Starting phenix.real_space_refine on Sat Sep 12 16:47:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6d6v_7821/09_2026/6d6v_7821.cif Found real_map, /net/cci-nas-00/data/ceres_data/6d6v_7821/09_2026/6d6v_7821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6d6v_7821/09_2026/6d6v_7821.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6d6v_7821/09_2026/6d6v_7821.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6d6v_7821/09_2026/6d6v_7821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6d6v_7821/09_2026/6d6v_7821.map" model { file = "/net/cci-nas-00/data/ceres_data/6d6v_7821/09_2026/6d6v_7821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6d6v_7821/09_2026/6d6v_7821.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 177 5.49 5 S 54 5.16 5 C 10405 2.51 5 N 2948 2.21 5 O 3732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17317 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 980, 8253 Classifications: {'peptide': 980} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 20, 'TRANS': 959} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1538 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 3, 'TRANS': 181} Chain: "F" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 919 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "E" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1207 Classifications: {'peptide': 149} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 143} Chain: "B" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3322 Classifications: {'RNAv2': 159} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 21, 'rna3p_pur': 59, 'rna3p_pyr': 60} Link IDs: {'rna2p': 38, 'rna3p': 120} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {' U%rna3p_pyr:plan': 1, ' G%rna3p_pur:plan': 2, ' G%rna3p_pur:plan2': 2} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 406 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "G" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 785 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'TRANS': 156} Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 157 Planarities with less than four sites: {'UNK:plan-1': 157} Unresolved non-hydrogen planarities: 157 Chain: "H" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 886 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8788 SG CYS D 575 71.318 62.077 84.962 1.00328.59 S Time building chain proxies: 3.52, per 1000 atoms: 0.20 Number of scatterers: 17317 At special positions: 0 Unit cell: (148.24, 160.48, 114.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 54 16.00 P 177 15.00 O 3732 8.00 N 2948 7.00 C 10405 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: 1.72 Conformation dependent library (CDL) restraints added in 624.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 801 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 575 " 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3282 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 13 sheets defined 51.5% alpha, 13.6% beta 43 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 19 through 26 Processing helix chain 'A' and resid 36 through 43 Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 88 through 99 Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 125 through 131 removed outlier: 3.583A pdb=" N GLN A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.751A pdb=" N TYR A 177 " --> pdb=" O CYS A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 301 through 320 Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 336 through 351 Processing helix chain 'A' and resid 355 through 368 Processing helix chain 'A' and resid 372 through 386 Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 394 through 411 removed outlier: 4.371A pdb=" N TYR A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 436 through 443 removed outlier: 3.679A pdb=" N ASN A 439 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 440 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LYS A 441 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 467 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 493 through 505 Processing helix chain 'A' and resid 506 through 509 removed outlier: 4.321A pdb=" N GLU A 509 " --> pdb=" O LYS A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 506 through 509' Processing helix chain 'A' and resid 551 through 579 removed outlier: 3.670A pdb=" N LYS A 555 " --> pdb=" O LYS A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 607 Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 711 through 717 removed outlier: 3.970A pdb=" N LEU A 715 " --> pdb=" O ASP A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 753 removed outlier: 3.836A pdb=" N ILE A 745 " --> pdb=" O THR A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 805 removed outlier: 3.686A pdb=" N GLU A 792 " --> pdb=" O LYS A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 840 Processing helix chain 'A' and resid 856 through 865 Processing helix chain 'A' and resid 894 through 900 Processing helix chain 'A' and resid 911 through 921 removed outlier: 4.249A pdb=" N ASN A 918 " --> pdb=" O SER A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 965 removed outlier: 3.639A pdb=" N LEU A 942 " --> pdb=" O SER A 938 " (cutoff:3.500A) Proline residue: A 959 - end of helix Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 974 through 980 Processing helix chain 'A' and resid 983 through 1003 removed outlier: 3.750A pdb=" N ASN A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1040 Processing helix chain 'A' and resid 1043 through 1075 removed outlier: 4.742A pdb=" N LYS A1049 " --> pdb=" O GLY A1045 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN A1070 " --> pdb=" O CYS A1066 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1093 Processing helix chain 'A' and resid 1099 through 1108 Proline residue: A1105 - end of helix Processing helix chain 'D' and resid 516 through 526 Processing helix chain 'D' and resid 604 through 613 Processing helix chain 'D' and resid 619 through 621 No H-bonds generated for 'chain 'D' and resid 619 through 621' Processing helix chain 'D' and resid 622 through 634 Processing helix chain 'D' and resid 635 through 646 removed outlier: 3.602A pdb=" N LEU D 646 " --> pdb=" O LEU D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 693 removed outlier: 3.816A pdb=" N SER D 684 " --> pdb=" O ILE D 680 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 21 removed outlier: 5.904A pdb=" N ALA F 19 " --> pdb=" O GLU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 110 removed outlier: 3.534A pdb=" N TYR F 102 " --> pdb=" O ASP F 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 49 removed outlier: 3.781A pdb=" N ILE E 39 " --> pdb=" O ASN E 35 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN E 41 " --> pdb=" O PHE E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 120 removed outlier: 5.566A pdb=" N GLU E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE E 118 " --> pdb=" O GLN E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 175 removed outlier: 3.920A pdb=" N ILE E 156 " --> pdb=" O ASP E 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 28 removed outlier: 3.896A pdb=" N UNK G 11 " --> pdb=" O UNK G 7 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N UNK G 13 " --> pdb=" O UNK G 9 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N UNK G 14 " --> pdb=" O UNK G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 72 removed outlier: 4.133A pdb=" N UNK G 71 " --> pdb=" O UNK G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 133 removed outlier: 3.627A pdb=" N UNK G 130 " --> pdb=" O UNK G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 154 Processing helix chain 'H' and resid 391 through 401 removed outlier: 3.501A pdb=" N VAL H 395 " --> pdb=" O LEU H 391 " (cutoff:3.500A) Processing helix chain 'H' and resid 468 through 479 Processing helix chain 'H' and resid 503 through 531 removed outlier: 4.041A pdb=" N PHE H 525 " --> pdb=" O PHE H 521 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN H 530 " --> pdb=" O PHE H 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 162 removed outlier: 7.938A pdb=" N PHE A 158 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A 169 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LYS A 160 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 167 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 476 through 481 removed outlier: 4.615A pdb=" N LYS A 481 " --> pdb=" O GLN A 487 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLN A 487 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 532 through 534 Processing sheet with id=AA5, first strand: chain 'A' and resid 613 through 618 Processing sheet with id=AA6, first strand: chain 'A' and resid 647 through 648 removed outlier: 4.202A pdb=" N ILE A 647 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 880 through 882 Processing sheet with id=AA8, first strand: chain 'D' and resid 551 through 554 removed outlier: 4.885A pdb=" N TYR D 670 " --> pdb=" O PRO D 599 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET D 601 " --> pdb=" O TYR D 670 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE D 603 " --> pdb=" O VAL D 672 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N LYS D 674 " --> pdb=" O PHE D 603 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TYR D 670 " --> pdb=" O GLU D 658 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLU D 658 " --> pdb=" O TYR D 670 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL D 672 " --> pdb=" O GLN D 656 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLN D 656 " --> pdb=" O VAL D 672 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 562 through 563 removed outlier: 3.671A pdb=" N PHE D 571 " --> pdb=" O LEU D 563 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 70 through 75 removed outlier: 6.670A pdb=" N ILE F 43 " --> pdb=" O CYS F 33 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU F 44 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N VAL F 83 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL F 55 " --> pdb=" O VAL F 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 31 through 33 removed outlier: 3.553A pdb=" N TYR E 146 " --> pdb=" O MET E 133 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LYS E 135 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU E 144 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LEU E 144 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL E 99 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N TYR E 146 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY E 94 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE E 85 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N MET E 86 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU E 76 " --> pdb=" O MET E 86 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS E 88 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 87 through 89 Processing sheet with id=AB4, first strand: chain 'H' and resid 406 through 411 removed outlier: 4.766A pdb=" N LEU H 487 " --> pdb=" O VAL H 498 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1806 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 194 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 3.68 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 5118 1.34 - 1.49: 6588 1.49 - 1.65: 6213 1.65 - 1.80: 63 1.80 - 1.95: 16 Bond restraints: 17998 Sorted by residual: bond pdb=" CA SER A 890 " pdb=" C SER A 890 " ideal model delta sigma weight residual 1.524 1.473 0.051 7.00e-03 2.04e+04 5.30e+01 bond pdb=" C3' DT C 9 " pdb=" O3' DT C 9 " ideal model delta sigma weight residual 1.435 1.523 -0.088 1.30e-02 5.92e+03 4.56e+01 bond pdb=" SD MET H 527 " pdb=" CE MET H 527 " ideal model delta sigma weight residual 1.791 1.952 -0.161 2.50e-02 1.60e+03 4.17e+01 bond pdb=" CG MET H 527 " pdb=" SD MET H 527 " ideal model delta sigma weight residual 1.803 1.955 -0.152 2.50e-02 1.60e+03 3.69e+01 bond pdb=" C3' DT C 15 " pdb=" O3' DT C 15 " ideal model delta sigma weight residual 1.435 1.360 0.075 1.30e-02 5.92e+03 3.32e+01 ... (remaining 17993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 23736 3.51 - 7.02: 1186 7.02 - 10.52: 147 10.52 - 14.03: 34 14.03 - 17.54: 9 Bond angle restraints: 25112 Sorted by residual: angle pdb=" O4' DT C 14 " pdb=" C1' DT C 14 " pdb=" N1 DT C 14 " ideal model delta sigma weight residual 108.00 114.44 -6.44 7.00e-01 2.04e+00 8.46e+01 angle pdb=" N ILE A 626 " pdb=" CA ILE A 626 " pdb=" C ILE A 626 " ideal model delta sigma weight residual 108.84 120.25 -11.41 1.32e+00 5.74e-01 7.47e+01 angle pdb=" C SER A 922 " pdb=" N LEU A 923 " pdb=" CA LEU A 923 " ideal model delta sigma weight residual 122.31 138.67 -16.36 2.00e+00 2.50e-01 6.69e+01 angle pdb=" C3' A B 3 " pdb=" O3' A B 3 " pdb=" P C B 4 " ideal model delta sigma weight residual 119.70 129.34 -9.64 1.20e+00 6.94e-01 6.46e+01 angle pdb=" N LYS A 849 " pdb=" CA LYS A 849 " pdb=" C LYS A 849 " ideal model delta sigma weight residual 108.07 118.55 -10.48 1.38e+00 5.25e-01 5.77e+01 ... (remaining 25107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 9819 35.72 - 71.44: 639 71.44 - 107.16: 37 107.16 - 142.88: 5 142.88 - 178.61: 4 Dihedral angle restraints: 10504 sinusoidal: 5462 harmonic: 5042 Sorted by residual: dihedral pdb=" C4' C B 88 " pdb=" C3' C B 88 " pdb=" C2' C B 88 " pdb=" C1' C B 88 " ideal model delta sinusoidal sigma weight residual 36.34 -42.68 79.03 1 3.10e+00 1.04e-01 8.09e+02 dihedral pdb=" C4' C B 39 " pdb=" C3' C B 39 " pdb=" C2' C B 39 " pdb=" C1' C B 39 " ideal model delta sinusoidal sigma weight residual 36.35 -40.88 77.23 1 3.10e+00 1.04e-01 7.78e+02 dihedral pdb=" C4' C B 109 " pdb=" C3' C B 109 " pdb=" C2' C B 109 " pdb=" C1' C B 109 " ideal model delta sinusoidal sigma weight residual 36.35 -40.66 77.00 1 3.10e+00 1.04e-01 7.74e+02 ... (remaining 10501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.200: 2685 0.200 - 0.400: 220 0.400 - 0.600: 17 0.600 - 0.800: 2 0.800 - 1.000: 1 Chirality restraints: 2925 Sorted by residual: chirality pdb=" C1' C B 46 " pdb=" O4' C B 46 " pdb=" C2' C B 46 " pdb=" N1 C B 46 " both_signs ideal model delta sigma weight residual False 2.46 1.46 1.00 2.00e-01 2.50e+01 2.50e+01 chirality pdb=" CG LEU A 565 " pdb=" CB LEU A 565 " pdb=" CD1 LEU A 565 " pdb=" CD2 LEU A 565 " both_signs ideal model delta sigma weight residual False -2.59 -1.81 -0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" C3' U B 42 " pdb=" C4' U B 42 " pdb=" O3' U B 42 " pdb=" C2' U B 42 " both_signs ideal model delta sigma weight residual False -2.50 -1.79 -0.71 2.00e-01 2.50e+01 1.26e+01 ... (remaining 2922 not shown) Planarity restraints: 2584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 585 " 0.053 2.00e-02 2.50e+03 3.15e-02 1.99e+01 pdb=" CG TYR A 585 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR A 585 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 585 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 585 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 585 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 585 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 585 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT C 15 " 0.059 2.00e-02 2.50e+03 2.82e-02 1.99e+01 pdb=" N1 DT C 15 " -0.029 2.00e-02 2.50e+03 pdb=" C2 DT C 15 " 0.011 2.00e-02 2.50e+03 pdb=" O2 DT C 15 " -0.030 2.00e-02 2.50e+03 pdb=" N3 DT C 15 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT C 15 " 0.012 2.00e-02 2.50e+03 pdb=" O4 DT C 15 " 0.020 2.00e-02 2.50e+03 pdb=" C5 DT C 15 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT C 15 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT C 15 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 46 " -0.056 2.00e-02 2.50e+03 2.93e-02 1.93e+01 pdb=" N1 C B 46 " 0.050 2.00e-02 2.50e+03 pdb=" C2 C B 46 " 0.038 2.00e-02 2.50e+03 pdb=" O2 C B 46 " -0.007 2.00e-02 2.50e+03 pdb=" N3 C B 46 " -0.010 2.00e-02 2.50e+03 pdb=" C4 C B 46 " -0.008 2.00e-02 2.50e+03 pdb=" N4 C B 46 " -0.019 2.00e-02 2.50e+03 pdb=" C5 C B 46 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C B 46 " 0.009 2.00e-02 2.50e+03 ... (remaining 2581 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 8 1.93 - 2.67: 1148 2.67 - 3.42: 26487 3.42 - 4.16: 48918 4.16 - 4.90: 75700 Nonbonded interactions: 152261 Sorted by model distance: nonbonded pdb=" OP2 G B 121 " pdb=" O LYS H 518 " model vdw 1.189 3.040 nonbonded pdb=" C5' G B 121 " pdb=" CB PHE H 521 " model vdw 1.441 3.840 nonbonded pdb=" O4' G B 121 " pdb=" O LYS H 517 " model vdw 1.447 3.040 nonbonded pdb=" CB UNK G 51 " pdb=" O UNK G 73 " model vdw 1.641 3.440 nonbonded pdb=" OE2 GLU E 65 " pdb=" O MET E 136 " model vdw 1.673 3.040 ... (remaining 152256 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.870 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 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 : 0.013 0.233 17999 Z= 0.702 Angle : 1.769 17.540 25112 Z= 0.905 Chirality : 0.111 1.000 2925 Planarity : 0.010 0.091 2584 Dihedral : 20.309 178.605 7222 Min Nonbonded Distance : 1.189 Molprobity Statistics. All-atom Clashscore : 25.73 Ramachandran Plot: Outliers : 0.73 % Allowed : 15.78 % Favored : 83.50 % Rotamer: Outliers : 0.97 % Allowed : 4.04 % Favored : 94.99 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 6.25 % Twisted General : 2.14 % 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: -4.28 (0.17), residues: 1515 helix: -2.30 (0.15), residues: 637 sheet: -2.50 (0.40), residues: 138 loop : -3.45 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.002 ARG A 727 TYR 0.070 0.006 TYR A 585 PHE 0.073 0.006 PHE A 634 TRP 0.018 0.004 TRP A1030 HIS 0.015 0.004 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.01335 / 0.70 (17998) covalent geometry : angle 1.76864 / 0.91 (25112) hydrogen bonds : bond 0.20647 / 13.43 ( 733) hydrogen bonds : angle 8.33635 / 5.53 ( 2000) metal coordination : bond 0.23275 / 12.25 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.613 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: symmetry clash REVERT: A 560 ASN cc_start: 0.8434 (m-40) cc_final: 0.8016 (m-40) REVERT: A 566 MET cc_start: 0.8902 (mmt) cc_final: 0.8675 (tpp) REVERT: A 631 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9180 (mt) REVERT: A 634 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.8099 (m-10) REVERT: A 701 ARG cc_start: 0.7806 (ptm160) cc_final: 0.7291 (ptt-90) REVERT: A 777 ILE cc_start: 0.9473 (pt) cc_final: 0.8941 (pt) REVERT: A 955 MET cc_start: 0.9326 (mtt) cc_final: 0.9120 (mmp) REVERT: D 586 MET cc_start: 0.6292 (tpp) cc_final: 0.6010 (tpp) REVERT: D 601 MET cc_start: 0.8038 (mtt) cc_final: 0.7479 (mtp) REVERT: H 397 LEU cc_start: 0.8459 (tp) cc_final: 0.8123 (pp) outliers start: 14 outliers final: 8 residues processed: 137 average time/residue: 0.1566 time to fit residues: 31.9487 Evaluate side-chains 89 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 ASN A 105 ASN A 181 GLN ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN A 317 ASN A 319 HIS ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN A 475 ASN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN A 590 ASN A 648 ASN A 697 ASN ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 ASN A 896 GLN A 900 ASN A 927 GLN ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN A1016 ASN A1098 GLN ** D 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN F 79 ASN ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN E 127 HIS ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 401 HIS H 461 GLN ** H 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 482 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.045936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.034032 restraints weight = 214474.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.034919 restraints weight = 143341.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.035628 restraints weight = 106968.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.036107 restraints weight = 86213.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.036431 restraints weight = 73600.812| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17999 Z= 0.274 Angle : 1.564 22.621 25112 Z= 0.673 Chirality : 0.151 2.738 2925 Planarity : 0.006 0.070 2584 Dihedral : 22.041 175.913 3896 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 23.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.73 % Favored : 86.14 % Rotamer: Outliers : 0.35 % Allowed : 2.44 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 1.21 % 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: -3.44 (0.19), residues: 1515 helix: -1.36 (0.18), residues: 647 sheet: -2.27 (0.41), residues: 135 loop : -3.20 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 22 TYR 0.034 0.003 TYR A1061 PHE 0.041 0.003 PHE A 634 TRP 0.041 0.003 TRP A 604 HIS 0.011 0.002 HIS A 948 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.27 (17998) covalent geometry : angle 1.56379 / 0.67 (25112) hydrogen bonds : bond 0.07381 / 4.66 ( 733) hydrogen bonds : angle 6.79474 / 4.48 ( 2000) metal coordination : bond 0.00976 / 0.51 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 0.579 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: symmetry clash revert: symmetry clash REVERT: A 130 THR cc_start: 0.8411 (m) cc_final: 0.8027 (p) REVERT: A 139 LEU cc_start: 0.9636 (mt) cc_final: 0.9325 (mt) REVERT: A 179 SER cc_start: 0.7501 (p) cc_final: 0.6879 (p) REVERT: A 634 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.8464 (m-10) REVERT: A 701 ARG cc_start: 0.7484 (ptm160) cc_final: 0.7190 (mtm180) REVERT: A 811 MET cc_start: 0.8763 (tmm) cc_final: 0.8416 (ppp) REVERT: A 912 LEU cc_start: 0.9324 (tp) cc_final: 0.8840 (tp) REVERT: D 586 MET cc_start: 0.6811 (tpp) cc_final: 0.5635 (tpp) REVERT: D 601 MET cc_start: 0.8649 (mtt) cc_final: 0.8155 (ppp) REVERT: F 59 TYR cc_start: 0.8988 (t80) cc_final: 0.8768 (t80) REVERT: E 86 MET cc_start: 0.8452 (tpp) cc_final: 0.8080 (tpp) REVERT: E 162 ASP cc_start: 0.9352 (m-30) cc_final: 0.9089 (m-30) outliers start: 5 outliers final: 2 residues processed: 136 average time/residue: 0.1466 time to fit residues: 30.2357 Evaluate side-chains 88 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 72 optimal weight: 9.9990 chunk 162 optimal weight: 20.0000 chunk 181 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 chunk 129 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 ASN A 163 GLN ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 GLN ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 592 GLN ** D 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 GLN ** H 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.045587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.033759 restraints weight = 219268.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.034588 restraints weight = 146972.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.035254 restraints weight = 110316.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.035740 restraints weight = 88970.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.036034 restraints weight = 76116.405| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 17999 Z= 0.255 Angle : 1.314 22.534 25112 Z= 0.582 Chirality : 0.119 2.131 2925 Planarity : 0.006 0.081 2584 Dihedral : 22.144 174.795 3896 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 23.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.25 % Favored : 84.62 % Rotamer: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 1.00 % 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: -2.99 (0.20), residues: 1515 helix: -0.89 (0.19), residues: 648 sheet: -2.14 (0.43), residues: 129 loop : -3.04 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 534 TYR 0.053 0.003 TYR D 565 PHE 0.056 0.003 PHE A 634 TRP 0.043 0.002 TRP A 604 HIS 0.011 0.002 HIS A 948 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.25 (17998) covalent geometry : angle 1.31359 / 0.58 (25112) hydrogen bonds : bond 0.07227 / 4.61 ( 733) hydrogen bonds : angle 6.34691 / 4.18 ( 2000) metal coordination : bond 0.00270 / 0.14 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.586 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: A 130 THR cc_start: 0.8591 (m) cc_final: 0.8212 (p) REVERT: A 139 LEU cc_start: 0.9648 (mt) cc_final: 0.9355 (mt) REVERT: A 566 MET cc_start: 0.8972 (tpt) cc_final: 0.8522 (tpt) REVERT: A 701 ARG cc_start: 0.7353 (ptm160) cc_final: 0.7036 (ptt-90) REVERT: A 811 MET cc_start: 0.8819 (tmm) cc_final: 0.8315 (ppp) REVERT: A 1040 LYS cc_start: 0.8678 (mtmt) cc_final: 0.8436 (mtmm) REVERT: D 586 MET cc_start: 0.6752 (tpp) cc_final: 0.5783 (tpp) REVERT: D 601 MET cc_start: 0.8091 (mtt) cc_final: 0.7889 (mtt) REVERT: F 59 TYR cc_start: 0.9073 (t80) cc_final: 0.8673 (t80) REVERT: F 61 ARG cc_start: 0.8661 (ttt-90) cc_final: 0.7841 (tmm160) REVERT: E 117 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7678 (mt-10) REVERT: E 146 TYR cc_start: 0.9156 (t80) cc_final: 0.8275 (t80) REVERT: E 162 ASP cc_start: 0.9390 (m-30) cc_final: 0.9057 (m-30) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1383 time to fit residues: 24.2237 Evaluate side-chains 79 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 18 optimal weight: 0.0030 chunk 103 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 165 optimal weight: 40.0000 chunk 38 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.045953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.034077 restraints weight = 218448.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.034886 restraints weight = 146071.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.035592 restraints weight = 109899.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.036013 restraints weight = 88748.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 71)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.036415 restraints weight = 76251.681| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17999 Z= 0.218 Angle : 1.218 18.637 25112 Z= 0.540 Chirality : 0.110 2.077 2925 Planarity : 0.005 0.054 2584 Dihedral : 21.794 175.671 3896 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 23.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.99 % Favored : 85.94 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.74 % 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: -2.70 (0.20), residues: 1515 helix: -0.58 (0.19), residues: 647 sheet: -2.23 (0.41), residues: 136 loop : -2.90 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 534 TYR 0.047 0.002 TYR A 650 PHE 0.029 0.002 PHE A 143 TRP 0.038 0.002 TRP A 604 HIS 0.007 0.002 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.22 (17998) covalent geometry : angle 1.21823 / 0.54 (25112) hydrogen bonds : bond 0.06434 / 4.03 ( 733) hydrogen bonds : angle 6.15144 / 4.05 ( 2000) metal coordination : bond 0.00133 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.591 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: A 139 LEU cc_start: 0.9686 (mt) cc_final: 0.9391 (mt) REVERT: A 566 MET cc_start: 0.8974 (tpt) cc_final: 0.8157 (tpt) REVERT: A 593 ILE cc_start: 0.9335 (tt) cc_final: 0.8969 (mt) REVERT: A 701 ARG cc_start: 0.7431 (ptm160) cc_final: 0.7039 (mtm180) REVERT: A 811 MET cc_start: 0.8841 (tmm) cc_final: 0.8469 (ppp) REVERT: A 1029 MET cc_start: 0.8987 (mmp) cc_final: 0.8771 (mmp) REVERT: A 1040 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8516 (mtmm) REVERT: D 586 MET cc_start: 0.6705 (tpp) cc_final: 0.5739 (tpp) REVERT: F 59 TYR cc_start: 0.9128 (t80) cc_final: 0.8807 (t80) REVERT: F 61 ARG cc_start: 0.8663 (ttt-90) cc_final: 0.7944 (ttp80) REVERT: E 86 MET cc_start: 0.8386 (tpp) cc_final: 0.8152 (tpp) REVERT: E 117 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7888 (mt-10) REVERT: E 146 TYR cc_start: 0.9208 (t80) cc_final: 0.8259 (t80) REVERT: E 162 ASP cc_start: 0.9330 (m-30) cc_final: 0.8955 (m-30) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1390 time to fit residues: 24.2019 Evaluate side-chains 77 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 44 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 HIS ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN A 804 ASN ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 401 HIS ** H 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.045902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.034019 restraints weight = 217277.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.034833 restraints weight = 145898.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.035548 restraints weight = 109787.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.036026 restraints weight = 88402.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.036366 restraints weight = 75730.486| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17999 Z= 0.224 Angle : 1.155 18.118 25112 Z= 0.519 Chirality : 0.100 1.981 2925 Planarity : 0.005 0.056 2584 Dihedral : 21.710 175.874 3896 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 23.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 15.51 % Favored : 84.42 % Rotamer: Outliers : 0.07 % Allowed : 2.51 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.74 % 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: -2.61 (0.21), residues: 1515 helix: -0.52 (0.19), residues: 650 sheet: -2.09 (0.41), residues: 137 loop : -2.86 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 766 TYR 0.037 0.002 TYR D 565 PHE 0.030 0.002 PHE A 819 TRP 0.050 0.002 TRP A 604 HIS 0.006 0.002 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.22 (17998) covalent geometry : angle 1.15522 / 0.52 (25112) hydrogen bonds : bond 0.06429 / 4.05 ( 733) hydrogen bonds : angle 6.03675 / 3.99 ( 2000) metal coordination : bond 0.00142 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.558 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: A 139 LEU cc_start: 0.9699 (mt) cc_final: 0.9399 (mt) REVERT: A 179 SER cc_start: 0.7096 (p) cc_final: 0.6877 (p) REVERT: A 566 MET cc_start: 0.8996 (tpt) cc_final: 0.8160 (tpt) REVERT: A 701 ARG cc_start: 0.7605 (ptm160) cc_final: 0.7115 (mtt180) REVERT: A 811 MET cc_start: 0.8858 (tmm) cc_final: 0.8459 (ppp) REVERT: A 912 LEU cc_start: 0.9441 (tp) cc_final: 0.8988 (tp) REVERT: A 954 VAL cc_start: 0.9500 (t) cc_final: 0.9172 (t) REVERT: A 1029 MET cc_start: 0.9010 (mmp) cc_final: 0.8751 (mmp) REVERT: A 1040 LYS cc_start: 0.8793 (mtmt) cc_final: 0.8532 (mtmm) REVERT: D 586 MET cc_start: 0.6938 (tpp) cc_final: 0.5962 (tpp) REVERT: D 601 MET cc_start: 0.8413 (mtt) cc_final: 0.8107 (mtt) REVERT: F 59 TYR cc_start: 0.9166 (t80) cc_final: 0.8717 (t80) REVERT: F 61 ARG cc_start: 0.8693 (ttt-90) cc_final: 0.7897 (tmm160) REVERT: E 86 MET cc_start: 0.8266 (tpp) cc_final: 0.7959 (tpp) REVERT: E 117 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7900 (mt-10) REVERT: E 146 TYR cc_start: 0.9143 (t80) cc_final: 0.8445 (t80) REVERT: E 162 ASP cc_start: 0.9262 (m-30) cc_final: 0.8914 (m-30) outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.1269 time to fit residues: 21.8690 Evaluate side-chains 74 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 1 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 160 optimal weight: 40.0000 chunk 91 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 GLN ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 HIS ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 GLN ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 GLN ** H 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.045366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.033623 restraints weight = 219639.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.034432 restraints weight = 146667.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.035086 restraints weight = 109948.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.035504 restraints weight = 89200.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.035905 restraints weight = 76755.013| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 17999 Z= 0.257 Angle : 1.155 18.008 25112 Z= 0.524 Chirality : 0.097 1.975 2925 Planarity : 0.005 0.053 2584 Dihedral : 21.561 178.705 3896 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 25.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 14.65 % Favored : 85.28 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -2.67 (0.21), residues: 1515 helix: -0.59 (0.19), residues: 663 sheet: -2.42 (0.40), residues: 141 loop : -2.84 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 12 TYR 0.030 0.003 TYR A 650 PHE 0.058 0.003 PHE A 634 TRP 0.046 0.002 TRP A 604 HIS 0.015 0.002 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.26 (17998) covalent geometry : angle 1.15455 / 0.52 (25112) hydrogen bonds : bond 0.06577 / 4.14 ( 733) hydrogen bonds : angle 6.06233 / 4.00 ( 2000) metal coordination : bond 0.00226 / 0.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.586 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: A 139 LEU cc_start: 0.9709 (mt) cc_final: 0.9445 (mt) REVERT: A 179 SER cc_start: 0.7203 (p) cc_final: 0.6992 (p) REVERT: A 566 MET cc_start: 0.8994 (tpt) cc_final: 0.8204 (tpt) REVERT: A 634 PHE cc_start: 0.8723 (m-80) cc_final: 0.8370 (m-10) REVERT: A 701 ARG cc_start: 0.7603 (ptm160) cc_final: 0.7379 (mtt180) REVERT: A 811 MET cc_start: 0.8938 (tmm) cc_final: 0.8475 (ppp) REVERT: A 948 HIS cc_start: 0.8592 (m-70) cc_final: 0.8266 (m-70) REVERT: A 954 VAL cc_start: 0.9555 (t) cc_final: 0.9270 (p) REVERT: A 955 MET cc_start: 0.9482 (mmt) cc_final: 0.9102 (mmm) REVERT: A 1029 MET cc_start: 0.9074 (mmp) cc_final: 0.8793 (mmp) REVERT: D 586 MET cc_start: 0.6714 (tpp) cc_final: 0.5711 (tpp) REVERT: D 601 MET cc_start: 0.8360 (mtt) cc_final: 0.7947 (mtt) REVERT: F 59 TYR cc_start: 0.9219 (t80) cc_final: 0.8715 (t80) REVERT: F 61 ARG cc_start: 0.8798 (ttt-90) cc_final: 0.7813 (tmm160) REVERT: E 86 MET cc_start: 0.8378 (tpp) cc_final: 0.8050 (tpp) REVERT: E 146 TYR cc_start: 0.9194 (t80) cc_final: 0.8570 (t80) REVERT: E 162 ASP cc_start: 0.9183 (m-30) cc_final: 0.8850 (m-30) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1290 time to fit residues: 20.4486 Evaluate side-chains 74 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 106 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 GLN A 465 ASN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN A 648 ASN ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 GLN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.046846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.034835 restraints weight = 211400.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.035703 restraints weight = 142506.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.036411 restraints weight = 107038.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.036846 restraints weight = 86803.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.037244 restraints weight = 74624.879| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17999 Z= 0.180 Angle : 1.083 17.337 25112 Z= 0.485 Chirality : 0.094 1.871 2925 Planarity : 0.005 0.068 2584 Dihedral : 21.432 178.727 3896 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.66 % Favored : 86.27 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.67 % 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: -2.38 (0.21), residues: 1515 helix: -0.22 (0.19), residues: 657 sheet: -2.33 (0.40), residues: 143 loop : -2.79 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 446 TYR 0.029 0.002 TYR D 565 PHE 0.039 0.002 PHE A 634 TRP 0.063 0.003 TRP A 604 HIS 0.005 0.001 HIS D 693 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 (17998) covalent geometry : angle 1.08339 / 0.49 (25112) hydrogen bonds : bond 0.05656 / 3.58 ( 733) hydrogen bonds : angle 5.79881 / 3.80 ( 2000) metal coordination : bond 0.00057 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.583 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: A 139 LEU cc_start: 0.9701 (mt) cc_final: 0.9431 (mt) REVERT: A 426 MET cc_start: 0.7938 (mmp) cc_final: 0.7713 (mmm) REVERT: A 562 ASN cc_start: 0.8319 (t0) cc_final: 0.7791 (t0) REVERT: A 566 MET cc_start: 0.9044 (tpt) cc_final: 0.8271 (tpt) REVERT: A 634 PHE cc_start: 0.8506 (m-80) cc_final: 0.8125 (m-10) REVERT: A 701 ARG cc_start: 0.7498 (ptm160) cc_final: 0.7222 (mtt180) REVERT: A 811 MET cc_start: 0.8912 (tmm) cc_final: 0.8197 (ppp) REVERT: A 818 LEU cc_start: 0.9397 (tp) cc_final: 0.9006 (mp) REVERT: A 948 HIS cc_start: 0.8547 (m-70) cc_final: 0.8166 (m-70) REVERT: A 950 SER cc_start: 0.9805 (m) cc_final: 0.9413 (p) REVERT: A 954 VAL cc_start: 0.9500 (t) cc_final: 0.9244 (p) REVERT: A 955 MET cc_start: 0.9506 (mmt) cc_final: 0.9182 (mmm) REVERT: A 1029 MET cc_start: 0.9158 (mmp) cc_final: 0.8921 (mmm) REVERT: D 586 MET cc_start: 0.6734 (tpp) cc_final: 0.5936 (tpp) REVERT: D 601 MET cc_start: 0.8314 (mtt) cc_final: 0.7989 (mtt) REVERT: F 59 TYR cc_start: 0.9161 (t80) cc_final: 0.8650 (t80) REVERT: F 61 ARG cc_start: 0.8640 (ttt-90) cc_final: 0.7689 (tmm160) REVERT: E 86 MET cc_start: 0.8318 (tpp) cc_final: 0.8067 (tpp) REVERT: E 117 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7728 (mt-10) REVERT: E 146 TYR cc_start: 0.9224 (t80) cc_final: 0.8553 (t80) REVERT: E 162 ASP cc_start: 0.9217 (m-30) cc_final: 0.8822 (m-30) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1259 time to fit residues: 22.0972 Evaluate side-chains 81 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 113 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 173 optimal weight: 0.7980 chunk 124 optimal weight: 20.0000 chunk 76 optimal weight: 8.9990 chunk 33 optimal weight: 0.1980 chunk 20 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 GLN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 GLN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 461 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 = 0.3341 r_free = 0.3341 target = 0.045936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.034068 restraints weight = 216506.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.034915 restraints weight = 145451.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.035609 restraints weight = 109085.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.036046 restraints weight = 88258.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.036352 restraints weight = 76036.847| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17999 Z= 0.227 Angle : 1.090 16.125 25112 Z= 0.493 Chirality : 0.091 1.850 2925 Planarity : 0.005 0.052 2584 Dihedral : 21.325 174.756 3896 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 23.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 14.06 % Favored : 85.87 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -2.40 (0.21), residues: 1515 helix: -0.28 (0.19), residues: 658 sheet: -2.39 (0.40), residues: 141 loop : -2.75 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 727 TYR 0.039 0.002 TYR D 565 PHE 0.040 0.002 PHE A 634 TRP 0.051 0.002 TRP A 604 HIS 0.017 0.002 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.23 (17998) covalent geometry : angle 1.09019 / 0.49 (25112) hydrogen bonds : bond 0.06130 / 3.89 ( 733) hydrogen bonds : angle 5.81371 / 3.82 ( 2000) metal coordination : bond 0.00196 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.677 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: A 139 LEU cc_start: 0.9712 (mt) cc_final: 0.9371 (mt) REVERT: A 179 SER cc_start: 0.7156 (p) cc_final: 0.6946 (p) REVERT: A 562 ASN cc_start: 0.8311 (t0) cc_final: 0.7646 (t0) REVERT: A 566 MET cc_start: 0.9014 (tpt) cc_final: 0.8212 (tpt) REVERT: A 811 MET cc_start: 0.8853 (tmm) cc_final: 0.8358 (ppp) REVERT: A 917 LYS cc_start: 0.9361 (mtmm) cc_final: 0.9154 (mttt) REVERT: A 948 HIS cc_start: 0.8428 (m-70) cc_final: 0.8140 (m90) REVERT: A 950 SER cc_start: 0.9793 (m) cc_final: 0.9422 (p) REVERT: A 954 VAL cc_start: 0.9542 (t) cc_final: 0.9277 (p) REVERT: A 955 MET cc_start: 0.9487 (mmt) cc_final: 0.9198 (mmm) REVERT: D 586 MET cc_start: 0.6609 (tpp) cc_final: 0.5938 (tpp) REVERT: F 59 TYR cc_start: 0.9158 (t80) cc_final: 0.8643 (t80) REVERT: F 61 ARG cc_start: 0.8752 (ttt-90) cc_final: 0.7761 (tmm160) REVERT: E 146 TYR cc_start: 0.9230 (t80) cc_final: 0.8618 (t80) REVERT: E 162 ASP cc_start: 0.9198 (m-30) cc_final: 0.8845 (m-30) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1221 time to fit residues: 19.6917 Evaluate side-chains 74 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 64 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 179 optimal weight: 50.0000 chunk 81 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 166 optimal weight: 20.0000 chunk 138 optimal weight: 1.9990 chunk 115 optimal weight: 0.1980 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 GLN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 GLN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 461 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 = 0.3376 r_free = 0.3376 target = 0.046938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.034934 restraints weight = 207544.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.035785 restraints weight = 139427.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.036478 restraints weight = 104860.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.036968 restraints weight = 84769.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.037291 restraints weight = 72615.587| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17999 Z= 0.173 Angle : 1.039 14.008 25112 Z= 0.466 Chirality : 0.088 1.784 2925 Planarity : 0.004 0.055 2584 Dihedral : 21.153 176.050 3896 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.47 % Favored : 86.47 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -2.20 (0.21), residues: 1515 helix: -0.06 (0.19), residues: 666 sheet: -2.24 (0.41), residues: 139 loop : -2.74 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 12 TYR 0.038 0.002 TYR D 565 PHE 0.033 0.002 PHE A 819 TRP 0.060 0.002 TRP A 604 HIS 0.014 0.002 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (17998) covalent geometry : angle 1.03891 / 0.47 (25112) hydrogen bonds : bond 0.05535 / 3.52 ( 733) hydrogen bonds : angle 5.65269 / 3.71 ( 2000) metal coordination : bond 0.00093 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9700 (mt) cc_final: 0.9362 (mt) REVERT: A 459 LEU cc_start: 0.9544 (mt) cc_final: 0.9344 (mt) REVERT: A 562 ASN cc_start: 0.7986 (t0) cc_final: 0.7224 (m-40) REVERT: A 566 MET cc_start: 0.8980 (tpt) cc_final: 0.8676 (tpt) REVERT: A 811 MET cc_start: 0.8877 (tmm) cc_final: 0.8363 (ppp) REVERT: A 912 LEU cc_start: 0.9343 (tp) cc_final: 0.9071 (tp) REVERT: A 948 HIS cc_start: 0.8485 (m-70) cc_final: 0.8194 (m90) REVERT: A 950 SER cc_start: 0.9797 (m) cc_final: 0.9437 (p) REVERT: A 954 VAL cc_start: 0.9543 (t) cc_final: 0.9124 (p) REVERT: A 955 MET cc_start: 0.9506 (mmt) cc_final: 0.9065 (mmm) REVERT: D 586 MET cc_start: 0.6801 (tpp) cc_final: 0.6040 (tpp) REVERT: F 59 TYR cc_start: 0.9150 (t80) cc_final: 0.8617 (t80) REVERT: F 61 ARG cc_start: 0.8715 (ttt-90) cc_final: 0.7738 (tmm160) REVERT: E 86 MET cc_start: 0.8214 (tpt) cc_final: 0.7915 (tpp) REVERT: E 136 MET cc_start: 0.9252 (mmp) cc_final: 0.9032 (mmp) REVERT: E 146 TYR cc_start: 0.9252 (t80) cc_final: 0.8461 (t80) REVERT: E 162 ASP cc_start: 0.9236 (m-30) cc_final: 0.9003 (m-30) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1243 time to fit residues: 20.8218 Evaluate side-chains 77 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 92 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 11 optimal weight: 0.0170 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 GLN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN A 633 ASN ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 ASN A 853 ASN ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 GLN ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 461 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 = 0.3398 r_free = 0.3398 target = 0.047639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.035658 restraints weight = 210272.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.036517 restraints weight = 140320.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.037261 restraints weight = 105113.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.037751 restraints weight = 84691.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.038049 restraints weight = 72333.534| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17999 Z= 0.165 Angle : 1.017 13.527 25112 Z= 0.457 Chirality : 0.085 1.729 2925 Planarity : 0.004 0.070 2584 Dihedral : 20.981 176.506 3896 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.40 % Favored : 86.60 % Rotamer: Outliers : 0.07 % Allowed : 0.42 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -1.97 (0.21), residues: 1515 helix: 0.16 (0.20), residues: 663 sheet: -1.95 (0.43), residues: 131 loop : -2.69 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 766 TYR 0.043 0.002 TYR D 565 PHE 0.034 0.002 PHE A 819 TRP 0.065 0.003 TRP A 604 HIS 0.015 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (17998) covalent geometry : angle 1.01675 / 0.46 (25112) hydrogen bonds : bond 0.05361 / 3.46 ( 733) hydrogen bonds : angle 5.53141 / 3.63 ( 2000) metal coordination : bond 0.00075 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.584 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: A 139 LEU cc_start: 0.9702 (mt) cc_final: 0.9354 (mt) REVERT: A 179 SER cc_start: 0.6392 (p) cc_final: 0.6185 (p) REVERT: A 562 ASN cc_start: 0.8311 (t0) cc_final: 0.7658 (m-40) REVERT: A 566 MET cc_start: 0.9078 (tpt) cc_final: 0.8725 (tpt) REVERT: A 573 ARG cc_start: 0.9282 (ttm110) cc_final: 0.9061 (ttm110) REVERT: A 811 MET cc_start: 0.8843 (tmm) cc_final: 0.8190 (ppp) REVERT: A 818 LEU cc_start: 0.9378 (tp) cc_final: 0.9047 (mt) REVERT: A 948 HIS cc_start: 0.8560 (m-70) cc_final: 0.8117 (m90) REVERT: A 950 SER cc_start: 0.9786 (m) cc_final: 0.9464 (p) REVERT: A 954 VAL cc_start: 0.9526 (t) cc_final: 0.9245 (t) REVERT: A 955 MET cc_start: 0.9481 (mmt) cc_final: 0.9070 (mmm) REVERT: A 961 MET cc_start: 0.9025 (ptp) cc_final: 0.8729 (tpp) REVERT: D 586 MET cc_start: 0.6511 (tpp) cc_final: 0.5835 (tpp) REVERT: D 661 GLU cc_start: 0.8694 (mp0) cc_final: 0.8493 (mp0) REVERT: F 59 TYR cc_start: 0.9143 (t80) cc_final: 0.8600 (t80) REVERT: F 61 ARG cc_start: 0.8689 (ttt-90) cc_final: 0.7707 (tmm160) REVERT: E 86 MET cc_start: 0.8204 (tpt) cc_final: 0.7983 (tpp) REVERT: E 136 MET cc_start: 0.9241 (mmp) cc_final: 0.9013 (mmm) REVERT: E 146 TYR cc_start: 0.9259 (t80) cc_final: 0.8882 (t80) REVERT: E 162 ASP cc_start: 0.9021 (m-30) cc_final: 0.8716 (m-30) REVERT: H 531 GLN cc_start: 0.9270 (mt0) cc_final: 0.8934 (pt0) outliers start: 1 outliers final: 0 residues processed: 116 average time/residue: 0.1321 time to fit residues: 24.1403 Evaluate side-chains 84 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 161 optimal weight: 30.0000 chunk 72 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 160 optimal weight: 40.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN A 633 ASN A 636 ASN ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 GLN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN ** H 461 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 = 0.3337 r_free = 0.3337 target = 0.045847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.033957 restraints weight = 217968.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.034799 restraints weight = 146260.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.035483 restraints weight = 109936.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.035941 restraints weight = 89176.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.036224 restraints weight = 76631.455| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 17999 Z= 0.255 Angle : 1.071 13.124 25112 Z= 0.493 Chirality : 0.085 1.707 2925 Planarity : 0.005 0.063 2584 Dihedral : 20.964 176.781 3896 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 25.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.13 % Favored : 85.87 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.18 (0.21), residues: 1515 helix: -0.09 (0.19), residues: 655 sheet: -2.33 (0.41), residues: 137 loop : -2.62 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 727 TYR 0.046 0.003 TYR D 565 PHE 0.034 0.003 PHE A 588 TRP 0.044 0.003 TRP A 604 HIS 0.013 0.002 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.26 (17998) covalent geometry : angle 1.07120 / 0.49 (25112) hydrogen bonds : bond 0.06299 / 4.02 ( 733) hydrogen bonds : angle 5.70109 / 3.77 ( 2000) metal coordination : bond 0.00232 / 0.12 ( 1) =============================================================================== Job complete usr+sys time: 3290.43 seconds wall clock time: 57 minutes 56.66 seconds (3476.66 seconds total)