc_final: 0.7617 (t) REVERT: F 48 MET cc_start: 0.8034 (tpp) cc_final: 0.7833 (tpp) REVERT: F 126 ARG cc_start: 0.7861 (mtt-85) cc_final: 0.6941 (tmt170) REVERT: F 501 MET cc_start: 0.3235 (mtt) cc_final: 0.2772 (ttt) REVERT: F 508 GLU cc_start: 0.5399 (OUTLIER) cc_final: 0.4712 (pm20) REVERT: F 532 ASP cc_start: 0.5930 (t0) cc_final: 0.5631 (t0) REVERT: A 58 LYS cc_start: 0.4744 (pttt) cc_final: 0.4110 (tttt) REVERT: A 461 GLU cc_start: 0.6257 (mm-30) cc_final: 0.5975 (mm-30) REVERT: E 31 ARG cc_start: 0.7652 (mtm-85) cc_final: 0.7444 (mtm-85) REVERT: E 138 LYS cc_start: 0.7084 (mttt) cc_final: 0.6449 (tttt) REVERT: E 472 GLN cc_start: 0.7898 (tp40) cc_final: 0.7521 (tp40) REVERT: E 524 ILE cc_start: 0.8818 (mt) cc_final: 0.8444 (mp) REVERT: D 77 MET cc_start: 0.8513 (tmm) cc_final: 0.8277 (tmm) outliers start: 34 outliers final: 25 residues processed: 425 average time/residue: 0.1817 time to fit residues: 103.4313 Evaluate side-chains 414 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 387 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 489 ASP Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 491 THR Chi-restraints excluded: chain I residue 508 VAL Chi-restraints excluded: chain I residue 535 VAL Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 508 GLU Chi-restraints excluded: chain A residue 499 CYS Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 426 TYR Chi-restraints excluded: chain E residue 482 ILE Chi-restraints excluded: chain E residue 499 ASP Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 101 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 18 optimal weight: 2.9990 chunk 85 optimal weight: 0.0970 chunk 56 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 189 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 28 optimal weight: 0.0470 chunk 6 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 GLN C 110 GLN H 71 GLN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN D 58 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.065313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.056316 restraints weight = 52718.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.057843 restraints weight = 26865.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.058866 restraints weight = 16815.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.059490 restraints weight = 12132.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.059957 restraints weight = 9712.138| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15375 Z= 0.140 Angle : 0.687 12.565 20778 Z= 0.355 Chirality : 0.040 0.170 2528 Planarity : 0.004 0.057 2668 Dihedral : 4.353 31.293 2120 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.69 % Allowed : 18.03 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.10 (0.19), residues: 1986 helix: 2.19 (0.14), residues: 1385 sheet: 0.52 (0.62), residues: 66 loop : -0.62 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 496 TYR 0.021 0.001 TYR D 73 PHE 0.023 0.001 PHE A 133 TRP 0.010 0.001 TRP H 435 HIS 0.007 0.001 HIS H 74 Details of bonding type rmsd covalent geometry : bond 0.00312 (15375) covalent geometry : angle 0.68681 (20778) hydrogen bonds : bond 0.04446 ( 1081) hydrogen bonds : angle 3.84244 ( 3198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 410 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 433 ARG cc_start: 0.3336 (mmt180) cc_final: 0.2360 (mtp85) REVERT: C 462 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.8002 (p0) REVERT: G 119 LYS cc_start: 0.9035 (mtmm) cc_final: 0.8642 (mtmm) REVERT: H 73 GLN cc_start: 0.8316 (pm20) cc_final: 0.7086 (pp30) REVERT: H 78 LYS cc_start: 0.8985 (tptp) cc_final: 0.8298 (tptp) REVERT: H 82 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7686 (mm-30) REVERT: F 126 ARG cc_start: 0.7883 (mtt-85) cc_final: 0.6922 (tmt170) REVERT: F 471 ILE cc_start: 0.7799 (mm) cc_final: 0.7460 (pt) REVERT: F 501 MET cc_start: 0.3156 (mtt) cc_final: 0.2805 (ttt) REVERT: F 508 GLU cc_start: 0.5281 (OUTLIER) cc_final: 0.4610 (pm20) REVERT: F 532 ASP cc_start: 0.5821 (t0) cc_final: 0.5566 (t0) REVERT: A 58 LYS cc_start: 0.4849 (pttt) cc_final: 0.4121 (tttt) REVERT: B 34 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8230 (mm-30) REVERT: B 486 ASP cc_start: 0.6524 (t0) cc_final: 0.6259 (t0) REVERT: E 31 ARG cc_start: 0.7657 (mtm-85) cc_final: 0.7443 (mtm-85) REVERT: E 138 LYS cc_start: 0.7098 (mttt) cc_final: 0.6456 (tttt) REVERT: E 456 SER cc_start: 0.8423 (t) cc_final: 0.8183 (t) REVERT: E 472 GLN cc_start: 0.7889 (tp40) cc_final: 0.7498 (tp40) REVERT: D 68 LYS cc_start: 0.8829 (tppt) cc_final: 0.8613 (tptp) outliers start: 44 outliers final: 31 residues processed: 432 average time/residue: 0.1768 time to fit residues: 102.7814 Evaluate side-chains 431 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 398 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 489 ASP Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 491 THR Chi-restraints excluded: chain I residue 508 VAL Chi-restraints excluded: chain I residue 512 LEU Chi-restraints excluded: chain I residue 535 VAL Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain F residue 508 GLU Chi-restraints excluded: chain F residue 515 GLN Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 499 CYS Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 426 TYR Chi-restraints excluded: chain E residue 482 ILE Chi-restraints excluded: chain E residue 499 ASP Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 107 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 57 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 105 optimal weight: 0.0970 chunk 98 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 GLN C 110 GLN H 71 GLN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN ** H 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.064343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.055298 restraints weight = 53806.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.056832 restraints weight = 27348.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.057848 restraints weight = 17161.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.058483 restraints weight = 12419.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.058948 restraints weight = 9977.773| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15375 Z= 0.157 Angle : 0.717 12.885 20778 Z= 0.369 Chirality : 0.041 0.232 2528 Planarity : 0.004 0.059 2668 Dihedral : 4.394 30.846 2120 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.18 % Allowed : 18.34 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.02 (0.19), residues: 1986 helix: 2.13 (0.14), residues: 1386 sheet: 0.49 (0.63), residues: 66 loop : -0.68 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 127 TYR 0.019 0.002 TYR D 73 PHE 0.019 0.002 PHE A 133 TRP 0.011 0.001 TRP H 435 HIS 0.007 0.001 HIS H 74 Details of bonding type rmsd covalent geometry : bond 0.00354 (15375) covalent geometry : angle 0.71665 (20778) hydrogen bonds : bond 0.04845 ( 1081) hydrogen bonds : angle 3.86346 ( 3198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 404 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 123 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8628 (tp) REVERT: C 433 ARG cc_start: 0.3495 (mmt180) cc_final: 0.2437 (mtp85) REVERT: G 119 LYS cc_start: 0.9066 (mtmm) cc_final: 0.8541 (mtmm) REVERT: H 78 LYS cc_start: 0.9023 (tptp) cc_final: 0.8345 (tptp) REVERT: H 82 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7745 (mm-30) REVERT: I 497 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8687 (mtmt) REVERT: F 126 ARG cc_start: 0.7862 (mtt-85) cc_final: 0.6902 (tmt170) REVERT: F 501 MET cc_start: 0.3190 (mtt) cc_final: 0.2830 (ttt) REVERT: F 508 GLU cc_start: 0.5204 (OUTLIER) cc_final: 0.4463 (pm20) REVERT: A 58 LYS cc_start: 0.4889 (pttt) cc_final: 0.4121 (tttt) REVERT: B 475 TYR cc_start: 0.7125 (OUTLIER) cc_final: 0.6924 (m-10) REVERT: B 486 ASP cc_start: 0.6524 (t0) cc_final: 0.6174 (t0) REVERT: E 31 ARG cc_start: 0.7679 (mtm-85) cc_final: 0.7472 (mtm-85) REVERT: E 138 LYS cc_start: 0.6996 (mttt) cc_final: 0.6372 (tttt) REVERT: E 456 SER cc_start: 0.8485 (t) cc_final: 0.8228 (t) REVERT: E 472 GLN cc_start: 0.7911 (tp40) cc_final: 0.7638 (tp40) outliers start: 52 outliers final: 35 residues processed: 430 average time/residue: 0.1706 time to fit residues: 99.0330 Evaluate side-chains 430 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 391 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 489 ASP Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 497 LYS Chi-restraints excluded: chain I residue 508 VAL Chi-restraints excluded: chain I residue 512 LEU Chi-restraints excluded: chain I residue 515 SER Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 508 GLU Chi-restraints excluded: chain F residue 515 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 499 CYS Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 426 TYR Chi-restraints excluded: chain E residue 482 ILE Chi-restraints excluded: chain E residue 499 ASP Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 107 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 96 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 113 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 178 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 GLN ** H 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.064018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.054940 restraints weight = 53600.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.056455 restraints weight = 27285.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.057466 restraints weight = 17150.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.058105 restraints weight = 12420.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.058494 restraints weight = 9953.128| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15375 Z= 0.162 Angle : 0.748 12.744 20778 Z= 0.385 Chirality : 0.042 0.245 2528 Planarity : 0.004 0.061 2668 Dihedral : 4.491 30.462 2120 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.57 % Allowed : 20.05 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.95 (0.19), residues: 1986 helix: 2.09 (0.14), residues: 1379 sheet: 0.76 (0.65), residues: 64 loop : -0.76 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 59 TYR 0.020 0.002 TYR D 73 PHE 0.018 0.002 PHE A 133 TRP 0.009 0.001 TRP H 435 HIS 0.005 0.001 HIS I 129 Details of bonding type rmsd covalent geometry : bond 0.00367 (15375) covalent geometry : angle 0.74835 (20778) hydrogen bonds : bond 0.04941 ( 1081) hydrogen bonds : angle 3.88900 ( 3198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 400 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 433 ARG cc_start: 0.3639 (mmt180) cc_final: 0.2581 (mtp85) REVERT: G 73 ASN cc_start: 0.9150 (m-40) cc_final: 0.8744 (m-40) REVERT: G 119 LYS cc_start: 0.9096 (mtmm) cc_final: 0.8671 (mtmm) REVERT: H 78 LYS cc_start: 0.9051 (tptp) cc_final: 0.8443 (tptp) REVERT: H 82 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7751 (mm-30) REVERT: H 85 ARG cc_start: 0.7731 (mmm160) cc_final: 0.7476 (mmm160) REVERT: F 126 ARG cc_start: 0.7862 (mtt-85) cc_final: 0.6952 (tmt170) REVERT: F 508 GLU cc_start: 0.5147 (OUTLIER) cc_final: 0.4401 (mp0) REVERT: B 475 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6871 (m-10) REVERT: B 486 ASP cc_start: 0.6574 (t0) cc_final: 0.6214 (t0) REVERT: E 31 ARG cc_start: 0.7694 (mtm-85) cc_final: 0.7476 (mtm-85) REVERT: E 138 LYS cc_start: 0.7019 (mttt) cc_final: 0.6350 (tttt) REVERT: E 456 SER cc_start: 0.8505 (t) cc_final: 0.8247 (t) REVERT: E 472 GLN cc_start: 0.7921 (tp40) cc_final: 0.7658 (tp40) REVERT: D 41 ASN cc_start: 0.8525 (m110) cc_final: 0.8227 (p0) outliers start: 42 outliers final: 32 residues processed: 423 average time/residue: 0.1715 time to fit residues: 97.9637 Evaluate side-chains 420 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 386 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 489 ASP Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 495 VAL Chi-restraints excluded: chain I residue 508 VAL Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 508 GLU Chi-restraints excluded: chain F residue 515 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 499 CYS Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 426 TYR Chi-restraints excluded: chain E residue 482 ILE Chi-restraints excluded: chain E residue 499 ASP Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 101 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 9 optimal weight: 3.9990 chunk 189 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 GLN H 87 GLN H 111 HIS H 116 GLN ** H 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 472 GLN B 86 GLN ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.062892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.053789 restraints weight = 53918.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.055302 restraints weight = 27565.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.056257 restraints weight = 17325.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.056943 restraints weight = 12646.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.057341 restraints weight = 10111.152| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15375 Z= 0.186 Angle : 0.784 13.262 20778 Z= 0.405 Chirality : 0.043 0.221 2528 Planarity : 0.005 0.062 2668 Dihedral : 4.658 30.289 2120 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.51 % Allowed : 19.99 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.74 (0.19), residues: 1986 helix: 1.96 (0.14), residues: 1379 sheet: 0.59 (0.64), residues: 64 loop : -0.89 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 40 TYR 0.023 0.002 TYR D 73 PHE 0.017 0.002 PHE A 133 TRP 0.007 0.001 TRP H 435 HIS 0.006 0.001 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.00429 (15375) covalent geometry : angle 0.78394 (20778) hydrogen bonds : bond 0.05392 ( 1081) hydrogen bonds : angle 3.99339 ( 3198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 383 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 433 ARG cc_start: 0.3571 (mmt180) cc_final: 0.2461 (mtp85) REVERT: G 119 LYS cc_start: 0.9135 (mtmm) cc_final: 0.8764 (mtmm) REVERT: H 69 GLU cc_start: 0.8435 (tp30) cc_final: 0.8127 (tp30) REVERT: H 85 ARG cc_start: 0.7778 (mmm160) cc_final: 0.7496 (mmm160) REVERT: H 478 TRP cc_start: 0.7953 (m100) cc_final: 0.7454 (m100) REVERT: F 126 ARG cc_start: 0.7860 (mtt-85) cc_final: 0.6925 (tmt170) REVERT: F 534 ARG cc_start: 0.8539 (mmt-90) cc_final: 0.8323 (mmm160) REVERT: A 58 LYS cc_start: 0.5024 (pttt) cc_final: 0.4184 (tttt) REVERT: A 461 GLU cc_start: 0.6311 (mm-30) cc_final: 0.6097 (mm-30) REVERT: B 475 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.6812 (m-10) REVERT: E 31 ARG cc_start: 0.7701 (mtm-85) cc_final: 0.7492 (mtm-85) REVERT: E 138 LYS cc_start: 0.7044 (mttt) cc_final: 0.6298 (ttmt) REVERT: E 456 SER cc_start: 0.8604 (t) cc_final: 0.8353 (t) REVERT: E 472 GLN cc_start: 0.7951 (tp40) cc_final: 0.7656 (tp40) outliers start: 41 outliers final: 32 residues processed: 404 average time/residue: 0.1724 time to fit residues: 93.7039 Evaluate side-chains 407 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 374 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain H residue 489 ASP Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 508 VAL Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 486 ASN Chi-restraints excluded: chain F residue 515 GLN Chi-restraints excluded: chain A residue 499 CYS Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 426 TYR Chi-restraints excluded: chain E residue 499 ASP Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 101 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 145 optimal weight: 0.0980 chunk 100 optimal weight: 0.5980 chunk 60 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 80 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 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 20 GLN H 87 GLN H 116 GLN ** H 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.064232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.055154 restraints weight = 53198.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.056663 restraints weight = 27070.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.057635 restraints weight = 17059.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.058315 restraints weight = 12427.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.058685 restraints weight = 9943.789| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15375 Z= 0.157 Angle : 0.768 13.135 20778 Z= 0.395 Chirality : 0.042 0.269 2528 Planarity : 0.004 0.059 2668 Dihedral : 4.600 29.569 2120 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.14 % Allowed : 20.66 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.36 % 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: 1.87 (0.19), residues: 1986 helix: 2.07 (0.14), residues: 1375 sheet: 0.59 (0.74), residues: 54 loop : -0.83 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 40 TYR 0.023 0.002 TYR D 73 PHE 0.019 0.002 PHE A 133 TRP 0.007 0.001 TRP H 478 HIS 0.004 0.001 HIS I 129 Details of bonding type rmsd covalent geometry : bond 0.00356 (15375) covalent geometry : angle 0.76838 (20778) hydrogen bonds : bond 0.04795 ( 1081) hydrogen bonds : angle 3.93974 ( 3198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3435.38 seconds wall clock time: 59 minutes 51.62 seconds (3591.62 seconds total)