Starting phenix.real_space_refine on Fri Jul 3 12:22:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j8f_36068/07_2026/8j8f_36068.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j8f_36068/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8j8f_36068/07_2026/8j8f_36068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j8f_36068/07_2026/8j8f_36068.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j8f_36068/07_2026/8j8f_36068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j8f_36068/07_2026/8j8f_36068.map" } 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-dev-6108/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, 28 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'DCP': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Time building chain proxies: 2.55, per 1000 atoms: 0.18 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: 0.86 Conformation dependent library (CDL) restraints added in 700.1 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: 1.64 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: 2.76 Time building geometry restraints manager: 1.24 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 3.460 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: 5.360 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.500 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:8.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.490 ------------------------------------------------------------------------------- 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= 0.333 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 0.51053 / 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 : 0.515 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: 0.6998 (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: 0.5996 time to fit residues: 178.0603 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 : 0.462 ------------------------------------------------------------------------------- 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: 7.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 964 GLN B 55 GLN B 111 ASN B 165 ASN C 134 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.215238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.177322 restraints weight = 17254.301| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 3.23 r_work: 0.3582 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1239 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= 0.144 Angle : 0.556 9.051 19800 Z= 0.310 Chirality : 0.042 0.160 2191 Planarity : 0.004 0.083 2390 Dihedral : 14.030 109.184 2252 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.98 % Allowed : 11.41 % Favored : 86.61 % 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: 0.08 (0.21), residues: 1634 helix: 1.30 (0.22), residues: 589 sheet: 0.03 (0.28), residues: 358 loop : -0.99 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 713 TYR 0.017 0.001 TYR A 668 PHE 0.022 0.001 PHE C 104 TRP 0.011 0.001 TRP A 470 HIS 0.003 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (14534) covalent geometry : angle 0.55646 / 0.31 (19800) hydrogen bonds : bond 0.05901 / 4.08 ( 585) hydrogen bonds : angle 4.73500 / 3.21 ( 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 196 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.561 Fit side-chains REVERT: A 596 TYR cc_start: 0.7980 (m-80) cc_final: 0.7755 (m-80) REVERT: A 837 LYS cc_start: 0.8398 (tppt) cc_final: 0.7996 (tppt) REVERT: A 853 MET cc_start: 0.5199 (OUTLIER) cc_final: 0.4460 (tpt) REVERT: A 859 MET cc_start: 0.3417 (mpp) cc_final: 0.2699 (tpt) REVERT: B 53 LEU cc_start: 0.7203 (mp) cc_final: 0.6414 (tt) REVERT: B 83 ASN cc_start: 0.7312 (m-40) cc_final: 0.6890 (m110) REVERT: C 63 GLU cc_start: 0.6502 (mm-30) cc_final: 0.6276 (pp20) REVERT: C 205 LEU cc_start: 0.4935 (mm) cc_final: 0.4498 (mt) outliers start: 30 outliers final: 12 residues processed: 181 average time/residue: 0.5464 time to fit residues: 109.8031 Evaluate side-chains 162 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 371 ILE 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 B residue 204 LEU 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: 1.9990 chunk 62 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 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: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN A 899 ASN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.208986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.159753 restraints weight = 17333.562| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.63 r_work: 0.3568 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14534 Z= 0.200 Angle : 0.608 8.832 19800 Z= 0.333 Chirality : 0.044 0.179 2191 Planarity : 0.005 0.081 2390 Dihedral : 14.174 87.668 2248 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.75 % Favored : 94.19 % Rotamer: Outliers : 2.90 % Allowed : 13.98 % 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: -0.31 (0.21), residues: 1634 helix: 0.98 (0.22), residues: 589 sheet: -0.21 (0.28), residues: 357 loop : -1.22 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 146 TYR 0.017 0.002 TYR A 668 PHE 0.021 0.002 PHE C 104 TRP 0.017 0.002 TRP C 136 HIS 0.004 0.001 HIS B 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (14534) covalent geometry : angle 0.60770 / 0.33 (19800) hydrogen bonds : bond 0.05898 / 3.98 ( 585) hydrogen bonds : angle 4.77848 / 3.22 ( 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 208 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7291 (mt) REVERT: A 640 MET cc_start: 0.8486 (ttm) cc_final: 0.8245 (mtp) REVERT: A 744 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6662 (mtm-85) REVERT: A 834 ASP cc_start: 0.8039 (p0) cc_final: 0.7837 (p0) REVERT: A 837 LYS cc_start: 0.8363 (tppt) cc_final: 0.8018 (tppt) REVERT: A 853 MET cc_start: 0.5148 (OUTLIER) cc_final: 0.4486 (tpt) REVERT: A 859 MET cc_start: 0.3391 (mpp) cc_final: 0.2436 (tpt) REVERT: B 8 HIS cc_start: 0.5136 (m90) cc_final: 0.4470 (m-70) REVERT: B 83 ASN cc_start: 0.7354 (m-40) cc_final: 0.6864 (m110) REVERT: C 63 GLU cc_start: 0.6628 (mm-30) cc_final: 0.6292 (pp20) REVERT: C 88 ILE cc_start: 0.6338 (mp) cc_final: 0.5797 (tt) REVERT: C 95 MET cc_start: 0.4827 (mmp) cc_final: 0.4070 (mpt) REVERT: C 98 LEU cc_start: 0.7865 (tt) cc_final: 0.7605 (pt) REVERT: C 205 LEU cc_start: 0.5126 (mm) cc_final: 0.4662 (mt) outliers start: 44 outliers final: 17 residues processed: 189 average time/residue: 0.5515 time to fit residues: 115.4971 Evaluate side-chains 169 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 107 optimal weight: 4.9990 chunk 74 optimal weight: 0.0170 chunk 28 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 chunk 153 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 = 0.4363 r_free = 0.4363 target = 0.211257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.169124 restraints weight = 17312.707| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 3.55 r_work: 0.3492 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14534 Z= 0.122 Angle : 0.537 10.906 19800 Z= 0.296 Chirality : 0.042 0.272 2191 Planarity : 0.004 0.083 2390 Dihedral : 14.181 88.565 2246 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.84 % Allowed : 15.83 % Favored : 81.33 % 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: -0.22 (0.21), residues: 1634 helix: 1.16 (0.22), residues: 589 sheet: -0.26 (0.28), residues: 357 loop : -1.21 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 0.00255 / 0.12 (14534) covalent geometry : angle 0.53687 / 0.30 (19800) hydrogen bonds : bond 0.04823 / 3.25 ( 585) hydrogen bonds : angle 4.58141 / 3.09 ( 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 201 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 158 time to evaluate : 0.561 Fit side-chains REVERT: A 132 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7185 (mp) REVERT: A 640 MET cc_start: 0.8373 (ttm) cc_final: 0.7990 (mtp) REVERT: A 688 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.7741 (m) REVERT: A 744 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.6641 (mtm-85) REVERT: A 834 ASP cc_start: 0.8006 (p0) cc_final: 0.7804 (p0) REVERT: A 837 LYS cc_start: 0.8276 (tppt) cc_final: 0.7962 (tppt) REVERT: A 853 MET cc_start: 0.5003 (OUTLIER) cc_final: 0.4363 (tpt) REVERT: A 859 MET cc_start: 0.3331 (mpp) cc_final: 0.2457 (tpt) REVERT: A 942 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.6751 (mtpp) REVERT: A 956 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.5972 (mmp-170) REVERT: B 8 HIS cc_start: 0.5110 (m90) cc_final: 0.4306 (m-70) REVERT: B 40 ASP cc_start: 0.5885 (t0) cc_final: 0.5407 (t0) REVERT: B 53 LEU cc_start: 0.7166 (mp) cc_final: 0.6363 (tt) REVERT: C 88 ILE cc_start: 0.6287 (mp) cc_final: 0.5719 (tt) REVERT: C 95 MET cc_start: 0.4973 (mmp) cc_final: 0.4097 (mpt) REVERT: C 98 LEU cc_start: 0.7840 (tt) cc_final: 0.7587 (pt) REVERT: C 205 LEU cc_start: 0.5140 (mm) cc_final: 0.4648 (mt) REVERT: C 365 GLU cc_start: 0.6783 (tp30) cc_final: 0.5574 (mp0) REVERT: C 397 ASN cc_start: 0.6578 (OUTLIER) cc_final: 0.6373 (t0) outliers start: 43 outliers final: 18 residues processed: 183 average time/residue: 0.5100 time to fit residues: 104.3796 Evaluate side-chains 167 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 132 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 227 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 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 65 CYS Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 124 ILE 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 397 ASN 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: 0.0170 chunk 43 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 131 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 74 optimal weight: 0.0060 chunk 130 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.5634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 964 GLN B 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.211305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.168952 restraints weight = 17137.920| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 3.42 r_work: 0.3498 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1946 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= 0.120 Angle : 0.523 6.697 19800 Z= 0.291 Chirality : 0.041 0.159 2191 Planarity : 0.004 0.082 2390 Dihedral : 14.144 88.511 2246 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.32 % Favored : 94.61 % Rotamer: Outliers : 3.23 % Allowed : 16.56 % 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: -0.14 (0.21), residues: 1634 helix: 1.24 (0.22), residues: 589 sheet: -0.28 (0.28), residues: 357 loop : -1.13 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 713 TYR 0.014 0.001 TYR A 668 PHE 0.020 0.001 PHE A 55 TRP 0.011 0.001 TRP C 136 HIS 0.005 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (14534) covalent geometry : angle 0.52250 / 0.29 (19800) hydrogen bonds : bond 0.04576 / 3.09 ( 585) hydrogen bonds : angle 4.50242 / 3.02 ( 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 210 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 161 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7249 (mp) REVERT: A 608 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6779 (mp) REVERT: A 688 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.7717 (m) REVERT: A 744 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6533 (mtm-85) REVERT: A 837 LYS cc_start: 0.8239 (tppt) cc_final: 0.7941 (tppt) REVERT: A 859 MET cc_start: 0.3328 (mpp) cc_final: 0.2427 (tpt) REVERT: A 917 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.7733 (t0) REVERT: A 956 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6001 (mmp-170) REVERT: B 8 HIS cc_start: 0.5008 (m90) cc_final: 0.4275 (m-70) REVERT: B 40 ASP cc_start: 0.5880 (t0) cc_final: 0.5354 (t0) REVERT: B 53 LEU cc_start: 0.7213 (mp) cc_final: 0.6415 (tt) REVERT: B 73 ASP cc_start: 0.7103 (t0) cc_final: 0.6452 (m-30) REVERT: C 88 ILE cc_start: 0.6193 (mp) cc_final: 0.5624 (tt) REVERT: C 98 LEU cc_start: 0.7899 (tt) cc_final: 0.7651 (pt) REVERT: C 205 LEU cc_start: 0.5308 (mm) cc_final: 0.4784 (mt) outliers start: 49 outliers final: 20 residues processed: 190 average time/residue: 0.5387 time to fit residues: 114.1446 Evaluate side-chains 174 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 132 LEU Chi-restraints excluded: chain A residue 199 LEU 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 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 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 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: 2.9990 chunk 61 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 12 optimal weight: 0.0980 chunk 10 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** 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 = 0.4353 r_free = 0.4353 target = 0.209963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.161338 restraints weight = 17132.639| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.76 r_work: 0.3574 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14534 Z= 0.144 Angle : 0.552 10.161 19800 Z= 0.304 Chirality : 0.041 0.171 2191 Planarity : 0.004 0.082 2390 Dihedral : 14.169 88.181 2246 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.63 % Favored : 94.31 % Rotamer: Outliers : 3.56 % Allowed : 17.22 % Favored : 79.22 % 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: -0.23 (0.21), residues: 1634 helix: 1.16 (0.22), residues: 588 sheet: -0.32 (0.28), residues: 357 loop : -1.17 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 713 TYR 0.015 0.001 TYR B 121 PHE 0.016 0.001 PHE A 992 TRP 0.009 0.001 TRP A 470 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (14534) covalent geometry : angle 0.55197 / 0.30 (19800) hydrogen bonds : bond 0.04724 / 3.15 ( 585) hydrogen bonds : angle 4.53647 / 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 203 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 149 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7376 (mt) REVERT: A 174 LYS cc_start: 0.7007 (mtmm) cc_final: 0.6791 (mtpp) REVERT: A 540 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7950 (mtt) REVERT: A 608 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6783 (mp) REVERT: A 688 THR cc_start: 0.8297 (OUTLIER) cc_final: 0.7760 (m) REVERT: A 706 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.5984 (pp20) REVERT: A 744 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6550 (mtm-85) REVERT: A 837 LYS cc_start: 0.8246 (tppt) cc_final: 0.7950 (tppt) REVERT: A 853 MET cc_start: 0.4940 (OUTLIER) cc_final: 0.4235 (tpt) REVERT: A 859 MET cc_start: 0.3382 (mpp) cc_final: 0.2390 (tpt) REVERT: A 956 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.5953 (mmp-170) REVERT: B 8 HIS cc_start: 0.4963 (m90) cc_final: 0.4268 (m-70) REVERT: B 40 ASP cc_start: 0.5876 (t0) cc_final: 0.5321 (t0) REVERT: B 73 ASP cc_start: 0.7108 (t0) cc_final: 0.6445 (m-30) REVERT: B 110 LEU cc_start: 0.4018 (OUTLIER) cc_final: 0.3787 (tt) REVERT: C 11 LYS cc_start: 0.5075 (OUTLIER) cc_final: 0.4453 (mmtp) REVERT: C 63 GLU cc_start: 0.6641 (mm-30) cc_final: 0.6275 (pp20) REVERT: C 88 ILE cc_start: 0.6157 (mp) cc_final: 0.5551 (tt) REVERT: C 95 MET cc_start: 0.4985 (mmp) cc_final: 0.3860 (mpt) REVERT: C 98 LEU cc_start: 0.7865 (tt) cc_final: 0.7632 (pt) REVERT: C 205 LEU cc_start: 0.5340 (mm) cc_final: 0.4841 (mt) outliers start: 54 outliers final: 22 residues processed: 183 average time/residue: 0.5318 time to fit residues: 108.4047 Evaluate side-chains 178 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 132 LEU 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 540 MET 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 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 B residue 177 ILE Chi-restraints excluded: chain C residue 11 LYS 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: 2.9990 chunk 64 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 135 optimal weight: 0.0980 chunk 96 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 107 optimal weight: 0.0370 chunk 31 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 964 GLN B 109 ASN 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 = 0.4349 r_free = 0.4349 target = 0.209413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.166944 restraints weight = 17014.959| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 3.18 r_work: 0.3493 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14534 Z= 0.137 Angle : 0.551 9.206 19800 Z= 0.303 Chirality : 0.041 0.167 2191 Planarity : 0.004 0.082 2390 Dihedral : 14.190 88.160 2246 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.39 % Favored : 94.55 % Rotamer: Outliers : 3.50 % Allowed : 17.94 % Favored : 78.56 % 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: -0.19 (0.21), residues: 1634 helix: 1.24 (0.22), residues: 588 sheet: -0.34 (0.27), residues: 357 loop : -1.17 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 255 TYR 0.015 0.001 TYR B 121 PHE 0.023 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 0.00303 / 0.14 (14534) covalent geometry : angle 0.55132 / 0.30 (19800) hydrogen bonds : bond 0.04622 / 3.06 ( 585) hydrogen bonds : angle 4.52924 / 3.05 ( 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 204 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 151 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7382 (mt) REVERT: A 540 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7827 (mtt) REVERT: A 608 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6764 (mp) REVERT: A 640 MET cc_start: 0.8368 (ttm) cc_final: 0.8127 (mtp) REVERT: A 688 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.7732 (m) REVERT: A 706 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.5872 (pp20) REVERT: A 744 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.6529 (mtm-85) REVERT: A 837 LYS cc_start: 0.8211 (tppt) cc_final: 0.7921 (tppt) REVERT: A 853 MET cc_start: 0.4922 (OUTLIER) cc_final: 0.4220 (tpt) REVERT: A 859 MET cc_start: 0.3416 (mpp) cc_final: 0.2405 (tpt) REVERT: A 916 LYS cc_start: 0.8481 (ptmt) cc_final: 0.7835 (mptm) REVERT: A 956 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.5947 (mmp-170) REVERT: B 8 HIS cc_start: 0.5019 (m90) cc_final: 0.4353 (m-70) REVERT: B 40 ASP cc_start: 0.5903 (t0) cc_final: 0.5365 (t0) REVERT: B 73 ASP cc_start: 0.7089 (t0) cc_final: 0.6450 (m-30) REVERT: B 110 LEU cc_start: 0.3727 (OUTLIER) cc_final: 0.3475 (tt) REVERT: B 158 LEU cc_start: 0.5507 (mt) cc_final: 0.5250 (mp) REVERT: C 11 LYS cc_start: 0.5044 (OUTLIER) cc_final: 0.4399 (mmtp) REVERT: C 88 ILE cc_start: 0.6140 (mp) cc_final: 0.5533 (tt) REVERT: C 95 MET cc_start: 0.4956 (mmp) cc_final: 0.3999 (mtt) REVERT: C 98 LEU cc_start: 0.7877 (tt) cc_final: 0.7652 (pt) REVERT: C 205 LEU cc_start: 0.5377 (mm) cc_final: 0.4876 (mt) REVERT: C 255 ARG cc_start: 0.6304 (mmm160) cc_final: 0.5849 (mtm180) REVERT: C 365 GLU cc_start: 0.6852 (tp30) cc_final: 0.6508 (mm-30) outliers start: 53 outliers final: 23 residues processed: 186 average time/residue: 0.5002 time to fit residues: 104.3141 Evaluate side-chains 178 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 132 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 540 MET 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 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 384 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 122 optimal weight: 3.9990 chunk 129 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 115 optimal weight: 0.1980 chunk 151 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 128 optimal weight: 30.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 907 ASN A 964 GLN 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 = 0.4350 r_free = 0.4350 target = 0.209456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.167329 restraints weight = 17065.110| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 3.38 r_work: 0.3479 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14534 Z= 0.136 Angle : 0.555 8.780 19800 Z= 0.305 Chirality : 0.042 0.170 2191 Planarity : 0.004 0.082 2390 Dihedral : 14.196 88.124 2246 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.39 % Favored : 94.55 % Rotamer: Outliers : 2.84 % Allowed : 18.60 % Favored : 78.56 % 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: 588 sheet: -0.38 (0.27), residues: 357 loop : -1.17 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 713 TYR 0.014 0.001 TYR B 121 PHE 0.038 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 0.00299 / 0.14 (14534) covalent geometry : angle 0.55494 / 0.30 (19800) hydrogen bonds : bond 0.04543 / 2.99 ( 585) hydrogen bonds : angle 4.52760 / 3.04 ( 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 192 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7393 (mt) REVERT: A 540 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7881 (mtt) REVERT: A 608 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6773 (mp) REVERT: A 640 MET cc_start: 0.8377 (ttm) cc_final: 0.8135 (mtp) REVERT: A 656 MET cc_start: 0.7591 (mtp) cc_final: 0.7359 (mtm) REVERT: A 688 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.7737 (m) REVERT: A 706 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.5974 (pp20) REVERT: A 744 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.6508 (mtm-85) REVERT: A 853 MET cc_start: 0.4922 (OUTLIER) cc_final: 0.4224 (tpt) REVERT: A 859 MET cc_start: 0.3463 (mpp) cc_final: 0.2445 (tpt) REVERT: A 916 LYS cc_start: 0.8507 (ptmt) cc_final: 0.7825 (mptm) REVERT: A 956 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.5931 (mmp-170) REVERT: B 8 HIS cc_start: 0.5037 (m90) cc_final: 0.4345 (m-70) REVERT: B 40 ASP cc_start: 0.5968 (t0) cc_final: 0.5380 (t0) REVERT: B 73 ASP cc_start: 0.7092 (t0) cc_final: 0.6441 (m-30) REVERT: C 11 LYS cc_start: 0.5052 (OUTLIER) cc_final: 0.4405 (mmtp) REVERT: C 88 ILE cc_start: 0.6137 (mp) cc_final: 0.5550 (tt) REVERT: C 95 MET cc_start: 0.4860 (mmp) cc_final: 0.3985 (mtt) REVERT: C 98 LEU cc_start: 0.7855 (tt) cc_final: 0.7630 (pt) REVERT: C 205 LEU cc_start: 0.5378 (mm) cc_final: 0.4883 (mt) REVERT: C 255 ARG cc_start: 0.6268 (mmm160) cc_final: 0.5811 (mtm180) REVERT: C 365 GLU cc_start: 0.6821 (tp30) cc_final: 0.6545 (mm-30) outliers start: 43 outliers final: 24 residues processed: 173 average time/residue: 0.5398 time to fit residues: 103.7023 Evaluate side-chains 173 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 132 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 205 GLU 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 423 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 540 MET 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 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 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 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: 2.9990 chunk 62 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 138 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4342 r_free = 0.4342 target = 0.208634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.167160 restraints weight = 17069.369| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 3.40 r_work: 0.3457 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14534 Z= 0.152 Angle : 0.577 9.084 19800 Z= 0.317 Chirality : 0.042 0.166 2191 Planarity : 0.004 0.082 2390 Dihedral : 14.234 87.800 2246 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.51 % Favored : 94.43 % Rotamer: Outliers : 2.90 % Allowed : 18.93 % 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: -0.27 (0.21), residues: 1634 helix: 1.15 (0.22), residues: 588 sheet: -0.40 (0.27), residues: 354 loop : -1.18 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 713 TYR 0.016 0.001 TYR B 121 PHE 0.020 0.001 PHE A 55 TRP 0.008 0.001 TRP A 470 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (14534) covalent geometry : angle 0.57718 / 0.32 (19800) hydrogen bonds : bond 0.04668 / 3.05 ( 585) hydrogen bonds : angle 4.56609 / 3.07 ( 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 184 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7390 (mt) REVERT: A 398 ASP cc_start: 0.7628 (t0) cc_final: 0.7079 (t0) REVERT: A 608 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6784 (mp) REVERT: A 640 MET cc_start: 0.8435 (ttm) cc_final: 0.8196 (mtp) REVERT: A 656 MET cc_start: 0.7682 (mtp) cc_final: 0.7410 (mtm) REVERT: A 688 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.7776 (m) REVERT: A 706 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6054 (pp20) REVERT: A 744 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6547 (mtm-85) REVERT: A 853 MET cc_start: 0.4949 (OUTLIER) cc_final: 0.4332 (tpt) REVERT: A 859 MET cc_start: 0.3487 (mpp) cc_final: 0.2416 (tpt) REVERT: A 916 LYS cc_start: 0.8525 (ptmt) cc_final: 0.7838 (mptm) REVERT: A 956 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.5957 (mmp-170) REVERT: B 8 HIS cc_start: 0.5169 (m90) cc_final: 0.4505 (m-70) REVERT: B 110 LEU cc_start: 0.3934 (OUTLIER) cc_final: 0.3687 (tt) REVERT: C 11 LYS cc_start: 0.5040 (OUTLIER) cc_final: 0.4371 (mmtp) REVERT: C 88 ILE cc_start: 0.6155 (mp) cc_final: 0.5564 (tt) REVERT: C 95 MET cc_start: 0.4844 (mmp) cc_final: 0.3991 (mtt) REVERT: C 98 LEU cc_start: 0.7862 (tt) cc_final: 0.7636 (pt) REVERT: C 205 LEU cc_start: 0.5328 (mm) cc_final: 0.4826 (mt) REVERT: C 255 ARG cc_start: 0.6321 (mmm160) cc_final: 0.5882 (mtm180) REVERT: C 365 GLU cc_start: 0.6875 (tp30) cc_final: 0.6637 (mm-30) outliers start: 44 outliers final: 23 residues processed: 168 average time/residue: 0.5386 time to fit residues: 100.5891 Evaluate side-chains 169 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 132 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 608 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 384 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 0.0970 chunk 41 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 127 optimal weight: 20.0000 chunk 1 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4344 r_free = 0.4344 target = 0.208893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.166397 restraints weight = 17069.065| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 3.44 r_work: 0.3470 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2390 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= 0.143 Angle : 0.584 9.037 19800 Z= 0.318 Chirality : 0.042 0.217 2191 Planarity : 0.004 0.082 2390 Dihedral : 14.236 87.818 2246 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.32 % Favored : 94.61 % Rotamer: Outliers : 2.37 % Allowed : 19.59 % Favored : 78.03 % 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: -0.29 (0.21), residues: 1634 helix: 1.11 (0.22), residues: 588 sheet: -0.31 (0.28), residues: 332 loop : -1.22 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 255 TYR 0.014 0.001 TYR B 121 PHE 0.017 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 0.00319 / 0.14 (14534) covalent geometry : angle 0.58445 / 0.32 (19800) hydrogen bonds : bond 0.04550 / 2.96 ( 585) hydrogen bonds : angle 4.56250 / 3.07 ( 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 174 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7405 (mt) REVERT: A 398 ASP cc_start: 0.7612 (t0) cc_final: 0.7052 (t0) REVERT: A 608 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6759 (mp) REVERT: A 640 MET cc_start: 0.8417 (ttm) cc_final: 0.8173 (mtp) REVERT: A 656 MET cc_start: 0.7638 (mtp) cc_final: 0.7374 (mtm) REVERT: A 688 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.7760 (m) REVERT: A 744 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6506 (mtm-85) REVERT: A 853 MET cc_start: 0.4943 (OUTLIER) cc_final: 0.4326 (tpt) REVERT: A 859 MET cc_start: 0.3479 (mpp) cc_final: 0.2429 (tpt) REVERT: A 956 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.5959 (mmp-170) REVERT: B 8 HIS cc_start: 0.5138 (m90) cc_final: 0.4456 (m-70) REVERT: B 23 MET cc_start: 0.6967 (mmp) cc_final: 0.6744 (mmm) REVERT: B 110 LEU cc_start: 0.3861 (OUTLIER) cc_final: 0.3634 (tt) REVERT: C 11 LYS cc_start: 0.5054 (OUTLIER) cc_final: 0.4395 (mmtp) REVERT: C 88 ILE cc_start: 0.6072 (mp) cc_final: 0.5441 (tt) REVERT: C 95 MET cc_start: 0.4831 (mmp) cc_final: 0.3990 (mtt) REVERT: C 98 LEU cc_start: 0.7861 (tt) cc_final: 0.7577 (pt) REVERT: C 205 LEU cc_start: 0.5347 (mm) cc_final: 0.4857 (mt) REVERT: C 255 ARG cc_start: 0.6238 (mmm160) cc_final: 0.5831 (mtm180) REVERT: C 365 GLU cc_start: 0.6855 (tp30) cc_final: 0.6596 (mm-30) outliers start: 36 outliers final: 22 residues processed: 163 average time/residue: 0.5428 time to fit residues: 98.4742 Evaluate side-chains 164 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 132 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 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 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 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: 0.6980 chunk 122 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 51 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.208378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.166144 restraints weight = 17138.077| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 3.54 r_work: 0.3459 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14534 Z= 0.149 Angle : 0.587 8.845 19800 Z= 0.320 Chirality : 0.043 0.193 2191 Planarity : 0.005 0.082 2390 Dihedral : 14.249 87.612 2246 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.26 % Favored : 94.68 % Rotamer: Outliers : 2.57 % Allowed : 19.66 % Favored : 77.77 % 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: 1.05 (0.22), residues: 588 sheet: -0.35 (0.28), residues: 333 loop : -1.21 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 713 TYR 0.015 0.001 TYR B 121 PHE 0.021 0.001 PHE A 55 TRP 0.009 0.001 TRP A 470 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (14534) covalent geometry : angle 0.58705 / 0.32 (19800) hydrogen bonds : bond 0.04595 / 2.98 ( 585) hydrogen bonds : angle 4.57801 / 3.07 ( 1656) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4726.91 seconds wall clock time: 81 minutes 34.92 seconds (4894.92 seconds total)