Starting phenix.real_space_refine on Fri Jul 3 19:39:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k9t_62198/07_2026/9k9t_62198.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k9t_62198/07_2026/9k9t_62198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k9t_62198/07_2026/9k9t_62198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k9t_62198/07_2026/9k9t_62198.map" model { file = "/net/cci-nas-00/data/ceres_data/9k9t_62198/07_2026/9k9t_62198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k9t_62198/07_2026/9k9t_62198.cif" } resolution = 2.96 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= 0.003 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2154 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 43 5.49 5 S 70 5.16 5 C 8933 2.51 5 N 2351 2.21 5 O 2742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 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: 14139 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 8106 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 952} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 409 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "P" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 473 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "C" Number of atoms: 3389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3389 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 10, 'TRANS': 405} Chain breaks: 1 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: {'PCIS': 2, 'PTRANS': 11, '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 Time building chain proxies: 3.03, per 1000 atoms: 0.21 Number of scatterers: 14139 At special positions: 0 Unit cell: (110.5, 126.65, 141.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 P 43 15.00 O 2742 8.00 N 2351 7.00 C 8933 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 541.4 milliseconds 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3110 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 18 sheets defined 39.8% alpha, 19.3% beta 12 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 44 through 48 Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.538A pdb=" N PHE A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.667A pdb=" N GLU A 229 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 230' Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 330 through 339 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 390 removed outlier: 3.529A pdb=" N THR A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 446 removed outlier: 3.889A pdb=" N ASP A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 474 removed outlier: 3.735A pdb=" N CYS A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.891A 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 489 through 493 removed outlier: 3.896A pdb=" N VAL A 493 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.639A pdb=" N ILE A 501 " --> pdb=" O ARG A 497 " (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 Processing helix chain 'A' and resid 622 through 643 removed outlier: 3.833A pdb=" N GLN A 643 " --> pdb=" O LYS A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 665 Processing helix chain 'A' and resid 666 through 672 removed outlier: 3.663A 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 782 Processing helix chain 'A' and resid 837 through 855 removed outlier: 3.782A pdb=" N SER A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 883 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.500A pdb=" N MET A 891 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 918 removed outlier: 4.185A pdb=" N TYR A 909 " --> pdb=" O ASN A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 949 removed outlier: 3.718A pdb=" N THR A 949 " --> pdb=" O ASN A 946 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 946 through 949' Processing helix chain 'A' and resid 967 through 982 removed outlier: 4.489A pdb=" N TYR A 971 " --> pdb=" O PHE A 967 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 982 " --> pdb=" O GLU A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 997 Processing helix chain 'C' and resid 3 through 19 removed outlier: 3.632A pdb=" N LEU C 7 " --> pdb=" O SER C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 42 Processing helix chain 'C' and resid 107 through 121 removed outlier: 4.057A pdb=" N ARG C 111 " --> pdb=" O PRO C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 159 removed outlier: 4.095A pdb=" N PHE C 152 " --> pdb=" O PRO C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 189 Processing helix chain 'C' and resid 249 through 257 Processing helix chain 'C' and resid 285 through 298 removed outlier: 4.132A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 323 Processing helix chain 'C' and resid 330 through 341 Processing helix chain 'C' and resid 344 through 351 Processing helix chain 'C' and resid 353 through 361 removed outlier: 3.666A pdb=" N LEU C 361 " --> pdb=" O SER C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 373 Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'C' and resid 397 through 425 removed outlier: 4.575A pdb=" N ASN C 408 " --> pdb=" O TYR C 404 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLN C 409 " --> pdb=" O GLY C 405 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 412 " --> pdb=" O ASN C 408 " (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 31 removed outlier: 4.044A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLN B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 27 " --> pdb=" O MET B 23 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 45 through 49 removed outlier: 4.199A pdb=" N PHE B 49 " --> pdb=" O PRO B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 55 Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 133 through 150 removed outlier: 5.610A pdb=" N LYS B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 205 removed outlier: 4.244A pdb=" N ILE B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP B 205 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 214 No H-bonds generated for 'chain 'B' and resid 212 through 214' Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 134 removed outlier: 8.282A pdb=" N TYR A 140 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE A 31 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N CYS A 142 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ARG A 33 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N PHE A 17 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLU A 10 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR A 19 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TRP A 8 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LYS A 21 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N CYS A 124 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 6.161A pdb=" N SER A 84 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG A 64 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA A 86 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS A 62 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N MET A 88 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.704A pdb=" N SER A 73 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A 568 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP A 616 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU A 611 " --> pdb=" O CYS A 601 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 removed outlier: 6.303A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL A 237 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR A 201 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N CYS A 239 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ILE A 203 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU A 163 " --> pdb=" O VAL A 260 " (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 302 Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 360 removed outlier: 6.990A pdb=" N MET A 357 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ASP A 373 " --> pdb=" O MET A 357 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 407 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N SER A 420 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A 405 " --> pdb=" O SER A 420 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 733 through 734 removed outlier: 5.469A pdb=" N SER A 747 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU A 758 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR A 749 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL A 545 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL A 794 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE A 547 " --> pdb=" O GLU A 792 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU A 798 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR A 807 " --> pdb=" O LEU A 798 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB1, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB2, first strand: chain 'C' and resid 70 through 71 removed outlier: 3.745A pdb=" N THR C 174 " --> pdb=" O ILE C 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 166 through 169 removed outlier: 3.897A pdb=" N GLN C 208 " --> pdb=" O TYR C 199 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 95 through 96 removed outlier: 8.144A pdb=" N ARG C 128 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU C 139 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL C 130 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE C 137 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU C 132 " --> pdb=" O ARG C 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 233 through 239 removed outlier: 4.009A pdb=" N SER C 222 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS C 214 " --> pdb=" O LYS C 268 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 375 through 380 removed outlier: 6.758A pdb=" N ARG C 376 " --> pdb=" O PHE C 387 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE C 387 " --> pdb=" O ARG C 376 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYS C 378 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 3 through 5 Processing sheet with id=AB8, first strand: chain 'B' and resid 115 through 120 removed outlier: 6.540A pdb=" N GLY B 115 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 117 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 107 through 108 578 hydrogen bonds defined for protein. 1641 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3682 1.33 - 1.45: 2859 1.45 - 1.57: 7800 1.57 - 1.69: 84 1.69 - 1.81: 107 Bond restraints: 14532 Sorted by residual: bond pdb=" C3' DA P 20 " pdb=" C2' DA P 20 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" N TYR A 74 " pdb=" CA TYR A 74 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.22e-02 6.72e+03 8.82e+00 bond pdb=" C3' DG P 18 " pdb=" C2' DG P 18 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.00e+00 bond pdb=" C3' DC P 9 " pdb=" C2' DC P 9 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.85e+00 bond pdb=" C3' DA P 16 " pdb=" C2' DA P 16 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.80e+00 ... (remaining 14527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 19410 2.17 - 4.34: 370 4.34 - 6.51: 32 6.51 - 8.68: 6 8.68 - 10.84: 4 Bond angle restraints: 19822 Sorted by residual: angle pdb=" C GLU A 852 " pdb=" N MET A 853 " pdb=" CA MET A 853 " ideal model delta sigma weight residual 122.38 113.28 9.10 1.81e+00 3.05e-01 2.53e+01 angle pdb=" N3 DT P 11 " pdb=" C4 DT P 11 " pdb=" O4 DT P 11 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT P 3 " pdb=" C4 DT P 3 " pdb=" O4 DT P 3 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT E 29 " pdb=" C4 DT E 29 " pdb=" O4 DT E 29 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT P 14 " pdb=" C4 DT P 14 " pdb=" O4 DT P 14 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.67e+01 ... (remaining 19817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.93: 8178 27.93 - 55.86: 457 55.86 - 83.79: 30 83.79 - 111.71: 2 111.71 - 139.64: 1 Dihedral angle restraints: 8668 sinusoidal: 3848 harmonic: 4820 Sorted by residual: dihedral pdb=" CA ARG C 135 " pdb=" C ARG C 135 " pdb=" N TRP C 136 " pdb=" CA TRP C 136 " ideal model delta harmonic sigma weight residual 180.00 -151.64 -28.36 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA THR A 209 " pdb=" C THR A 209 " pdb=" N GLU A 210 " pdb=" CA GLU A 210 " ideal model delta harmonic sigma weight residual 180.00 -154.70 -25.30 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ARG A 832 " pdb=" C ARG A 832 " pdb=" N ARG A 833 " pdb=" CA ARG A 833 " ideal model delta harmonic sigma weight residual -180.00 -156.23 -23.77 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 8665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1873 0.066 - 0.132: 309 0.132 - 0.198: 11 0.198 - 0.264: 3 0.264 - 0.329: 1 Chirality restraints: 2197 Sorted by residual: chirality pdb=" CB ILE C 313 " pdb=" CA ILE C 313 " pdb=" CG1 ILE C 313 " pdb=" CG2 ILE C 313 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB VAL A 365 " pdb=" CA VAL A 365 " pdb=" CG1 VAL A 365 " pdb=" CG2 VAL A 365 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CG LEU C 131 " pdb=" CB LEU C 131 " pdb=" CD1 LEU C 131 " pdb=" CD2 LEU C 131 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 2194 not shown) Planarity restraints: 2370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 73 " 0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C SER A 73 " -0.069 2.00e-02 2.50e+03 pdb=" O SER A 73 " 0.025 2.00e-02 2.50e+03 pdb=" N TYR A 74 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 231 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.32e+00 pdb=" C ASN C 231 " -0.050 2.00e-02 2.50e+03 pdb=" O ASN C 231 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE C 232 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 592 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.41e+00 pdb=" N PRO A 593 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 593 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 593 " -0.037 5.00e-02 4.00e+02 ... (remaining 2367 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2393 2.77 - 3.30: 13429 3.30 - 3.83: 23232 3.83 - 4.37: 26467 4.37 - 4.90: 44455 Nonbonded interactions: 109976 Sorted by model distance: nonbonded pdb=" O ASN A 181 " pdb=" OH TYR A 271 " model vdw 2.236 3.040 nonbonded pdb=" O TYR A 909 " pdb=" OG1 THR A 912 " model vdw 2.242 3.040 nonbonded pdb=" OE2 GLU C 97 " pdb=" N GLY C 101 " model vdw 2.258 3.120 nonbonded pdb=" NE ARG C 227 " pdb=" O GLY C 229 " model vdw 2.262 3.120 nonbonded pdb=" O ASP C 72 " pdb=" OH TYR C 76 " model vdw 2.271 3.040 ... (remaining 109971 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.900 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 : 0.004 0.071 14532 Z= 0.234 Angle : 0.707 10.844 19822 Z= 0.440 Chirality : 0.047 0.329 2197 Planarity : 0.005 0.068 2370 Dihedral : 15.457 139.642 5558 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.22 % Favored : 95.66 % Rotamer: Outliers : 0.27 % Allowed : 0.53 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.21), residues: 1612 helix: 0.89 (0.22), residues: 564 sheet: 0.34 (0.29), residues: 301 loop : -1.15 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 693 TYR 0.019 0.001 TYR A 74 PHE 0.023 0.002 PHE B 49 TRP 0.028 0.001 TRP C 136 HIS 0.004 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.23 (14532) covalent geometry : angle 0.70730 / 0.44 (19822) hydrogen bonds : bond 0.15773 / 10.38 ( 602) hydrogen bonds : angle 6.35494 / 4.30 ( 1697) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 384 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7338 (p0) cc_final: 0.7093 (p0) REVERT: A 230 MET cc_start: 0.7460 (tmm) cc_final: 0.6387 (tmt) REVERT: A 413 ASN cc_start: 0.8264 (p0) cc_final: 0.7945 (p0) REVERT: A 577 ARG cc_start: 0.7889 (mtt180) cc_final: 0.7626 (mtt180) REVERT: A 794 VAL cc_start: 0.8075 (t) cc_final: 0.7704 (p) REVERT: A 878 SER cc_start: 0.9206 (t) cc_final: 0.8908 (p) REVERT: A 965 ARG cc_start: 0.7295 (ppt170) cc_final: 0.6868 (ppt170) REVERT: A 966 ILE cc_start: 0.8574 (mt) cc_final: 0.8095 (mt) REVERT: C 95 MET cc_start: 0.4864 (tpt) cc_final: 0.4051 (tmt) REVERT: C 154 LEU cc_start: 0.8663 (pp) cc_final: 0.8460 (pp) REVERT: C 181 TYR cc_start: 0.8433 (t80) cc_final: 0.8193 (t80) REVERT: C 251 ASP cc_start: 0.8468 (m-30) cc_final: 0.7850 (m-30) REVERT: C 252 HIS cc_start: 0.7698 (t-170) cc_final: 0.6909 (t-170) REVERT: C 264 VAL cc_start: 0.7218 (p) cc_final: 0.6595 (t) REVERT: C 300 ASP cc_start: 0.7974 (p0) cc_final: 0.7719 (t0) REVERT: C 323 LEU cc_start: 0.8298 (mm) cc_final: 0.7732 (mm) REVERT: C 367 ASP cc_start: 0.7585 (m-30) cc_final: 0.7348 (m-30) REVERT: C 371 LEU cc_start: 0.8221 (tt) cc_final: 0.7929 (tm) REVERT: B 60 LYS cc_start: 0.8622 (mmtp) cc_final: 0.8420 (mmtp) REVERT: B 114 ASP cc_start: 0.7938 (p0) cc_final: 0.7735 (p0) REVERT: B 155 LEU cc_start: 0.8306 (tp) cc_final: 0.8084 (tp) outliers start: 4 outliers final: 3 residues processed: 385 average time/residue: 0.5531 time to fit residues: 233.5526 Evaluate side-chains 335 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 332 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 334 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.0030 chunk 122 optimal weight: 0.0870 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.9772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 393 ASN A 524 GLN ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.156817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.120265 restraints weight = 29342.000| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 3.01 r_work: 0.3528 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14532 Z= 0.168 Angle : 0.674 11.607 19822 Z= 0.361 Chirality : 0.046 0.253 2197 Planarity : 0.005 0.056 2370 Dihedral : 14.830 149.910 2271 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.91 % Favored : 95.97 % Rotamer: Outliers : 2.40 % Allowed : 13.41 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.21), residues: 1612 helix: 1.05 (0.22), residues: 574 sheet: 0.39 (0.29), residues: 297 loop : -1.16 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 135 TYR 0.018 0.001 TYR C 199 PHE 0.018 0.002 PHE C 152 TRP 0.023 0.002 TRP C 136 HIS 0.007 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (14532) covalent geometry : angle 0.67407 / 0.36 (19822) hydrogen bonds : bond 0.05513 / 3.60 ( 602) hydrogen bonds : angle 4.85338 / 3.28 ( 1697) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 339 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7864 (pm20) REVERT: A 105 ASP cc_start: 0.8080 (p0) cc_final: 0.7784 (p0) REVERT: A 144 ASP cc_start: 0.8229 (t0) cc_final: 0.7727 (t0) REVERT: A 413 ASN cc_start: 0.8575 (p0) cc_final: 0.8150 (p0) REVERT: A 446 ASP cc_start: 0.8041 (p0) cc_final: 0.7796 (p0) REVERT: A 577 ARG cc_start: 0.8446 (mtt180) cc_final: 0.7735 (mpp80) REVERT: A 742 ARG cc_start: 0.6095 (OUTLIER) cc_final: 0.5875 (tpp-160) REVERT: A 794 VAL cc_start: 0.8167 (t) cc_final: 0.7774 (p) REVERT: A 809 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7893 (mpp) REVERT: A 834 ASP cc_start: 0.7482 (t0) cc_final: 0.7244 (t0) REVERT: A 842 MET cc_start: 0.7958 (tpp) cc_final: 0.7615 (tpp) REVERT: A 878 SER cc_start: 0.9280 (t) cc_final: 0.8914 (p) REVERT: A 883 ARG cc_start: 0.8254 (mtp85) cc_final: 0.8009 (mtt90) REVERT: A 895 MET cc_start: 0.7769 (tmt) cc_final: 0.7259 (tmm) REVERT: A 965 ARG cc_start: 0.7688 (ppt170) cc_final: 0.7416 (ppt170) REVERT: A 966 ILE cc_start: 0.8706 (mt) cc_final: 0.8498 (mt) REVERT: C 95 MET cc_start: 0.4965 (tpt) cc_final: 0.4293 (tmt) REVERT: C 340 LYS cc_start: 0.8646 (pptt) cc_final: 0.8393 (pptt) REVERT: C 367 ASP cc_start: 0.8163 (m-30) cc_final: 0.7921 (m-30) REVERT: C 379 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8583 (pt) REVERT: C 380 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7633 (tm-30) REVERT: B 23 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.7374 (tmm) REVERT: B 155 LEU cc_start: 0.8401 (tp) cc_final: 0.8148 (tp) REVERT: B 210 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7359 (pt) REVERT: B 212 TRP cc_start: 0.7853 (OUTLIER) cc_final: 0.7453 (m100) outliers start: 36 outliers final: 14 residues processed: 349 average time/residue: 0.5663 time to fit residues: 216.3757 Evaluate side-chains 348 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 327 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 742 ARG Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 212 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 90 optimal weight: 0.6980 chunk 114 optimal weight: 20.0000 chunk 140 optimal weight: 4.9990 chunk 110 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.156288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.119652 restraints weight = 29295.850| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 3.02 r_work: 0.3525 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14532 Z= 0.157 Angle : 0.652 12.671 19822 Z= 0.345 Chirality : 0.044 0.179 2197 Planarity : 0.005 0.063 2370 Dihedral : 14.748 152.242 2265 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.85 % Favored : 96.03 % Rotamer: Outliers : 2.80 % Allowed : 16.54 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.21), residues: 1612 helix: 1.08 (0.22), residues: 575 sheet: 0.36 (0.30), residues: 293 loop : -1.16 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 519 TYR 0.018 0.001 TYR C 307 PHE 0.016 0.001 PHE A 200 TRP 0.016 0.001 TRP C 136 HIS 0.006 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (14532) covalent geometry : angle 0.65181 / 0.35 (19822) hydrogen bonds : bond 0.05047 / 3.33 ( 602) hydrogen bonds : angle 4.71028 / 3.19 ( 1697) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 336 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8134 (p0) cc_final: 0.7837 (p0) REVERT: A 144 ASP cc_start: 0.8223 (t0) cc_final: 0.7657 (t0) REVERT: A 339 GLU cc_start: 0.8207 (tp30) cc_final: 0.7931 (tp30) REVERT: A 413 ASN cc_start: 0.8553 (p0) cc_final: 0.8096 (p0) REVERT: A 427 ASP cc_start: 0.7580 (m-30) cc_final: 0.6921 (t0) REVERT: A 577 ARG cc_start: 0.8440 (mtt180) cc_final: 0.7711 (mpt-90) REVERT: A 643 GLN cc_start: 0.8311 (pp30) cc_final: 0.8086 (pp30) REVERT: A 729 ILE cc_start: 0.7964 (pt) cc_final: 0.7648 (pp) REVERT: A 742 ARG cc_start: 0.6250 (tpp-160) cc_final: 0.6001 (tpp-160) REVERT: A 794 VAL cc_start: 0.8149 (t) cc_final: 0.7772 (p) REVERT: C 95 MET cc_start: 0.4999 (tpt) cc_final: 0.4398 (tmt) REVERT: C 233 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.7141 (m-10) REVERT: C 302 TYR cc_start: 0.7610 (p90) cc_final: 0.7364 (p90) REVERT: C 367 ASP cc_start: 0.8130 (m-30) cc_final: 0.7879 (m-30) REVERT: C 375 MET cc_start: 0.7941 (pmm) cc_final: 0.7396 (pmm) REVERT: C 379 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8651 (pt) REVERT: C 422 LYS cc_start: 0.8502 (tttt) cc_final: 0.8117 (tppt) REVERT: B 153 SER cc_start: 0.8907 (m) cc_final: 0.8558 (t) REVERT: B 203 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7805 (mm-30) REVERT: B 206 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8327 (p0) outliers start: 42 outliers final: 19 residues processed: 355 average time/residue: 0.5495 time to fit residues: 213.6886 Evaluate side-chains 351 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 329 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 206 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 147 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 143 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 133 ASN ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.154768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.118153 restraints weight = 29407.575| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.99 r_work: 0.3499 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14532 Z= 0.201 Angle : 0.692 12.545 19822 Z= 0.365 Chirality : 0.047 0.544 2197 Planarity : 0.005 0.050 2370 Dihedral : 14.820 152.658 2265 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.97 % Favored : 95.91 % Rotamer: Outliers : 3.40 % Allowed : 18.15 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.21), residues: 1612 helix: 1.00 (0.22), residues: 574 sheet: 0.27 (0.30), residues: 294 loop : -1.18 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 255 TYR 0.021 0.001 TYR C 307 PHE 0.022 0.002 PHE A 958 TRP 0.022 0.002 TRP B 212 HIS 0.007 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (14532) covalent geometry : angle 0.69176 / 0.37 (19822) hydrogen bonds : bond 0.05161 / 3.44 ( 602) hydrogen bonds : angle 4.70602 / 3.19 ( 1697) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 336 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8182 (p0) cc_final: 0.7900 (p0) REVERT: A 144 ASP cc_start: 0.8281 (t0) cc_final: 0.7735 (t0) REVERT: A 413 ASN cc_start: 0.8550 (p0) cc_final: 0.8077 (p0) REVERT: A 427 ASP cc_start: 0.7625 (m-30) cc_final: 0.7075 (t70) REVERT: A 794 VAL cc_start: 0.8194 (t) cc_final: 0.7824 (p) REVERT: A 892 LEU cc_start: 0.7610 (mm) cc_final: 0.7397 (mp) REVERT: A 895 MET cc_start: 0.7774 (tmt) cc_final: 0.7306 (tmm) REVERT: C 95 MET cc_start: 0.5190 (tpt) cc_final: 0.4688 (tmt) REVERT: C 227 ARG cc_start: 0.8062 (tpp-160) cc_final: 0.7714 (mmm-85) REVERT: C 367 ASP cc_start: 0.8093 (m-30) cc_final: 0.7861 (m-30) REVERT: C 379 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8672 (pt) REVERT: C 422 LYS cc_start: 0.8522 (tttt) cc_final: 0.8154 (tppt) REVERT: B 153 SER cc_start: 0.8924 (m) cc_final: 0.8586 (t) REVERT: B 155 LEU cc_start: 0.8392 (tp) cc_final: 0.8050 (tm) REVERT: B 203 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7883 (mm-30) outliers start: 51 outliers final: 25 residues processed: 356 average time/residue: 0.5223 time to fit residues: 204.2025 Evaluate side-chains 350 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 324 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 210 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 73 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 41 optimal weight: 0.3980 chunk 116 optimal weight: 6.9990 chunk 93 optimal weight: 0.0170 chunk 127 optimal weight: 3.9990 overall best weight: 1.0824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.154891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.118427 restraints weight = 29298.916| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.00 r_work: 0.3508 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14532 Z= 0.168 Angle : 0.683 13.568 19822 Z= 0.360 Chirality : 0.045 0.181 2197 Planarity : 0.005 0.070 2370 Dihedral : 14.862 153.705 2265 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.09 % Favored : 95.78 % Rotamer: Outliers : 3.20 % Allowed : 20.75 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.21), residues: 1612 helix: 0.99 (0.22), residues: 576 sheet: 0.11 (0.29), residues: 312 loop : -1.17 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 255 TYR 0.026 0.001 TYR C 307 PHE 0.023 0.002 PHE B 29 TRP 0.025 0.002 TRP B 212 HIS 0.006 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (14532) covalent geometry : angle 0.68326 / 0.36 (19822) hydrogen bonds : bond 0.04789 / 3.18 ( 602) hydrogen bonds : angle 4.63023 / 3.13 ( 1697) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 335 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8221 (p0) cc_final: 0.7954 (p0) REVERT: A 144 ASP cc_start: 0.8298 (t0) cc_final: 0.7667 (t0) REVERT: A 413 ASN cc_start: 0.8528 (p0) cc_final: 0.8056 (p0) REVERT: A 427 ASP cc_start: 0.7599 (m-30) cc_final: 0.7048 (t70) REVERT: A 577 ARG cc_start: 0.8448 (mtt180) cc_final: 0.7852 (mpt-90) REVERT: A 729 ILE cc_start: 0.7888 (pt) cc_final: 0.7596 (pp) REVERT: A 742 ARG cc_start: 0.6356 (tpp-160) cc_final: 0.6043 (tpp-160) REVERT: A 794 VAL cc_start: 0.8148 (t) cc_final: 0.7768 (p) REVERT: A 834 ASP cc_start: 0.7547 (t0) cc_final: 0.7297 (t70) REVERT: A 842 MET cc_start: 0.8028 (tpp) cc_final: 0.7734 (tpp) REVERT: A 859 MET cc_start: 0.5883 (mmp) cc_final: 0.5499 (mmp) REVERT: A 895 MET cc_start: 0.7844 (tmt) cc_final: 0.7325 (tmm) REVERT: C 95 MET cc_start: 0.5190 (tpt) cc_final: 0.4697 (tmt) REVERT: C 154 LEU cc_start: 0.8838 (tm) cc_final: 0.8316 (pp) REVERT: C 179 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8213 (mp0) REVERT: C 227 ARG cc_start: 0.8020 (tpp-160) cc_final: 0.7798 (mmm-85) REVERT: C 367 ASP cc_start: 0.8113 (m-30) cc_final: 0.7861 (m-30) REVERT: C 375 MET cc_start: 0.7745 (pmm) cc_final: 0.7188 (pmm) REVERT: C 379 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8696 (pt) REVERT: C 422 LYS cc_start: 0.8502 (tttt) cc_final: 0.8099 (tppt) REVERT: B 153 SER cc_start: 0.8907 (m) cc_final: 0.8564 (t) REVERT: B 155 LEU cc_start: 0.8368 (tp) cc_final: 0.8044 (tm) REVERT: B 203 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7845 (mm-30) outliers start: 48 outliers final: 27 residues processed: 355 average time/residue: 0.5684 time to fit residues: 220.9353 Evaluate side-chains 349 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 321 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 964 GLN Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 152 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 82 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 0.0980 chunk 11 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 841 ASN ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.155550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.118942 restraints weight = 29113.880| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 3.02 r_work: 0.3518 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14532 Z= 0.148 Angle : 0.686 14.978 19822 Z= 0.357 Chirality : 0.044 0.198 2197 Planarity : 0.005 0.055 2370 Dihedral : 14.869 154.196 2265 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.85 % Favored : 96.03 % Rotamer: Outliers : 3.20 % Allowed : 21.68 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.21), residues: 1612 helix: 1.03 (0.22), residues: 576 sheet: 0.27 (0.30), residues: 292 loop : -1.10 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 693 TYR 0.027 0.001 TYR C 307 PHE 0.028 0.002 PHE A 958 TRP 0.025 0.001 TRP B 212 HIS 0.005 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (14532) covalent geometry : angle 0.68604 / 0.36 (19822) hydrogen bonds : bond 0.04541 / 3.01 ( 602) hydrogen bonds : angle 4.57789 / 3.10 ( 1697) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 333 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8201 (p0) cc_final: 0.7935 (p0) REVERT: A 144 ASP cc_start: 0.8293 (t0) cc_final: 0.7673 (t0) REVERT: A 413 ASN cc_start: 0.8532 (p0) cc_final: 0.8044 (p0) REVERT: A 427 ASP cc_start: 0.7633 (m-30) cc_final: 0.7095 (t70) REVERT: A 577 ARG cc_start: 0.8397 (mtt180) cc_final: 0.7797 (mpt-90) REVERT: A 729 ILE cc_start: 0.7953 (pt) cc_final: 0.7655 (pp) REVERT: A 742 ARG cc_start: 0.6479 (tpp-160) cc_final: 0.6275 (tpp-160) REVERT: A 794 VAL cc_start: 0.8122 (t) cc_final: 0.7730 (p) REVERT: A 834 ASP cc_start: 0.7562 (t0) cc_final: 0.7213 (t70) REVERT: A 859 MET cc_start: 0.5900 (mmp) cc_final: 0.5279 (mmp) REVERT: A 895 MET cc_start: 0.7818 (tmt) cc_final: 0.7288 (tmm) REVERT: A 965 ARG cc_start: 0.7493 (ppt170) cc_final: 0.7150 (ptt-90) REVERT: C 95 MET cc_start: 0.5222 (tpt) cc_final: 0.4298 (tmt) REVERT: C 154 LEU cc_start: 0.8869 (tm) cc_final: 0.8360 (pp) REVERT: C 367 ASP cc_start: 0.8135 (m-30) cc_final: 0.7880 (m-30) REVERT: C 375 MET cc_start: 0.7737 (pmm) cc_final: 0.7189 (pmm) REVERT: C 379 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8699 (pt) REVERT: C 422 LYS cc_start: 0.8555 (tttt) cc_final: 0.8086 (tppt) REVERT: C 425 PHE cc_start: 0.8263 (m-10) cc_final: 0.7929 (m-10) REVERT: B 23 MET cc_start: 0.7843 (ttp) cc_final: 0.7585 (tmm) REVERT: B 153 SER cc_start: 0.8890 (m) cc_final: 0.8545 (t) REVERT: B 155 LEU cc_start: 0.8368 (tp) cc_final: 0.8042 (tm) REVERT: B 203 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7835 (mm-30) outliers start: 48 outliers final: 29 residues processed: 355 average time/residue: 0.5272 time to fit residues: 205.1402 Evaluate side-chains 352 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 322 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 152 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 33 optimal weight: 0.0980 chunk 122 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 chunk 120 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.155138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.118249 restraints weight = 29206.527| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.04 r_work: 0.3509 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14532 Z= 0.156 Angle : 0.695 11.788 19822 Z= 0.365 Chirality : 0.045 0.189 2197 Planarity : 0.007 0.236 2370 Dihedral : 14.895 154.414 2265 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.09 % Favored : 95.78 % Rotamer: Outliers : 3.07 % Allowed : 22.75 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.21), residues: 1612 helix: 1.00 (0.22), residues: 575 sheet: 0.26 (0.30), residues: 300 loop : -1.04 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 693 TYR 0.029 0.001 TYR C 307 PHE 0.022 0.001 PHE C 104 TRP 0.030 0.002 TRP B 212 HIS 0.005 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (14532) covalent geometry : angle 0.69537 / 0.36 (19822) hydrogen bonds : bond 0.04591 / 3.05 ( 602) hydrogen bonds : angle 4.60547 / 3.11 ( 1697) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 332 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8212 (p0) cc_final: 0.7949 (p0) REVERT: A 144 ASP cc_start: 0.8304 (t0) cc_final: 0.7666 (t0) REVERT: A 413 ASN cc_start: 0.8542 (p0) cc_final: 0.8049 (p0) REVERT: A 427 ASP cc_start: 0.7662 (m-30) cc_final: 0.7135 (t70) REVERT: A 577 ARG cc_start: 0.8381 (mtt180) cc_final: 0.7786 (mpt-90) REVERT: A 729 ILE cc_start: 0.7973 (pt) cc_final: 0.7669 (pp) REVERT: A 742 ARG cc_start: 0.6477 (tpp-160) cc_final: 0.6259 (tpp-160) REVERT: A 794 VAL cc_start: 0.8095 (t) cc_final: 0.7705 (p) REVERT: A 834 ASP cc_start: 0.7546 (t0) cc_final: 0.7177 (t70) REVERT: A 859 MET cc_start: 0.5851 (mmp) cc_final: 0.5591 (mmp) REVERT: A 895 MET cc_start: 0.7882 (tmt) cc_final: 0.7326 (tmm) REVERT: A 965 ARG cc_start: 0.7499 (ppt170) cc_final: 0.7170 (ptt-90) REVERT: C 95 MET cc_start: 0.5279 (tpt) cc_final: 0.4391 (tmt) REVERT: C 154 LEU cc_start: 0.8856 (tm) cc_final: 0.8353 (pp) REVERT: C 227 ARG cc_start: 0.8142 (ttm-80) cc_final: 0.7832 (tpm170) REVERT: C 264 VAL cc_start: 0.7433 (p) cc_final: 0.7106 (t) REVERT: C 278 TYR cc_start: 0.6702 (t80) cc_final: 0.6428 (t80) REVERT: C 337 GLU cc_start: 0.8700 (pp20) cc_final: 0.8482 (pm20) REVERT: C 367 ASP cc_start: 0.8150 (m-30) cc_final: 0.7893 (m-30) REVERT: C 374 ASN cc_start: 0.7727 (OUTLIER) cc_final: 0.6960 (m110) REVERT: C 375 MET cc_start: 0.7826 (pmm) cc_final: 0.7281 (pmm) REVERT: C 379 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8778 (pt) REVERT: C 422 LYS cc_start: 0.8584 (tttt) cc_final: 0.8076 (tppt) REVERT: C 425 PHE cc_start: 0.8346 (m-80) cc_final: 0.8027 (m-10) REVERT: B 23 MET cc_start: 0.7968 (ttp) cc_final: 0.7766 (tmm) REVERT: B 203 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7854 (mm-30) outliers start: 46 outliers final: 32 residues processed: 355 average time/residue: 0.5509 time to fit residues: 213.6690 Evaluate side-chains 352 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 318 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 374 ASN Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 152 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 115 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.155401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.118651 restraints weight = 29182.706| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 3.02 r_work: 0.3514 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14532 Z= 0.151 Angle : 0.706 12.672 19822 Z= 0.370 Chirality : 0.045 0.192 2197 Planarity : 0.005 0.061 2370 Dihedral : 14.887 154.591 2265 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.85 % Favored : 96.03 % Rotamer: Outliers : 3.40 % Allowed : 23.75 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.21), residues: 1612 helix: 1.02 (0.22), residues: 576 sheet: 0.29 (0.30), residues: 300 loop : -1.02 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 98 TYR 0.029 0.001 TYR C 307 PHE 0.027 0.002 PHE A 958 TRP 0.031 0.001 TRP B 212 HIS 0.005 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (14532) covalent geometry : angle 0.70638 / 0.37 (19822) hydrogen bonds : bond 0.04467 / 2.97 ( 602) hydrogen bonds : angle 4.56696 / 3.09 ( 1697) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 327 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8201 (p0) cc_final: 0.7949 (p0) REVERT: A 144 ASP cc_start: 0.8311 (t0) cc_final: 0.7691 (t0) REVERT: A 413 ASN cc_start: 0.8519 (p0) cc_final: 0.8037 (p0) REVERT: A 427 ASP cc_start: 0.7644 (m-30) cc_final: 0.7173 (t70) REVERT: A 577 ARG cc_start: 0.8315 (mtt180) cc_final: 0.7830 (mpt-90) REVERT: A 729 ILE cc_start: 0.7982 (pt) cc_final: 0.7668 (pp) REVERT: A 742 ARG cc_start: 0.6465 (tpp-160) cc_final: 0.6259 (tpp-160) REVERT: A 794 VAL cc_start: 0.8095 (t) cc_final: 0.7696 (p) REVERT: A 805 LYS cc_start: 0.8543 (mtpt) cc_final: 0.8343 (mtpp) REVERT: A 832 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7407 (ttm-80) REVERT: A 834 ASP cc_start: 0.7544 (t0) cc_final: 0.7180 (t70) REVERT: A 883 ARG cc_start: 0.8229 (mtp85) cc_final: 0.8002 (mtp85) REVERT: A 965 ARG cc_start: 0.7518 (ppt170) cc_final: 0.7194 (ptt-90) REVERT: A 985 ASN cc_start: 0.7764 (t0) cc_final: 0.6673 (m-40) REVERT: C 95 MET cc_start: 0.5335 (tpt) cc_final: 0.4381 (tmt) REVERT: C 154 LEU cc_start: 0.8842 (tm) cc_final: 0.8332 (pp) REVERT: C 179 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8247 (mp0) REVERT: C 227 ARG cc_start: 0.8163 (ttm-80) cc_final: 0.7603 (ttm-80) REVERT: C 367 ASP cc_start: 0.8149 (m-30) cc_final: 0.7887 (m-30) REVERT: C 374 ASN cc_start: 0.7741 (OUTLIER) cc_final: 0.7448 (m110) REVERT: C 375 MET cc_start: 0.7816 (pmm) cc_final: 0.7466 (pmm) REVERT: C 379 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8745 (pt) REVERT: B 23 MET cc_start: 0.7974 (ttp) cc_final: 0.7764 (tmm) REVERT: B 146 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7867 (mt0) REVERT: B 155 LEU cc_start: 0.8381 (tp) cc_final: 0.8054 (tm) REVERT: B 202 LEU cc_start: 0.8184 (tt) cc_final: 0.7907 (pp) outliers start: 51 outliers final: 32 residues processed: 352 average time/residue: 0.6175 time to fit residues: 237.2349 Evaluate side-chains 349 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 313 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 832 ARG Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 964 GLN Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 374 ASN Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 152 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 164 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 5 optimal weight: 0.1980 chunk 128 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.156028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.119303 restraints weight = 29173.682| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 3.04 r_work: 0.3525 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14532 Z= 0.146 Angle : 0.719 13.614 19822 Z= 0.378 Chirality : 0.045 0.204 2197 Planarity : 0.005 0.064 2370 Dihedral : 14.895 154.912 2265 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.54 % Favored : 96.34 % Rotamer: Outliers : 2.67 % Allowed : 24.88 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.21), residues: 1612 helix: 1.01 (0.22), residues: 580 sheet: 0.27 (0.30), residues: 300 loop : -1.01 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 255 TYR 0.033 0.001 TYR C 307 PHE 0.025 0.001 PHE C 104 TRP 0.031 0.001 TRP B 212 HIS 0.004 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (14532) covalent geometry : angle 0.71917 / 0.38 (19822) hydrogen bonds : bond 0.04381 / 2.90 ( 602) hydrogen bonds : angle 4.53738 / 3.08 ( 1697) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 317 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8198 (p0) cc_final: 0.7934 (p0) REVERT: A 144 ASP cc_start: 0.8288 (t0) cc_final: 0.7680 (t0) REVERT: A 427 ASP cc_start: 0.7650 (m-30) cc_final: 0.7184 (t70) REVERT: A 577 ARG cc_start: 0.8274 (mtt180) cc_final: 0.7759 (mpt-90) REVERT: A 729 ILE cc_start: 0.7987 (pt) cc_final: 0.7672 (pp) REVERT: A 742 ARG cc_start: 0.6430 (tpp-160) cc_final: 0.6209 (tpp-160) REVERT: A 794 VAL cc_start: 0.8064 (t) cc_final: 0.7674 (p) REVERT: A 832 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7416 (ttm-80) REVERT: A 834 ASP cc_start: 0.7511 (t0) cc_final: 0.7297 (t70) REVERT: A 895 MET cc_start: 0.7731 (tmt) cc_final: 0.7170 (tmm) REVERT: A 965 ARG cc_start: 0.7560 (ppt170) cc_final: 0.7179 (ptt-90) REVERT: A 985 ASN cc_start: 0.7787 (t0) cc_final: 0.6396 (m-40) REVERT: C 95 MET cc_start: 0.5335 (tpt) cc_final: 0.4518 (tmt) REVERT: C 154 LEU cc_start: 0.8834 (tm) cc_final: 0.8328 (pp) REVERT: C 179 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8236 (mp0) REVERT: C 227 ARG cc_start: 0.8131 (ttm-80) cc_final: 0.7717 (ttm-80) REVERT: C 300 ASP cc_start: 0.8203 (p0) cc_final: 0.7422 (t0) REVERT: C 367 ASP cc_start: 0.8148 (m-30) cc_final: 0.7884 (m-30) REVERT: C 374 ASN cc_start: 0.7712 (OUTLIER) cc_final: 0.7392 (m110) REVERT: C 375 MET cc_start: 0.7792 (pmm) cc_final: 0.7431 (pmm) REVERT: B 146 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7858 (mt0) REVERT: B 202 LEU cc_start: 0.8139 (tt) cc_final: 0.7893 (pp) outliers start: 40 outliers final: 28 residues processed: 339 average time/residue: 0.6317 time to fit residues: 234.0041 Evaluate side-chains 345 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 314 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 832 ARG Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 374 ASN Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 197 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 34 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 146 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.154842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.118017 restraints weight = 29146.792| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.02 r_work: 0.3500 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14532 Z= 0.183 Angle : 0.760 13.638 19822 Z= 0.396 Chirality : 0.047 0.254 2197 Planarity : 0.005 0.087 2370 Dihedral : 14.928 155.070 2265 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.34 % Favored : 95.53 % Rotamer: Outliers : 2.54 % Allowed : 25.15 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1612 helix: 0.96 (0.22), residues: 578 sheet: 0.08 (0.29), residues: 310 loop : -1.01 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 98 TYR 0.028 0.001 TYR B 156 PHE 0.029 0.002 PHE A 958 TRP 0.033 0.002 TRP B 212 HIS 0.005 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (14532) covalent geometry : angle 0.75956 / 0.40 (19822) hydrogen bonds : bond 0.04738 / 3.15 ( 602) hydrogen bonds : angle 4.58977 / 3.10 ( 1697) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 326 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8247 (p0) cc_final: 0.7991 (p0) REVERT: A 144 ASP cc_start: 0.8330 (t0) cc_final: 0.7720 (t0) REVERT: A 230 MET cc_start: 0.7707 (tmm) cc_final: 0.5832 (tmt) REVERT: A 282 GLU cc_start: 0.7231 (tp30) cc_final: 0.6754 (tp30) REVERT: A 427 ASP cc_start: 0.7669 (m-30) cc_final: 0.7214 (t70) REVERT: A 577 ARG cc_start: 0.8334 (mtt180) cc_final: 0.7762 (mpt-90) REVERT: A 692 ARG cc_start: 0.8558 (ttm110) cc_final: 0.8311 (mtp-110) REVERT: A 729 ILE cc_start: 0.8029 (pt) cc_final: 0.7708 (pp) REVERT: A 742 ARG cc_start: 0.6419 (tpp-160) cc_final: 0.6218 (tpp-160) REVERT: A 794 VAL cc_start: 0.8125 (t) cc_final: 0.7740 (p) REVERT: A 832 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7364 (ttm-80) REVERT: A 834 ASP cc_start: 0.7544 (t0) cc_final: 0.7332 (t70) REVERT: A 880 PHE cc_start: 0.8906 (t80) cc_final: 0.8583 (t80) REVERT: A 883 ARG cc_start: 0.8223 (mtp85) cc_final: 0.7884 (mtt90) REVERT: A 895 MET cc_start: 0.7788 (tmt) cc_final: 0.7299 (tmm) REVERT: A 965 ARG cc_start: 0.7544 (ppt170) cc_final: 0.7178 (ptt-90) REVERT: A 976 THR cc_start: 0.9043 (t) cc_final: 0.8837 (t) REVERT: C 95 MET cc_start: 0.5267 (tpt) cc_final: 0.4497 (tmt) REVERT: C 104 PHE cc_start: 0.7182 (t80) cc_final: 0.6951 (p90) REVERT: C 154 LEU cc_start: 0.8823 (tm) cc_final: 0.8318 (pp) REVERT: C 227 ARG cc_start: 0.8125 (ttm-80) cc_final: 0.7737 (ttm-80) REVERT: C 233 PHE cc_start: 0.6974 (OUTLIER) cc_final: 0.5858 (m-10) REVERT: C 300 ASP cc_start: 0.8171 (p0) cc_final: 0.7395 (t0) REVERT: C 359 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7865 (mm-30) REVERT: C 367 ASP cc_start: 0.8144 (m-30) cc_final: 0.7895 (m-30) REVERT: C 374 ASN cc_start: 0.7738 (OUTLIER) cc_final: 0.7069 (m110) REVERT: C 375 MET cc_start: 0.7781 (pmm) cc_final: 0.7305 (pmm) REVERT: B 16 HIS cc_start: 0.7767 (t70) cc_final: 0.7382 (t70) REVERT: B 146 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7880 (mt0) REVERT: B 202 LEU cc_start: 0.8142 (tt) cc_final: 0.7915 (pp) outliers start: 38 outliers final: 27 residues processed: 347 average time/residue: 0.5791 time to fit residues: 219.5628 Evaluate side-chains 345 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 314 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 832 ARG Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 374 ASN Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 8 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 0.0000 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.156017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.119352 restraints weight = 29226.797| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 3.03 r_work: 0.3523 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14532 Z= 0.154 Angle : 0.759 14.819 19822 Z= 0.397 Chirality : 0.047 0.204 2197 Planarity : 0.005 0.089 2370 Dihedral : 14.945 155.529 2265 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.66 % Favored : 96.22 % Rotamer: Outliers : 2.07 % Allowed : 25.68 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.21), residues: 1612 helix: 0.91 (0.22), residues: 580 sheet: 0.27 (0.30), residues: 300 loop : -0.98 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 255 TYR 0.032 0.001 TYR B 156 PHE 0.024 0.001 PHE C 217 TRP 0.036 0.002 TRP B 212 HIS 0.004 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (14532) covalent geometry : angle 0.75947 / 0.40 (19822) hydrogen bonds : bond 0.04433 / 2.94 ( 602) hydrogen bonds : angle 4.53881 / 3.08 ( 1697) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5976.70 seconds wall clock time: 102 minutes 22.81 seconds (6142.81 seconds total)