Starting phenix.real_space_refine on Sun Sep 13 05:52:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rok_54122/09_2026/9rok_54122_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rok_54122/09_2026/9rok_54122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rok_54122/09_2026/9rok_54122_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rok_54122/09_2026/9rok_54122_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rok_54122/09_2026/9rok_54122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rok_54122/09_2026/9rok_54122.map" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.022 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 S 60 5.16 5 Na 1 4.78 5 C 6502 2.51 5 N 1672 2.21 5 O 1888 1.98 5 H 10018 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 20141 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 15035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 969, 15035 Classifications: {'peptide': 969} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 927} Chain breaks: 2 Chain: "B" Number of atoms: 4436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 4436 Classifications: {'peptide': 274} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 253} Chain breaks: 1 Chain: "C" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 543 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 85 Unusual residues: {' NA': 1, 'CLR': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.42, per 1000 atoms: 0.17 Number of scatterers: 20141 At special positions: 0 Unit cell: (79.666, 84.89, 172.392, 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) S 60 16.00 Na 1 11.00 O 1888 8.00 N 1672 7.00 C 6502 6.00 H 10018 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied NAG-ASN " NAG B 401 " - " ASN B 158 " " NAG B 402 " - " ASN B 193 " " NAG B 403 " - " ASN B 265 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 541.5 milliseconds 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2354 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 9 sheets defined 50.6% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 37 through 45 Processing helix chain 'A' and resid 54 through 66 Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.668A pdb=" N LYS A 81 " --> pdb=" O PRO A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 109 removed outlier: 4.241A pdb=" N LEU A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 155 removed outlier: 3.729A pdb=" N TYR A 121 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 272 through 304 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 324 through 344 removed outlier: 4.497A pdb=" N ALA A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 359 removed outlier: 3.788A pdb=" N THR A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 358 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 419 removed outlier: 4.061A pdb=" N ASN A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 454 Processing helix chain 'A' and resid 456 through 464 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 521 through 538 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 610 through 622 Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 646 through 650 Processing helix chain 'A' and resid 657 through 662 removed outlier: 4.314A pdb=" N ASP A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 675 Processing helix chain 'A' and resid 684 through 698 Processing helix chain 'A' and resid 708 through 710 No H-bonds generated for 'chain 'A' and resid 708 through 710' Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'A' and resid 745 through 769 removed outlier: 4.335A pdb=" N VAL A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR A 750 " --> pdb=" O ALA A 746 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE A 759 " --> pdb=" O GLY A 755 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 786 Proline residue: A 779 - end of helix Processing helix chain 'A' and resid 793 through 805 Processing helix chain 'A' and resid 806 through 813 removed outlier: 3.610A pdb=" N ILE A 810 " --> pdb=" O MET A 806 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA A 813 " --> pdb=" O ALA A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 824 removed outlier: 3.569A pdb=" N ARG A 824 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 846 removed outlier: 4.007A pdb=" N GLN A 846 " --> pdb=" O MET A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 866 removed outlier: 3.806A pdb=" N ILE A 850 " --> pdb=" O GLN A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 876 through 882 Processing helix chain 'A' and resid 897 through 927 removed outlier: 3.897A pdb=" N ARG A 901 " --> pdb=" O THR A 897 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA A 922 " --> pdb=" O VAL A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 941 through 961 Processing helix chain 'A' and resid 975 through 980 Processing helix chain 'A' and resid 981 through 1002 Processing helix chain 'A' and resid 1005 through 1012 Processing helix chain 'B' and resid 28 through 61 Processing helix chain 'B' and resid 69 through 73 Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 111 through 118 removed outlier: 6.027A pdb=" N ASP B 114 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N SER B 115 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 161 removed outlier: 6.539A pdb=" N ASN B 158 " --> pdb=" O TRP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 223 Processing helix chain 'B' and resid 246 through 251 removed outlier: 4.235A pdb=" N LEU B 250 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 56 removed outlier: 3.602A pdb=" N LEU C 36 " --> pdb=" O ASP C 32 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 163 Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 184 removed outlier: 6.175A pdb=" N ASP A 179 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL A 248 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LYS A 202 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY A 242 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLY A 200 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA A 244 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA A 198 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLY A 246 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE A 196 " --> pdb=" O GLY A 246 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N VAL A 248 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ARG A 194 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 348 removed outlier: 6.155A pdb=" N GLY A 721 " --> pdb=" O MET A 738 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU A 740 " --> pdb=" O GLY A 721 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA A 723 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET A 724 " --> pdb=" O GLY A 706 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP A 366 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE A 363 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL A 606 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N SER A 365 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL A 603 " --> pdb=" O ILE A 678 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N PHE A 680 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N MET A 605 " --> pdb=" O PHE A 680 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 389 removed outlier: 6.025A pdb=" N VAL A 378 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE A 582 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS A 380 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 9.810A pdb=" N LEU A 573 " --> pdb=" O TYR A 549 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N TYR A 549 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N PHE A 575 " --> pdb=" O HIS A 547 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N HIS A 547 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A 577 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET A 579 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A 480 " --> pdb=" O GLU A 469 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU A 469 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 482 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 389 removed outlier: 6.025A pdb=" N VAL A 378 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE A 582 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS A 380 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS A 508 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N PHE A 575 " --> pdb=" O CYS A 508 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR A 510 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N GLY A 577 " --> pdb=" O THR A 510 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N LEU A 512 " --> pdb=" O GLY A 577 " (cutoff:3.500A) removed outlier: 12.851A pdb=" N MET A 579 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 888 through 889 Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AA8, first strand: chain 'B' and resid 88 through 90 removed outlier: 3.739A pdb=" N PHE B 90 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 123 through 124 522 hydrogen bonds defined for protein. 1467 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.76 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9992 1.03 - 1.23: 32 1.23 - 1.42: 4188 1.42 - 1.62: 6053 1.62 - 1.81: 88 Bond restraints: 20353 Sorted by residual: bond pdb=" C1 NAG B 402 " pdb=" O5 NAG B 402 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C1 NAG B 403 " pdb=" O5 NAG B 403 " ideal model delta sigma weight residual 1.406 1.428 -0.022 2.00e-02 2.50e+03 1.23e+00 bond pdb=" C5 NAG B 403 " pdb=" O5 NAG B 403 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.21e+00 bond pdb=" C5 NAG B 401 " pdb=" O5 NAG B 401 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.20e+00 bond pdb=" C1 NAG B 401 " pdb=" O5 NAG B 401 " ideal model delta sigma weight residual 1.406 1.427 -0.021 2.00e-02 2.50e+03 1.11e+00 ... (remaining 20348 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 36483 1.72 - 3.44: 318 3.44 - 5.15: 37 5.15 - 6.87: 3 6.87 - 8.59: 2 Bond angle restraints: 36843 Sorted by residual: angle pdb=" CB MET A 842 " pdb=" CG MET A 842 " pdb=" SD MET A 842 " ideal model delta sigma weight residual 112.70 121.29 -8.59 3.00e+00 1.11e-01 8.19e+00 angle pdb=" CB MET A 605 " pdb=" CG MET A 605 " pdb=" SD MET A 605 " ideal model delta sigma weight residual 112.70 119.72 -7.02 3.00e+00 1.11e-01 5.48e+00 angle pdb=" CB MET A 148 " pdb=" CG MET A 148 " pdb=" SD MET A 148 " ideal model delta sigma weight residual 112.70 119.24 -6.54 3.00e+00 1.11e-01 4.75e+00 angle pdb=" N GLY A 134 " pdb=" CA GLY A 134 " pdb=" C GLY A 134 " ideal model delta sigma weight residual 113.18 108.46 4.72 2.37e+00 1.78e-01 3.97e+00 angle pdb=" CB MET A 581 " pdb=" CG MET A 581 " pdb=" SD MET A 581 " ideal model delta sigma weight residual 112.70 118.64 -5.94 3.00e+00 1.11e-01 3.93e+00 ... (remaining 36838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 8654 17.97 - 35.95: 773 35.95 - 53.92: 252 53.92 - 71.90: 59 71.90 - 89.87: 18 Dihedral angle restraints: 9756 sinusoidal: 5475 harmonic: 4281 Sorted by residual: dihedral pdb=" CA LYS B 216 " pdb=" C LYS B 216 " pdb=" N ARG B 217 " pdb=" CA ARG B 217 " ideal model delta harmonic sigma weight residual -180.00 -154.08 -25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ASP A 490 " pdb=" C ASP A 490 " pdb=" N ASN A 491 " pdb=" CA ASN A 491 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA GLU A 469 " pdb=" C GLU A 469 " pdb=" N ILE A 470 " pdb=" CA ILE A 470 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 9753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1104 0.034 - 0.068: 348 0.068 - 0.101: 106 0.101 - 0.135: 42 0.135 - 0.169: 4 Chirality restraints: 1604 Sorted by residual: chirality pdb=" C1 NAG B 401 " pdb=" ND2 ASN B 158 " pdb=" C2 NAG B 401 " pdb=" O5 NAG B 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA ILE A 470 " pdb=" N ILE A 470 " pdb=" C ILE A 470 " pdb=" CB ILE A 470 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA ILE A 430 " pdb=" N ILE A 430 " pdb=" C ILE A 430 " pdb=" CB ILE A 430 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 1601 not shown) Planarity restraints: 2998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 130 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.81e+00 pdb=" C VAL A 130 " 0.038 2.00e-02 2.50e+03 pdb=" O VAL A 130 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE A 131 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 129 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C VAL A 129 " 0.031 2.00e-02 2.50e+03 pdb=" O VAL A 129 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL A 130 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 132 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C ILE A 132 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE A 132 " 0.011 2.00e-02 2.50e+03 pdb=" N THR A 133 " 0.010 2.00e-02 2.50e+03 ... (remaining 2995 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 748 2.13 - 2.75: 38171 2.75 - 3.37: 59786 3.37 - 3.98: 74059 3.98 - 4.60: 115208 Nonbonded interactions: 287972 Sorted by model distance: nonbonded pdb=" OE1 GLU B 63 " pdb=" H GLU B 63 " model vdw 1.514 2.450 nonbonded pdb=" O ASN A 476 " pdb="HH12 ARG A 503 " model vdw 1.577 2.450 nonbonded pdb="HE22 GLN A 851 " pdb=" OE1 GLN A 920 " model vdw 1.591 2.450 nonbonded pdb=" O VAL A 709 " pdb=" HG SER A 712 " model vdw 1.597 2.450 nonbonded pdb=" O ASP B 114 " pdb=" HE ARG B 118 " model vdw 1.599 2.450 ... (remaining 287967 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=0.00 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.240 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 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 : 0.008 0.804 10342 Z= 0.802 Angle : 0.545 8.588 14037 Z= 0.275 Chirality : 0.039 0.169 1604 Planarity : 0.003 0.033 1786 Dihedral : 15.397 89.163 4038 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.09 % Favored : 93.83 % Rotamer: Outliers : 0.36 % Allowed : 15.51 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.24), residues: 1265 helix: 0.75 (0.22), residues: 574 sheet: -0.41 (0.42), residues: 151 loop : -0.82 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 463 TYR 0.012 0.001 TYR A 859 PHE 0.028 0.001 PHE A 90 TRP 0.005 0.001 TRP A 408 HIS 0.003 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (10335) covalent geometry : angle 0.53721 / 0.27 (14022) SS BOND : bond 0.00182 / 0.09 ( 3) SS BOND : angle 0.74671 / 0.36 ( 6) hydrogen bonds : bond 0.16205 / 10.73 ( 515) hydrogen bonds : angle 7.02020 / 5.01 ( 1467) Misc. bond : bond 0.80366 / 42.30 ( 1) link_NAG-ASN : bond 0.00169 / 0.08 ( 3) link_NAG-ASN : angle 3.63398 / 1.84 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 772 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.549 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: symmetry clash REVERT: B 199 TYR cc_start: 0.6406 (OUTLIER) cc_final: 0.4407 (p90) outliers start: 4 outliers final: 2 residues processed: 82 average time/residue: 0.2017 time to fit residues: 24.5914 Evaluate side-chains 80 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 199 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.4980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 20.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN A 108 GLN ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 HIS ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.102534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.071202 restraints weight = 100422.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.074212 restraints weight = 39444.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.076081 restraints weight = 22851.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.077100 restraints weight = 16690.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.077787 restraints weight = 14130.143| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.0659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10342 Z= 0.141 Angle : 0.548 7.080 14037 Z= 0.287 Chirality : 0.040 0.159 1604 Planarity : 0.004 0.040 1786 Dihedral : 7.044 58.911 1636 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.30 % Favored : 94.62 % Rotamer: Outliers : 1.46 % Allowed : 13.59 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.24), residues: 1265 helix: 1.11 (0.21), residues: 591 sheet: -0.60 (0.44), residues: 143 loop : -0.95 (0.29), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 27 TYR 0.014 0.001 TYR A 105 PHE 0.011 0.001 PHE B 295 TRP 0.006 0.001 TRP A 408 HIS 0.004 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (10335) covalent geometry : angle 0.54133 / 0.29 (14022) SS BOND : bond 0.00124 / 0.06 ( 3) SS BOND : angle 0.74054 / 0.35 ( 6) hydrogen bonds : bond 0.04967 / 3.47 ( 515) hydrogen bonds : angle 5.34278 / 3.78 ( 1467) Misc. bond : bond 0.00404 / 0.21 ( 1) link_NAG-ASN : bond 0.00166 / 0.08 ( 3) link_NAG-ASN : angle 3.29699 / 1.69 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 772 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.600 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: B 57 MET cc_start: 0.8627 (tmm) cc_final: 0.8372 (tmm) REVERT: B 199 TYR cc_start: 0.6230 (OUTLIER) cc_final: 0.3909 (p90) outliers start: 16 outliers final: 12 residues processed: 92 average time/residue: 0.1871 time to fit residues: 26.4404 Evaluate side-chains 88 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 42 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 75 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 GLN B 292 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.101584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.070284 restraints weight = 100698.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.073237 restraints weight = 39945.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.075088 restraints weight = 23202.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.076108 restraints weight = 16970.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.076781 restraints weight = 14345.448| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10342 Z= 0.184 Angle : 0.549 6.349 14037 Z= 0.288 Chirality : 0.040 0.160 1604 Planarity : 0.004 0.037 1786 Dihedral : 6.998 58.523 1636 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.85 % Favored : 94.07 % Rotamer: Outliers : 1.82 % Allowed : 14.14 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.24), residues: 1265 helix: 1.18 (0.21), residues: 591 sheet: -0.66 (0.45), residues: 143 loop : -1.00 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 586 TYR 0.016 0.001 TYR A 105 PHE 0.010 0.001 PHE B 295 TRP 0.007 0.001 TRP A 408 HIS 0.004 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (10335) covalent geometry : angle 0.54321 / 0.29 (14022) SS BOND : bond 0.00140 / 0.07 ( 3) SS BOND : angle 0.76693 / 0.37 ( 6) hydrogen bonds : bond 0.04414 / 3.05 ( 515) hydrogen bonds : angle 5.18400 / 3.67 ( 1467) Misc. bond : bond 0.00071 / 0.04 ( 1) link_NAG-ASN : bond 0.00241 / 0.12 ( 3) link_NAG-ASN : angle 3.11451 / 1.57 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 772 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.588 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: B 170 LYS cc_start: 0.9417 (OUTLIER) cc_final: 0.9079 (ptpp) REVERT: B 199 TYR cc_start: 0.5879 (OUTLIER) cc_final: 0.3282 (p90) REVERT: B 268 MET cc_start: 0.7697 (tpp) cc_final: 0.7255 (tpp) outliers start: 20 outliers final: 16 residues processed: 91 average time/residue: 0.2007 time to fit residues: 28.0158 Evaluate side-chains 95 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 42 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 62 optimal weight: 0.0770 chunk 108 optimal weight: 3.9990 chunk 106 optimal weight: 0.0070 chunk 63 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN A 920 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.102753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.071390 restraints weight = 100062.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.074415 restraints weight = 39297.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.076272 restraints weight = 22770.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.077393 restraints weight = 16693.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.077891 restraints weight = 13970.896| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10342 Z= 0.115 Angle : 0.517 6.925 14037 Z= 0.264 Chirality : 0.040 0.162 1604 Planarity : 0.003 0.038 1786 Dihedral : 6.714 59.713 1635 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.43 % Favored : 95.49 % Rotamer: Outliers : 1.92 % Allowed : 14.32 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.25), residues: 1265 helix: 1.42 (0.21), residues: 592 sheet: -0.54 (0.45), residues: 140 loop : -0.90 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 901 TYR 0.017 0.001 TYR A 105 PHE 0.010 0.001 PHE B 295 TRP 0.005 0.001 TRP A 408 HIS 0.004 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (10335) covalent geometry : angle 0.51149 / 0.26 (14022) SS BOND : bond 0.00188 / 0.09 ( 3) SS BOND : angle 0.82659 / 0.40 ( 6) hydrogen bonds : bond 0.03886 / 2.68 ( 515) hydrogen bonds : angle 4.85075 / 3.43 ( 1467) Misc. bond : bond 0.00003 / 0.00 ( 1) link_NAG-ASN : bond 0.00190 / 0.10 ( 3) link_NAG-ASN : angle 2.98713 / 1.50 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 772 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.489 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: B 57 MET cc_start: 0.8542 (tmm) cc_final: 0.8338 (tmm) REVERT: B 170 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9078 (ptpp) REVERT: B 199 TYR cc_start: 0.5914 (OUTLIER) cc_final: 0.3250 (p90) REVERT: B 224 VAL cc_start: 0.6118 (OUTLIER) cc_final: 0.5835 (m) REVERT: B 268 MET cc_start: 0.7883 (tpp) cc_final: 0.7459 (tpp) outliers start: 21 outliers final: 16 residues processed: 97 average time/residue: 0.1896 time to fit residues: 28.4782 Evaluate side-chains 96 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 42 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 50 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 54 optimal weight: 0.3980 chunk 88 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 24 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 96 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.103386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.072149 restraints weight = 99765.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.075194 restraints weight = 39286.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.077024 restraints weight = 22671.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.078178 restraints weight = 16632.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.078753 restraints weight = 13890.298| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10342 Z= 0.098 Angle : 0.506 6.251 14037 Z= 0.256 Chirality : 0.040 0.156 1604 Planarity : 0.003 0.038 1786 Dihedral : 6.335 57.268 1635 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.27 % Favored : 95.65 % Rotamer: Outliers : 1.82 % Allowed : 14.51 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.25), residues: 1265 helix: 1.58 (0.22), residues: 594 sheet: -0.44 (0.46), residues: 140 loop : -0.81 (0.29), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 901 TYR 0.015 0.001 TYR A 105 PHE 0.010 0.001 PHE B 108 TRP 0.004 0.001 TRP A 408 HIS 0.003 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (10335) covalent geometry : angle 0.50046 / 0.25 (14022) SS BOND : bond 0.00219 / 0.10 ( 3) SS BOND : angle 0.84024 / 0.40 ( 6) hydrogen bonds : bond 0.03638 / 2.50 ( 515) hydrogen bonds : angle 4.68007 / 3.31 ( 1467) Misc. bond : bond 0.00000 / 0.00 ( 1) link_NAG-ASN : bond 0.00220 / 0.11 ( 3) link_NAG-ASN : angle 2.92954 / 1.47 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 772 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.522 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 581 MET cc_start: 0.7610 (mmp) cc_final: 0.7385 (mmp) REVERT: A 973 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8747 (mp) REVERT: B 170 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9042 (ptpp) REVERT: B 224 VAL cc_start: 0.5963 (OUTLIER) cc_final: 0.5679 (m) REVERT: B 268 MET cc_start: 0.7923 (tpp) cc_final: 0.7557 (tpp) outliers start: 20 outliers final: 16 residues processed: 96 average time/residue: 0.1892 time to fit residues: 27.9713 Evaluate side-chains 94 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 546 CYS Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 42 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.101917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.070680 restraints weight = 101129.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.073647 restraints weight = 40026.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.075523 restraints weight = 23240.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.076551 restraints weight = 16962.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.077010 restraints weight = 14310.753| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10342 Z= 0.176 Angle : 0.531 6.255 14037 Z= 0.275 Chirality : 0.040 0.154 1604 Planarity : 0.003 0.037 1786 Dihedral : 6.200 59.722 1633 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.53 % Favored : 94.39 % Rotamer: Outliers : 2.37 % Allowed : 14.87 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.25), residues: 1265 helix: 1.56 (0.21), residues: 593 sheet: -0.57 (0.45), residues: 143 loop : -0.93 (0.29), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 877 TYR 0.016 0.001 TYR A 859 PHE 0.010 0.001 PHE B 295 TRP 0.006 0.001 TRP A 408 HIS 0.004 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (10335) covalent geometry : angle 0.52604 / 0.27 (14022) SS BOND : bond 0.00113 / 0.06 ( 3) SS BOND : angle 0.76860 / 0.38 ( 6) hydrogen bonds : bond 0.03623 / 2.46 ( 515) hydrogen bonds : angle 4.77015 / 3.37 ( 1467) Misc. bond : bond 0.00001 / 0.00 ( 1) link_NAG-ASN : bond 0.00293 / 0.15 ( 3) link_NAG-ASN : angle 2.87568 / 1.45 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 772 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.626 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: A 754 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8345 (mp0) REVERT: A 973 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.8900 (mp) REVERT: B 57 MET cc_start: 0.8598 (tmm) cc_final: 0.8348 (tmm) REVERT: B 79 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8110 (pp30) REVERT: B 170 LYS cc_start: 0.9438 (OUTLIER) cc_final: 0.9085 (ptpp) REVERT: B 199 TYR cc_start: 0.6099 (OUTLIER) cc_final: 0.3487 (p90) REVERT: B 268 MET cc_start: 0.8137 (tpp) cc_final: 0.7792 (tpp) outliers start: 26 outliers final: 18 residues processed: 96 average time/residue: 0.2034 time to fit residues: 29.8088 Evaluate side-chains 99 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 546 CYS Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 42 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.102627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.070906 restraints weight = 103508.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.073985 restraints weight = 40740.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.075939 restraints weight = 23689.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.077067 restraints weight = 17265.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.077523 restraints weight = 14482.631| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10342 Z= 0.131 Angle : 0.517 6.941 14037 Z= 0.264 Chirality : 0.040 0.159 1604 Planarity : 0.003 0.037 1786 Dihedral : 5.953 53.673 1633 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.90 % Favored : 95.02 % Rotamer: Outliers : 2.37 % Allowed : 15.15 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.25), residues: 1265 helix: 1.61 (0.22), residues: 594 sheet: -0.49 (0.46), residues: 140 loop : -0.89 (0.29), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 877 TYR 0.014 0.001 TYR A 105 PHE 0.010 0.001 PHE B 295 TRP 0.005 0.001 TRP A 408 HIS 0.003 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (10335) covalent geometry : angle 0.51195 / 0.26 (14022) SS BOND : bond 0.00176 / 0.09 ( 3) SS BOND : angle 0.81834 / 0.39 ( 6) hydrogen bonds : bond 0.03519 / 2.38 ( 515) hydrogen bonds : angle 4.64759 / 3.29 ( 1467) Misc. bond : bond 0.00008 / 0.00 ( 1) link_NAG-ASN : bond 0.00188 / 0.09 ( 3) link_NAG-ASN : angle 2.79086 / 1.41 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 772 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.420 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 973 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.8892 (mp) REVERT: B 57 MET cc_start: 0.8613 (tmm) cc_final: 0.8336 (tmm) REVERT: B 79 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8091 (pp30) REVERT: B 170 LYS cc_start: 0.9435 (OUTLIER) cc_final: 0.9080 (ptpp) REVERT: B 199 TYR cc_start: 0.6124 (OUTLIER) cc_final: 0.3497 (p90) REVERT: B 224 VAL cc_start: 0.5921 (OUTLIER) cc_final: 0.5653 (m) REVERT: B 268 MET cc_start: 0.8189 (tpp) cc_final: 0.7810 (tpp) outliers start: 26 outliers final: 20 residues processed: 96 average time/residue: 0.1769 time to fit residues: 26.1136 Evaluate side-chains 100 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 546 CYS Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 43 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 0 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.101434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.071318 restraints weight = 104992.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.073919 restraints weight = 39615.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.073581 restraints weight = 25279.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.073948 restraints weight = 24635.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.074286 restraints weight = 22198.710| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10342 Z= 0.201 Angle : 0.550 7.127 14037 Z= 0.287 Chirality : 0.040 0.160 1604 Planarity : 0.004 0.036 1786 Dihedral : 6.008 59.219 1633 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.01 % Favored : 93.91 % Rotamer: Outliers : 2.55 % Allowed : 15.24 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.25), residues: 1265 helix: 1.48 (0.21), residues: 593 sheet: -0.69 (0.45), residues: 143 loop : -1.00 (0.29), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 586 TYR 0.017 0.001 TYR A 859 PHE 0.010 0.001 PHE A 281 TRP 0.007 0.001 TRP A 408 HIS 0.004 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (10335) covalent geometry : angle 0.54575 / 0.29 (14022) SS BOND : bond 0.00143 / 0.07 ( 3) SS BOND : angle 0.80927 / 0.40 ( 6) hydrogen bonds : bond 0.03649 / 2.46 ( 515) hydrogen bonds : angle 4.77263 / 3.38 ( 1467) Misc. bond : bond 0.00009 / 0.00 ( 1) link_NAG-ASN : bond 0.00331 / 0.17 ( 3) link_NAG-ASN : angle 2.77696 / 1.39 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 772 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.388 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: A 710 ASN cc_start: 0.8509 (t0) cc_final: 0.7997 (p0) REVERT: A 754 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8384 (mp0) REVERT: A 973 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.8892 (mp) REVERT: B 57 MET cc_start: 0.8611 (tmm) cc_final: 0.8359 (tmm) REVERT: B 170 LYS cc_start: 0.9478 (OUTLIER) cc_final: 0.9103 (ptpp) REVERT: B 199 TYR cc_start: 0.6358 (OUTLIER) cc_final: 0.3982 (p90) REVERT: B 224 VAL cc_start: 0.5968 (OUTLIER) cc_final: 0.5663 (m) REVERT: B 268 MET cc_start: 0.8298 (tpp) cc_final: 0.7932 (tpp) outliers start: 28 outliers final: 18 residues processed: 96 average time/residue: 0.1897 time to fit residues: 27.9991 Evaluate side-chains 96 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 546 CYS Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 43 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.101474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.071395 restraints weight = 104194.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.073800 restraints weight = 39782.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.073590 restraints weight = 25522.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.073964 restraints weight = 25055.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.074230 restraints weight = 22429.444| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10342 Z= 0.190 Angle : 0.555 8.057 14037 Z= 0.288 Chirality : 0.041 0.160 1604 Planarity : 0.004 0.036 1786 Dihedral : 5.802 56.871 1633 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.45 % Favored : 94.47 % Rotamer: Outliers : 2.37 % Allowed : 15.60 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.24), residues: 1265 helix: 1.44 (0.21), residues: 593 sheet: -0.80 (0.44), residues: 143 loop : -1.03 (0.29), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 586 TYR 0.017 0.001 TYR A 859 PHE 0.010 0.001 PHE B 295 TRP 0.006 0.001 TRP A 408 HIS 0.004 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (10335) covalent geometry : angle 0.55068 / 0.29 (14022) SS BOND : bond 0.00144 / 0.07 ( 3) SS BOND : angle 0.84763 / 0.41 ( 6) hydrogen bonds : bond 0.03652 / 2.46 ( 515) hydrogen bonds : angle 4.75302 / 3.37 ( 1467) Misc. bond : bond 0.00015 / 0.01 ( 1) link_NAG-ASN : bond 0.00262 / 0.13 ( 3) link_NAG-ASN : angle 2.70057 / 1.36 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 772 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.560 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: A 710 ASN cc_start: 0.8490 (t0) cc_final: 0.7941 (p0) REVERT: A 754 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8377 (mp0) REVERT: B 57 MET cc_start: 0.8649 (tmm) cc_final: 0.8390 (tmm) REVERT: B 170 LYS cc_start: 0.9481 (OUTLIER) cc_final: 0.9113 (ptpp) REVERT: B 199 TYR cc_start: 0.6465 (OUTLIER) cc_final: 0.4152 (p90) REVERT: B 224 VAL cc_start: 0.6113 (OUTLIER) cc_final: 0.5830 (m) REVERT: B 268 MET cc_start: 0.8324 (tpp) cc_final: 0.7961 (tpp) outliers start: 26 outliers final: 20 residues processed: 91 average time/residue: 0.1958 time to fit residues: 27.4158 Evaluate side-chains 97 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 546 CYS Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 43 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 60 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 106 optimal weight: 0.0870 chunk 81 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.101001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.070971 restraints weight = 105075.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.073396 restraints weight = 39986.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.073534 restraints weight = 25527.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.073925 restraints weight = 24944.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.074131 restraints weight = 21313.852| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10342 Z= 0.193 Angle : 0.553 8.217 14037 Z= 0.288 Chirality : 0.040 0.159 1604 Planarity : 0.004 0.036 1786 Dihedral : 5.815 57.617 1633 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.09 % Favored : 93.83 % Rotamer: Outliers : 2.37 % Allowed : 15.69 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.24), residues: 1265 helix: 1.46 (0.21), residues: 592 sheet: -0.68 (0.45), residues: 141 loop : -1.09 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 586 TYR 0.017 0.001 TYR A 859 PHE 0.010 0.001 PHE B 295 TRP 0.009 0.001 TRP A 307 HIS 0.004 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (10335) covalent geometry : angle 0.54933 / 0.29 (14022) SS BOND : bond 0.00150 / 0.07 ( 3) SS BOND : angle 0.82994 / 0.40 ( 6) hydrogen bonds : bond 0.03629 / 2.44 ( 515) hydrogen bonds : angle 4.74962 / 3.37 ( 1467) Misc. bond : bond 0.00004 / 0.00 ( 1) link_NAG-ASN : bond 0.00278 / 0.14 ( 3) link_NAG-ASN : angle 2.68272 / 1.34 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 772 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.525 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: A 710 ASN cc_start: 0.8484 (t0) cc_final: 0.7897 (p0) REVERT: A 754 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8379 (mp0) REVERT: A 973 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8763 (mp) REVERT: B 57 MET cc_start: 0.8652 (tmm) cc_final: 0.8370 (tmm) REVERT: B 199 TYR cc_start: 0.6392 (OUTLIER) cc_final: 0.3996 (p90) REVERT: B 224 VAL cc_start: 0.6255 (OUTLIER) cc_final: 0.5966 (m) REVERT: B 268 MET cc_start: 0.8338 (tpp) cc_final: 0.7978 (tpp) outliers start: 26 outliers final: 19 residues processed: 92 average time/residue: 0.1962 time to fit residues: 27.5174 Evaluate side-chains 95 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 546 CYS Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 43 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 68 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.100618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.069291 restraints weight = 101662.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.072202 restraints weight = 40956.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.074037 restraints weight = 24069.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.075024 restraints weight = 17710.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.075727 restraints weight = 15049.690| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10342 Z= 0.161 Angle : 0.545 9.037 14037 Z= 0.280 Chirality : 0.040 0.161 1604 Planarity : 0.004 0.037 1786 Dihedral : 5.769 59.017 1633 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.30 % Favored : 94.62 % Rotamer: Outliers : 2.19 % Allowed : 15.88 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.25), residues: 1265 helix: 1.53 (0.21), residues: 593 sheet: -0.70 (0.43), residues: 147 loop : -1.00 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 682 TYR 0.016 0.001 TYR A 859 PHE 0.010 0.001 PHE B 295 TRP 0.006 0.001 TRP A 408 HIS 0.003 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (10335) covalent geometry : angle 0.54047 / 0.28 (14022) SS BOND : bond 0.00164 / 0.08 ( 3) SS BOND : angle 0.85893 / 0.42 ( 6) hydrogen bonds : bond 0.03574 / 2.41 ( 515) hydrogen bonds : angle 4.64305 / 3.28 ( 1467) Misc. bond : bond 0.00005 / 0.00 ( 1) link_NAG-ASN : bond 0.00206 / 0.10 ( 3) link_NAG-ASN : angle 2.65826 / 1.33 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3282.99 seconds wall clock time: 57 minutes 19.77 seconds (3439.77 seconds total)