Starting phenix.real_space_refine on Thu Aug 6 07:08:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j8f_36068/08_2026/8j8f_36068.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j8f_36068/08_2026/8j8f_36068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j8f_36068/08_2026/8j8f_36068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j8f_36068/08_2026/8j8f_36068.map" model { file = "/net/cci-nas-00/data/ceres_data/8j8f_36068/08_2026/8j8f_36068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j8f_36068/08_2026/8j8f_36068.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 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 Ca 3 9.91 5 P 39 5.49 5 S 71 5.16 5 C 8957 2.51 5 N 2340 2.21 5 O 2749 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14159 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 8212 Classifications: {'peptide': 1005} Link IDs: {'PTRANS': 37, 'TRANS': 967} Chain: "B" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1762 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 13, 'TRANS': 204} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3418 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 10, 'TRANS': 408} Chain breaks: 1 Chain: "P" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 291 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 445 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 31 Unusual residues: {' CA': 3, 'DCP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.07, per 1000 atoms: 0.22 Number of scatterers: 14159 At special positions: 0 Unit cell: (95.76, 123.48, 146.16, 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) Ca 3 19.99 S 71 16.00 P 39 15.00 O 2749 8.00 N 2340 7.00 C 8957 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 602.8 milliseconds 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3140 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 20 sheets defined 39.5% alpha, 18.9% beta 10 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.595A pdb=" N GLU A 229 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 390 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 448 through 474 removed outlier: 3.631A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.559A pdb=" N ILE A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 514 Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 576 through 591 removed outlier: 3.902A pdb=" N GLN A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 642 Processing helix chain 'A' and resid 646 through 672 removed outlier: 3.528A pdb=" N GLY A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 703 Processing helix chain 'A' and resid 763 through 781 Processing helix chain 'A' and resid 837 through 857 Processing helix chain 'A' and resid 862 through 883 removed outlier: 3.509A pdb=" N ARG A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.977A pdb=" N MET A 891 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 918 Processing helix chain 'A' and resid 967 through 981 removed outlier: 3.953A pdb=" N TYR A 971 " --> pdb=" O PHE A 967 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 997 removed outlier: 3.978A pdb=" N MET A 996 " --> pdb=" O PHE A 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 18 No H-bonds generated for 'chain 'B' and resid 16 through 18' Processing helix chain 'B' and resid 19 through 38 removed outlier: 4.094A pdb=" N MET B 23 " --> pdb=" O TRP B 19 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLN B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLU B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER B 35 " --> pdb=" O ASN B 31 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TRP B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 101 removed outlier: 4.036A pdb=" N GLU B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 133 through 151 removed outlier: 5.569A pdb=" N LYS B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS B 151 " --> pdb=" O HIS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 removed outlier: 3.672A pdb=" N LEU B 170 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 removed outlier: 3.692A pdb=" N GLU B 190 " --> pdb=" O HIS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'C' and resid 4 through 19 removed outlier: 3.571A pdb=" N SER C 19 " --> pdb=" O SER C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 42 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 107 through 117 Processing helix chain 'C' and resid 147 through 158 Processing helix chain 'C' and resid 177 through 188 Processing helix chain 'C' and resid 249 through 257 removed outlier: 3.544A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 288 through 298 Processing helix chain 'C' and resid 315 through 323 removed outlier: 3.516A pdb=" N LEU C 319 " --> pdb=" O GLY C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 341 removed outlier: 3.527A pdb=" N SER C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 351 Processing helix chain 'C' and resid 352 through 362 removed outlier: 3.628A pdb=" N LEU C 361 " --> pdb=" O SER C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 374 Processing helix chain 'C' and resid 391 through 395 removed outlier: 3.592A pdb=" N CYS C 394 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 405 Processing helix chain 'C' and resid 406 through 425 removed outlier: 4.001A pdb=" N ARG C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 127 removed outlier: 6.971A pdb=" N LYS A 21 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TRP A 8 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TYR A 19 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLU A 10 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE A 17 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N TYR A 140 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE A 31 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N CYS A 142 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ARG A 33 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N HIS A 141 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LYS A 134 " --> pdb=" O HIS A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 3.647A pdb=" N GLY A 61 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU A 90 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU A 92 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ALA A 57 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N ILE A 516 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG A 64 " --> pdb=" O ILE A 516 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL A 518 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ILE A 66 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.256A pdb=" N LEU A 568 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP A 616 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 574 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 610 " --> pdb=" O SER A 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 removed outlier: 6.542A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL A 259 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 304 removed outlier: 3.600A pdb=" N ASN A 315 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 362 removed outlier: 6.814A pdb=" N THR A 369 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG A 407 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 533 through 534 removed outlier: 4.399A pdb=" N GLY A 750 " --> pdb=" O PHE A 534 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 706 " --> pdb=" O ARG A 713 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 533 through 534 removed outlier: 4.399A pdb=" N GLY A 750 " --> pdb=" O PHE A 534 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N SER A 747 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLU A 758 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR A 749 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA A 793 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASP A 549 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N PHE A 791 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU A 798 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR A 807 " --> pdb=" O LEU A 798 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB2, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB3, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.805A pdb=" N ILE B 117 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B 64 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N CYS B 63 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU B 155 " --> pdb=" O ILE B 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 69 through 70 Processing sheet with id=AB5, first strand: chain 'C' and resid 77 through 82 removed outlier: 4.037A pdb=" N SER C 196 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR C 199 " --> pdb=" O GLN C 208 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN C 208 " --> pdb=" O TYR C 199 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 85 through 87 removed outlier: 4.479A pdb=" N SER C 85 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 131 " --> pdb=" O SER C 85 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 124 through 126 removed outlier: 7.452A pdb=" N ILE C 142 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 222 through 227 removed outlier: 4.239A pdb=" N VAL C 237 " --> pdb=" O ILE C 245 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 266 through 268 Processing sheet with id=AC1, first strand: chain 'C' and resid 302 through 304 Processing sheet with id=AC2, first strand: chain 'C' and resid 375 through 380 removed outlier: 3.799A pdb=" N ASN C 386 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLU C 380 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL C 384 " --> pdb=" O GLU C 380 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1614 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 2.94 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3985 1.34 - 1.45: 2554 1.45 - 1.57: 7812 1.57 - 1.69: 75 1.69 - 1.81: 108 Bond restraints: 14534 Sorted by residual: bond pdb=" O3B DCP A1101 " pdb=" PG DCP A1101 " ideal model delta sigma weight residual 1.746 1.600 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" O3A DCP A1101 " pdb=" PB DCP A1101 " ideal model delta sigma weight residual 1.672 1.592 0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" O5' DCP A1101 " pdb=" PA DCP A1101 " ideal model delta sigma weight residual 1.654 1.578 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C3' DT P 22 " pdb=" C2' DT P 22 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DC T 8 " pdb=" C2' DC T 8 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.60e+00 ... (remaining 14529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 19719 2.79 - 5.57: 74 5.57 - 8.36: 5 8.36 - 11.15: 1 11.15 - 13.93: 1 Bond angle restraints: 19800 Sorted by residual: angle pdb=" PB DCP A1101 " pdb=" O3B DCP A1101 " pdb=" PG DCP A1101 " ideal model delta sigma weight residual 125.87 139.80 -13.93 3.00e+00 1.11e-01 2.16e+01 angle pdb=" N3 DT T 15 " pdb=" C4 DT T 15 " pdb=" O4 DT T 15 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT P 18 " pdb=" C4 DT P 18 " pdb=" O4 DT P 18 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT T 5 " pdb=" C4 DT T 5 " pdb=" O4 DT T 5 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT P 25 " pdb=" C4 DT P 25 " pdb=" O4 DT P 25 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 19795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 7664 17.66 - 35.32: 805 35.32 - 52.98: 191 52.98 - 70.63: 42 70.63 - 88.29: 9 Dihedral angle restraints: 8711 sinusoidal: 3840 harmonic: 4871 Sorted by residual: dihedral pdb=" CA PRO A 593 " pdb=" C PRO A 593 " pdb=" N PRO A 594 " pdb=" CA PRO A 594 " ideal model delta harmonic sigma weight residual 180.00 148.94 31.06 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA ASP A 751 " pdb=" C ASP A 751 " pdb=" N THR A 752 " pdb=" CA THR A 752 " ideal model delta harmonic sigma weight residual 180.00 157.04 22.96 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA THR A 752 " pdb=" C THR A 752 " pdb=" N ASP A 753 " pdb=" CA ASP A 753 " ideal model delta harmonic sigma weight residual 180.00 159.95 20.05 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 8708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1560 0.036 - 0.072: 427 0.072 - 0.109: 156 0.109 - 0.145: 47 0.145 - 0.181: 1 Chirality restraints: 2191 Sorted by residual: chirality pdb=" C1' DCP A1101 " pdb=" C2' DCP A1101 " pdb=" N1 DCP A1101 " pdb=" O4' DCP A1101 " both_signs ideal model delta sigma weight residual False 2.25 2.43 -0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" CA GLU B 20 " pdb=" N GLU B 20 " pdb=" C GLU B 20 " pdb=" CB GLU B 20 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA SER A 51 " pdb=" N SER A 51 " pdb=" C SER A 51 " pdb=" CB SER A 51 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.50e-01 ... (remaining 2188 not shown) Planarity restraints: 2390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 593 " -0.055 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO A 594 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 594 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 594 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 751 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C ASP A 751 " 0.030 2.00e-02 2.50e+03 pdb=" O ASP A 751 " -0.012 2.00e-02 2.50e+03 pdb=" N THR A 752 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 273 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C THR A 273 " 0.030 2.00e-02 2.50e+03 pdb=" O THR A 273 " -0.011 2.00e-02 2.50e+03 pdb=" N ASN A 274 " -0.010 2.00e-02 2.50e+03 ... (remaining 2387 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 56 2.47 - 3.08: 9197 3.08 - 3.68: 21105 3.68 - 4.29: 31213 4.29 - 4.90: 51607 Nonbonded interactions: 113178 Sorted by model distance: nonbonded pdb="CA CA A1103 " pdb="CA CA A1104 " model vdw 1.861 1.980 nonbonded pdb=" O TRP A 112 " pdb=" OG SER A 116 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR A 749 " pdb=" O LYS A 803 " model vdw 2.208 3.040 nonbonded pdb=" O ILE A 183 " pdb=" ND2 ASN A 204 " model vdw 2.244 3.120 nonbonded pdb=" O ASN A 181 " pdb=" OH TYR A 271 " model vdw 2.244 3.040 ... (remaining 113173 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.590 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 : 0.003 0.146 14534 Z= 0.207 Angle : 0.511 13.934 19800 Z= 0.334 Chirality : 0.041 0.181 2191 Planarity : 0.003 0.084 2390 Dihedral : 15.339 88.293 5571 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.07 % Allowed : 0.40 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: 0.21 (0.22), residues: 1634 helix: 1.31 (0.22), residues: 583 sheet: 0.24 (0.30), residues: 337 loop : -0.87 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 97 TYR 0.016 0.001 TYR A 668 PHE 0.012 0.001 PHE C 22 TRP 0.005 0.001 TRP C 136 HIS 0.005 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.21 (14534) covalent geometry : angle 0.51109 / 0.33 (19800) hydrogen bonds : bond 0.16269 / 10.98 ( 585) hydrogen bonds : angle 5.92144 / 4.04 ( 1656) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 270 time to evaluate : 0.556 Fit side-chains REVERT: A 859 MET cc_start: 0.3607 (mpp) cc_final: 0.2866 (tpt) REVERT: B 8 HIS cc_start: 0.4994 (m90) cc_final: 0.4673 (m-70) REVERT: B 83 ASN cc_start: 0.7304 (m-40) cc_final: 0.6997 (m110) REVERT: C 53 VAL cc_start: 0.5731 (t) cc_final: 0.5339 (p) REVERT: C 205 LEU cc_start: 0.4724 (mm) cc_final: 0.4376 (mt) outliers start: 1 outliers final: 3 residues processed: 271 average time/residue: 0.6089 time to fit residues: 180.9292 Evaluate side-chains 159 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 156 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain B residue 68 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.0010 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 899 ASN A 964 GLN B 55 GLN B 111 ASN B 165 ASN C 134 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.213538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.171736 restraints weight = 17205.388| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 3.51 r_work: 0.3512 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14534 Z= 0.141 Angle : 0.557 8.833 19800 Z= 0.310 Chirality : 0.042 0.177 2191 Planarity : 0.004 0.083 2390 Dihedral : 14.089 106.423 2252 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.85 % Allowed : 11.74 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: 0.07 (0.21), residues: 1634 helix: 1.31 (0.22), residues: 584 sheet: 0.01 (0.28), residues: 358 loop : -1.01 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 713 TYR 0.017 0.001 TYR A 668 PHE 0.021 0.001 PHE C 104 TRP 0.011 0.001 TRP A 470 HIS 0.004 0.001 HIS B 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (14534) covalent geometry : angle 0.55708 / 0.31 (19800) hydrogen bonds : bond 0.05636 / 3.88 ( 585) hydrogen bonds : angle 4.70191 / 3.19 ( 1656) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.536 Fit side-chains REVERT: A 596 TYR cc_start: 0.7995 (m-80) cc_final: 0.7776 (m-80) REVERT: A 853 MET cc_start: 0.5072 (OUTLIER) cc_final: 0.4390 (tpt) REVERT: A 859 MET cc_start: 0.3456 (mpp) cc_final: 0.2736 (tpt) REVERT: B 53 LEU cc_start: 0.7178 (mp) cc_final: 0.6386 (tt) REVERT: B 83 ASN cc_start: 0.7318 (m-40) cc_final: 0.6888 (m110) REVERT: C 63 GLU cc_start: 0.6724 (mm-30) cc_final: 0.6301 (pp20) REVERT: C 205 LEU cc_start: 0.4949 (mm) cc_final: 0.4547 (mt) outliers start: 28 outliers final: 14 residues processed: 182 average time/residue: 0.5063 time to fit residues: 102.8517 Evaluate side-chains 161 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 308 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 121 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.0870 chunk 136 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 154 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN A 964 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.209848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.167916 restraints weight = 17326.495| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 3.70 r_work: 0.3437 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14534 Z= 0.180 Angle : 0.579 8.972 19800 Z= 0.319 Chirality : 0.043 0.200 2191 Planarity : 0.004 0.082 2390 Dihedral : 14.198 88.137 2248 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.45 % Favored : 94.49 % Rotamer: Outliers : 2.97 % Allowed : 13.92 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -0.20 (0.21), residues: 1634 helix: 1.08 (0.22), residues: 589 sheet: -0.18 (0.28), residues: 357 loop : -1.15 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 713 TYR 0.016 0.001 TYR A 668 PHE 0.019 0.002 PHE C 104 TRP 0.018 0.002 TRP C 136 HIS 0.004 0.001 HIS B 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (14534) covalent geometry : angle 0.57882 / 0.32 (19800) hydrogen bonds : bond 0.05633 / 3.81 ( 585) hydrogen bonds : angle 4.68781 / 3.15 ( 1656) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 160 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7311 (mt) REVERT: A 174 LYS cc_start: 0.7019 (ptpt) cc_final: 0.6804 (mtmm) REVERT: A 640 MET cc_start: 0.8503 (ttm) cc_final: 0.8076 (mtp) REVERT: A 744 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6754 (mtm-85) REVERT: A 834 ASP cc_start: 0.8003 (p0) cc_final: 0.7783 (p0) REVERT: A 837 LYS cc_start: 0.8403 (tppt) cc_final: 0.8039 (tppt) REVERT: A 853 MET cc_start: 0.5004 (OUTLIER) cc_final: 0.4330 (tpt) REVERT: A 859 MET cc_start: 0.3365 (mpp) cc_final: 0.2482 (tpt) REVERT: B 8 HIS cc_start: 0.5167 (m90) cc_final: 0.4495 (m-70) REVERT: B 83 ASN cc_start: 0.7315 (m-40) cc_final: 0.6820 (m110) REVERT: C 63 GLU cc_start: 0.6677 (mm-30) cc_final: 0.6246 (pp20) REVERT: C 88 ILE cc_start: 0.6346 (mp) cc_final: 0.5830 (tt) REVERT: C 95 MET cc_start: 0.4779 (mmp) cc_final: 0.3945 (mpt) REVERT: C 98 LEU cc_start: 0.7769 (tt) cc_final: 0.7533 (pt) REVERT: C 205 LEU cc_start: 0.5180 (mm) cc_final: 0.4703 (mt) outliers start: 45 outliers final: 18 residues processed: 186 average time/residue: 0.4832 time to fit residues: 100.0568 Evaluate side-chains 173 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 308 PHE Chi-restraints excluded: chain C residue 311 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 82 optimal weight: 0.5980 chunk 107 optimal weight: 0.0980 chunk 74 optimal weight: 0.0070 chunk 28 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 153 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN A 964 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.212125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.170168 restraints weight = 17267.248| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 3.52 r_work: 0.3507 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14534 Z= 0.115 Angle : 0.523 10.642 19800 Z= 0.289 Chirality : 0.041 0.227 2191 Planarity : 0.004 0.083 2390 Dihedral : 14.218 89.038 2246 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.37 % Allowed : 15.63 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -0.10 (0.21), residues: 1634 helix: 1.25 (0.22), residues: 589 sheet: -0.18 (0.28), residues: 354 loop : -1.14 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 713 TYR 0.014 0.001 TYR A 668 PHE 0.026 0.001 PHE A 992 TRP 0.012 0.001 TRP A 470 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (14534) covalent geometry : angle 0.52282 / 0.29 (19800) hydrogen bonds : bond 0.04622 / 3.14 ( 585) hydrogen bonds : angle 4.48855 / 3.02 ( 1656) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.536 Fit side-chains REVERT: A 596 TYR cc_start: 0.7926 (m-80) cc_final: 0.7666 (m-80) REVERT: A 640 MET cc_start: 0.8394 (ttm) cc_final: 0.7992 (mtp) REVERT: A 688 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.7686 (m) REVERT: A 744 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6620 (mtm-85) REVERT: A 859 MET cc_start: 0.3280 (mpp) cc_final: 0.2465 (tpt) REVERT: A 942 LYS cc_start: 0.7612 (mmtt) cc_final: 0.6753 (mtpp) REVERT: A 956 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.5954 (mmp-170) REVERT: B 8 HIS cc_start: 0.5176 (m90) cc_final: 0.4398 (m-70) REVERT: B 40 ASP cc_start: 0.5812 (t0) cc_final: 0.5306 (t0) REVERT: B 53 LEU cc_start: 0.7170 (mp) cc_final: 0.6373 (tt) REVERT: B 73 ASP cc_start: 0.7092 (t0) cc_final: 0.6567 (m-30) REVERT: C 88 ILE cc_start: 0.6260 (mp) cc_final: 0.5733 (tt) REVERT: C 95 MET cc_start: 0.4899 (mmp) cc_final: 0.4040 (mpt) REVERT: C 98 LEU cc_start: 0.7802 (tt) cc_final: 0.7568 (pt) REVERT: C 205 LEU cc_start: 0.5079 (mm) cc_final: 0.4600 (mt) outliers start: 36 outliers final: 11 residues processed: 184 average time/residue: 0.4840 time to fit residues: 99.7016 Evaluate side-chains 164 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 956 ARG Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 308 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 151 optimal weight: 7.9990 chunk 49 optimal weight: 0.1980 chunk 43 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 964 GLN B 109 ASN C 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.208224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.165849 restraints weight = 17085.866| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 3.45 r_work: 0.3443 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14534 Z= 0.188 Angle : 0.592 6.864 19800 Z= 0.325 Chirality : 0.043 0.157 2191 Planarity : 0.005 0.081 2390 Dihedral : 14.365 87.487 2246 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.88 % Favored : 94.06 % Rotamer: Outliers : 3.43 % Allowed : 16.36 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -0.36 (0.21), residues: 1634 helix: 1.04 (0.22), residues: 588 sheet: -0.39 (0.28), residues: 358 loop : -1.24 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 713 TYR 0.016 0.002 TYR A 668 PHE 0.018 0.002 PHE A 992 TRP 0.013 0.002 TRP C 136 HIS 0.004 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (14534) covalent geometry : angle 0.59198 / 0.32 (19800) hydrogen bonds : bond 0.05448 / 3.61 ( 585) hydrogen bonds : angle 4.68153 / 3.13 ( 1656) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 161 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7307 (mt) REVERT: A 368 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7820 (tpt) REVERT: A 608 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.6796 (mp) REVERT: A 640 MET cc_start: 0.8516 (ttm) cc_final: 0.8284 (mtp) REVERT: A 688 THR cc_start: 0.8374 (OUTLIER) cc_final: 0.7897 (m) REVERT: A 744 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6788 (mtm-85) REVERT: A 837 LYS cc_start: 0.8360 (tppt) cc_final: 0.8050 (tppt) REVERT: A 853 MET cc_start: 0.4978 (OUTLIER) cc_final: 0.4259 (tpt) REVERT: A 859 MET cc_start: 0.3549 (mpp) cc_final: 0.2469 (tpt) REVERT: A 956 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.5927 (mmp-170) REVERT: B 8 HIS cc_start: 0.5088 (m90) cc_final: 0.4316 (m-70) REVERT: B 40 ASP cc_start: 0.5858 (t0) cc_final: 0.5362 (t0) REVERT: C 11 LYS cc_start: 0.5001 (OUTLIER) cc_final: 0.4431 (mmtp) REVERT: C 63 GLU cc_start: 0.6646 (mm-30) cc_final: 0.6365 (pp20) REVERT: C 88 ILE cc_start: 0.6283 (mp) cc_final: 0.5696 (tt) REVERT: C 95 MET cc_start: 0.5016 (mmp) cc_final: 0.3980 (mpt) REVERT: C 98 LEU cc_start: 0.7889 (tt) cc_final: 0.7648 (pt) REVERT: C 205 LEU cc_start: 0.5268 (mm) cc_final: 0.4738 (mt) outliers start: 52 outliers final: 23 residues processed: 195 average time/residue: 0.5424 time to fit residues: 117.4555 Evaluate side-chains 178 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 956 ARG Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 308 PHE Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 9 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 127 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.0980 chunk 13 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 907 ASN A 964 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.210179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.160305 restraints weight = 17057.323| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.61 r_work: 0.3596 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14534 Z= 0.122 Angle : 0.537 6.846 19800 Z= 0.299 Chirality : 0.041 0.164 2191 Planarity : 0.004 0.083 2390 Dihedral : 14.326 88.315 2246 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.14 % Favored : 94.80 % Rotamer: Outliers : 2.51 % Allowed : 17.94 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -0.20 (0.21), residues: 1634 helix: 1.23 (0.22), residues: 587 sheet: -0.29 (0.28), residues: 353 loop : -1.20 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 713 TYR 0.015 0.001 TYR B 121 PHE 0.012 0.001 PHE A 992 TRP 0.012 0.001 TRP A 470 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (14534) covalent geometry : angle 0.53698 / 0.30 (19800) hydrogen bonds : bond 0.04553 / 3.03 ( 585) hydrogen bonds : angle 4.53465 / 3.05 ( 1656) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7469 (ttt90) cc_final: 0.7222 (tpt170) REVERT: A 640 MET cc_start: 0.8434 (ttm) cc_final: 0.8074 (mtp) REVERT: A 688 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.7728 (m) REVERT: A 706 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.5967 (pp20) REVERT: A 744 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6557 (mtm-85) REVERT: A 853 MET cc_start: 0.4993 (OUTLIER) cc_final: 0.4284 (tpt) REVERT: A 859 MET cc_start: 0.3491 (mpp) cc_final: 0.2457 (tpt) REVERT: A 916 LYS cc_start: 0.8263 (mmtp) cc_final: 0.7973 (ptmt) REVERT: A 956 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6000 (mmp-170) REVERT: B 8 HIS cc_start: 0.5035 (m90) cc_final: 0.4343 (m-70) REVERT: B 40 ASP cc_start: 0.5902 (t0) cc_final: 0.5397 (t0) REVERT: B 53 LEU cc_start: 0.7158 (mp) cc_final: 0.6354 (tt) REVERT: B 73 ASP cc_start: 0.7111 (t0) cc_final: 0.6393 (m-30) REVERT: C 88 ILE cc_start: 0.6199 (mp) cc_final: 0.5685 (tt) REVERT: C 98 LEU cc_start: 0.7856 (tt) cc_final: 0.7635 (pt) REVERT: C 205 LEU cc_start: 0.5303 (mm) cc_final: 0.4785 (mt) outliers start: 38 outliers final: 19 residues processed: 184 average time/residue: 0.5663 time to fit residues: 115.4954 Evaluate side-chains 167 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 956 ARG Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 308 PHE Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 126 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 135 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 964 GLN B 109 ASN C 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.207575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.164969 restraints weight = 17041.631| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 3.57 r_work: 0.3446 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14534 Z= 0.172 Angle : 0.591 9.214 19800 Z= 0.323 Chirality : 0.043 0.170 2191 Planarity : 0.005 0.081 2390 Dihedral : 14.386 87.363 2246 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.81 % Favored : 94.12 % Rotamer: Outliers : 3.43 % Allowed : 18.34 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -0.37 (0.21), residues: 1634 helix: 1.05 (0.22), residues: 590 sheet: -0.44 (0.28), residues: 355 loop : -1.25 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 255 TYR 0.018 0.001 TYR B 121 PHE 0.020 0.002 PHE A 55 TRP 0.008 0.001 TRP C 136 HIS 0.004 0.001 HIS B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (14534) covalent geometry : angle 0.59148 / 0.32 (19800) hydrogen bonds : bond 0.05080 / 3.34 ( 585) hydrogen bonds : angle 4.65461 / 3.12 ( 1656) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 147 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7412 (mt) REVERT: A 146 ARG cc_start: 0.7492 (ttt90) cc_final: 0.7243 (tpt170) REVERT: A 398 ASP cc_start: 0.7648 (t0) cc_final: 0.7102 (t0) REVERT: A 640 MET cc_start: 0.8524 (ttm) cc_final: 0.8309 (mtp) REVERT: A 688 THR cc_start: 0.8350 (OUTLIER) cc_final: 0.7861 (m) REVERT: A 706 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.5963 (pp20) REVERT: A 744 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6594 (mtm-85) REVERT: A 853 MET cc_start: 0.4855 (OUTLIER) cc_final: 0.4143 (tpt) REVERT: A 859 MET cc_start: 0.3494 (mpp) cc_final: 0.2407 (tpt) REVERT: A 916 LYS cc_start: 0.8198 (mmtp) cc_final: 0.7987 (ptmt) REVERT: A 956 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.5923 (mmp-170) REVERT: B 8 HIS cc_start: 0.5028 (m90) cc_final: 0.4353 (m-70) REVERT: B 40 ASP cc_start: 0.5971 (t0) cc_final: 0.5664 (t0) REVERT: B 110 LEU cc_start: 0.3970 (OUTLIER) cc_final: 0.3709 (tt) REVERT: C 11 LYS cc_start: 0.5012 (OUTLIER) cc_final: 0.4411 (mmtp) REVERT: C 88 ILE cc_start: 0.6233 (mp) cc_final: 0.5649 (tt) REVERT: C 95 MET cc_start: 0.5031 (mmp) cc_final: 0.3844 (mpt) REVERT: C 98 LEU cc_start: 0.7888 (tt) cc_final: 0.7660 (pt) REVERT: C 124 ILE cc_start: 0.3936 (mm) cc_final: 0.3692 (mm) REVERT: C 205 LEU cc_start: 0.5408 (mm) cc_final: 0.4878 (mt) REVERT: C 255 ARG cc_start: 0.6287 (mmm160) cc_final: 0.5858 (mtm180) REVERT: C 365 GLU cc_start: 0.6905 (tp30) cc_final: 0.6679 (mm-30) outliers start: 52 outliers final: 25 residues processed: 182 average time/residue: 0.4900 time to fit residues: 99.4071 Evaluate side-chains 181 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 956 ARG Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 308 PHE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 122 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 43 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 151 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 128 optimal weight: 20.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 964 GLN B 211 ASN C 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.208563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.168330 restraints weight = 17087.110| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 3.59 r_work: 0.3432 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14534 Z= 0.139 Angle : 0.573 11.202 19800 Z= 0.312 Chirality : 0.042 0.173 2191 Planarity : 0.005 0.083 2390 Dihedral : 14.367 87.643 2246 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.08 % Favored : 94.86 % Rotamer: Outliers : 2.70 % Allowed : 19.13 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -0.33 (0.21), residues: 1634 helix: 1.16 (0.22), residues: 588 sheet: -0.46 (0.28), residues: 354 loop : -1.25 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 713 TYR 0.016 0.001 TYR B 121 PHE 0.026 0.001 PHE A 992 TRP 0.010 0.001 TRP A 470 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (14534) covalent geometry : angle 0.57339 / 0.31 (19800) hydrogen bonds : bond 0.04642 / 3.04 ( 585) hydrogen bonds : angle 4.58575 / 3.08 ( 1656) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7424 (mt) REVERT: A 146 ARG cc_start: 0.7551 (ttt90) cc_final: 0.7296 (tpt170) REVERT: A 656 MET cc_start: 0.7735 (mtp) cc_final: 0.7506 (mtm) REVERT: A 688 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.7792 (m) REVERT: A 706 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6023 (pp20) REVERT: A 744 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6618 (mtm-85) REVERT: A 853 MET cc_start: 0.4847 (OUTLIER) cc_final: 0.4160 (tpt) REVERT: A 859 MET cc_start: 0.3486 (mpp) cc_final: 0.2409 (tpt) REVERT: A 956 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.5971 (mmp-170) REVERT: B 8 HIS cc_start: 0.5197 (m90) cc_final: 0.4468 (m-70) REVERT: B 40 ASP cc_start: 0.5997 (t0) cc_final: 0.5700 (t0) REVERT: B 73 ASP cc_start: 0.7156 (t0) cc_final: 0.6517 (m-30) REVERT: B 158 LEU cc_start: 0.5689 (mt) cc_final: 0.5381 (mp) REVERT: C 11 LYS cc_start: 0.5067 (OUTLIER) cc_final: 0.4391 (mmtp) REVERT: C 88 ILE cc_start: 0.6222 (mp) cc_final: 0.5630 (tt) REVERT: C 95 MET cc_start: 0.5056 (mmp) cc_final: 0.3814 (mpt) REVERT: C 98 LEU cc_start: 0.7898 (tt) cc_final: 0.7677 (pt) REVERT: C 205 LEU cc_start: 0.5508 (mm) cc_final: 0.4971 (mt) REVERT: C 255 ARG cc_start: 0.6301 (mmm160) cc_final: 0.5849 (mtm180) REVERT: C 365 GLU cc_start: 0.6890 (tp30) cc_final: 0.6606 (mm-30) outliers start: 41 outliers final: 25 residues processed: 176 average time/residue: 0.5342 time to fit residues: 104.8481 Evaluate side-chains 173 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 956 ARG Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 308 PHE Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 163 optimal weight: 9.9990 chunk 43 optimal weight: 0.4980 chunk 62 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 0.0670 chunk 81 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 161 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 607 ASN A 964 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN C 134 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.209710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.168251 restraints weight = 17070.580| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 3.29 r_work: 0.3481 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14534 Z= 0.124 Angle : 0.556 8.910 19800 Z= 0.305 Chirality : 0.041 0.166 2191 Planarity : 0.004 0.082 2390 Dihedral : 14.284 87.980 2246 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.39 % Favored : 94.55 % Rotamer: Outliers : 2.44 % Allowed : 19.72 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -0.21 (0.21), residues: 1634 helix: 1.24 (0.22), residues: 587 sheet: -0.41 (0.28), residues: 343 loop : -1.15 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 713 TYR 0.015 0.001 TYR B 121 PHE 0.039 0.001 PHE A 992 TRP 0.012 0.001 TRP A 470 HIS 0.005 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (14534) covalent geometry : angle 0.55557 / 0.31 (19800) hydrogen bonds : bond 0.04266 / 2.79 ( 585) hydrogen bonds : angle 4.51420 / 3.02 ( 1656) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7490 (ttt90) cc_final: 0.7251 (tpt170) REVERT: A 398 ASP cc_start: 0.7606 (t0) cc_final: 0.7077 (t0) REVERT: A 540 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7814 (mtt) REVERT: A 596 TYR cc_start: 0.7938 (m-80) cc_final: 0.7658 (m-80) REVERT: A 688 THR cc_start: 0.8239 (OUTLIER) cc_final: 0.7703 (m) REVERT: A 706 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6085 (pp20) REVERT: A 744 ARG cc_start: 0.6901 (OUTLIER) cc_final: 0.6453 (mtm-85) REVERT: A 853 MET cc_start: 0.4805 (OUTLIER) cc_final: 0.4218 (tpt) REVERT: A 859 MET cc_start: 0.3448 (mpp) cc_final: 0.2404 (tpt) REVERT: A 956 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.5956 (mmp-170) REVERT: B 8 HIS cc_start: 0.5092 (m90) cc_final: 0.4411 (m-70) REVERT: B 40 ASP cc_start: 0.5895 (t0) cc_final: 0.5650 (t0) REVERT: B 73 ASP cc_start: 0.7162 (t0) cc_final: 0.6523 (m-30) REVERT: C 11 LYS cc_start: 0.5033 (OUTLIER) cc_final: 0.4385 (mmtp) REVERT: C 88 ILE cc_start: 0.6146 (mp) cc_final: 0.5539 (tt) REVERT: C 95 MET cc_start: 0.4878 (mmp) cc_final: 0.3944 (mtt) REVERT: C 98 LEU cc_start: 0.7853 (tt) cc_final: 0.7643 (pt) REVERT: C 205 LEU cc_start: 0.5432 (mm) cc_final: 0.4912 (mt) REVERT: C 255 ARG cc_start: 0.6288 (mmm160) cc_final: 0.5860 (mtm180) REVERT: C 365 GLU cc_start: 0.6813 (tp30) cc_final: 0.6564 (mm-30) outliers start: 37 outliers final: 23 residues processed: 171 average time/residue: 0.4924 time to fit residues: 93.7652 Evaluate side-chains 172 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 956 ARG Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 308 PHE Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 71 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 82 optimal weight: 0.2980 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 964 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN C 134 ASN C 339 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.207101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.167082 restraints weight = 17092.560| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 3.55 r_work: 0.3411 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14534 Z= 0.183 Angle : 0.624 12.639 19800 Z= 0.335 Chirality : 0.044 0.195 2191 Planarity : 0.005 0.082 2390 Dihedral : 14.389 87.146 2246 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.37 % Allowed : 20.12 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -0.45 (0.21), residues: 1634 helix: 0.99 (0.22), residues: 588 sheet: -0.55 (0.27), residues: 356 loop : -1.25 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 255 TYR 0.017 0.002 TYR B 121 PHE 0.015 0.002 PHE A 560 TRP 0.007 0.001 TRP A 940 HIS 0.004 0.001 HIS B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (14534) covalent geometry : angle 0.62381 / 0.34 (19800) hydrogen bonds : bond 0.05042 / 3.26 ( 585) hydrogen bonds : angle 4.68325 / 3.13 ( 1656) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7730 (t0) cc_final: 0.7198 (t0) REVERT: A 540 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8034 (mtt) REVERT: A 688 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.7891 (m) REVERT: A 744 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6636 (mtm-85) REVERT: A 853 MET cc_start: 0.4936 (OUTLIER) cc_final: 0.4342 (tpt) REVERT: A 859 MET cc_start: 0.3543 (mpp) cc_final: 0.2379 (tpt) REVERT: A 956 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6052 (mmp-170) REVERT: B 8 HIS cc_start: 0.5320 (m90) cc_final: 0.4740 (m-70) REVERT: C 11 LYS cc_start: 0.5101 (OUTLIER) cc_final: 0.4419 (mmtp) REVERT: C 88 ILE cc_start: 0.6139 (mp) cc_final: 0.5536 (tt) REVERT: C 95 MET cc_start: 0.4940 (mmp) cc_final: 0.3998 (mtt) REVERT: C 98 LEU cc_start: 0.7859 (tt) cc_final: 0.7652 (pt) REVERT: C 205 LEU cc_start: 0.5431 (mm) cc_final: 0.4921 (mt) REVERT: C 255 ARG cc_start: 0.6249 (mmm160) cc_final: 0.5835 (mtm180) outliers start: 36 outliers final: 21 residues processed: 166 average time/residue: 0.5259 time to fit residues: 96.9714 Evaluate side-chains 164 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 956 ARG Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 308 PHE Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 136 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 35 optimal weight: 0.0670 chunk 105 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 130 optimal weight: 30.0000 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 964 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN C 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.208597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.166723 restraints weight = 17147.918| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 3.37 r_work: 0.3468 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14534 Z= 0.136 Angle : 0.583 8.847 19800 Z= 0.317 Chirality : 0.042 0.344 2191 Planarity : 0.005 0.082 2390 Dihedral : 14.354 87.523 2246 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.26 % Favored : 94.68 % Rotamer: Outliers : 1.98 % Allowed : 20.78 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -0.36 (0.21), residues: 1634 helix: 1.09 (0.22), residues: 588 sheet: -0.44 (0.28), residues: 339 loop : -1.24 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 713 TYR 0.013 0.001 TYR A 668 PHE 0.020 0.001 PHE A 55 TRP 0.012 0.001 TRP A 470 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (14534) covalent geometry : angle 0.58284 / 0.32 (19800) hydrogen bonds : bond 0.04425 / 2.86 ( 585) hydrogen bonds : angle 4.60060 / 3.08 ( 1656) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4496.39 seconds wall clock time: 77 minutes 35.36 seconds (4655.36 seconds total)