Starting phenix.real_space_refine on Sat Jun 14 06:34:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k9t_62198/06_2025/9k9t_62198.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k9t_62198/06_2025/9k9t_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_62198/06_2025/9k9t_62198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k9t_62198/06_2025/9k9t_62198.map" model { file = "/net/cci-nas-00/data/ceres_data/9k9t_62198/06_2025/9k9t_62198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k9t_62198/06_2025/9k9t_62198.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.76, per 1000 atoms: 0.55 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: 3.09 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 4.30 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: 4.96 Time building geometry restraints manager: 3.72 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=" 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=" N ASP A 77 " pdb=" CA ASP A 77 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.27e-02 6.20e+03 5.35e+00 bond pdb=" N LEU A 76 " pdb=" CA LEU A 76 " ideal model delta sigma weight residual 1.458 1.484 -0.027 1.25e-02 6.40e+03 4.55e+00 bond pdb=" N ASN A 860 " pdb=" CA ASN A 860 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.25e+00 bond pdb=" C TYR A 74 " pdb=" O TYR A 74 " ideal model delta sigma weight residual 1.236 1.214 0.021 1.38e-02 5.25e+03 2.37e+00 ... (remaining 14527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 19450 2.17 - 4.34: 330 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=" N MET A 853 " pdb=" CA MET A 853 " pdb=" CB MET A 853 " ideal model delta sigma weight residual 110.44 116.09 -5.65 1.53e+00 4.27e-01 1.37e+01 angle pdb=" CB MET A 357 " pdb=" CG MET A 357 " pdb=" SD MET A 357 " ideal model delta sigma weight residual 112.70 123.54 -10.84 3.00e+00 1.11e-01 1.31e+01 angle pdb=" C ASP A 77 " pdb=" N ILE A 78 " pdb=" CA ILE A 78 " ideal model delta sigma weight residual 123.19 118.96 4.23 1.24e+00 6.50e-01 1.16e+01 angle pdb=" CA LEU A 76 " pdb=" C LEU A 76 " pdb=" O LEU A 76 " ideal model delta sigma weight residual 120.32 117.00 3.32 1.02e+00 9.61e-01 1.06e+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: 1908 0.066 - 0.132: 274 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 34.140 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:10.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 14532 Z= 0.157 Angle : 0.684 10.844 19822 Z= 0.383 Chirality : 0.045 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.028 0.001 TRP C 136 HIS 0.004 0.001 HIS A 170 PHE 0.023 0.002 PHE B 49 TYR 0.019 0.001 TYR A 74 ARG 0.010 0.000 ARG A 693 Details of bonding type rmsd hydrogen bonds : bond 0.15773 ( 602) hydrogen bonds : angle 6.35494 ( 1697) covalent geometry : bond 0.00322 (14532) covalent geometry : angle 0.68401 (19822) *********************** 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 : 1.476 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: 0.7725 (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: 1.2777 time to fit residues: 539.1347 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 : 1.580 ------------------------------------------------------------------------------- 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 139 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 42 optimal weight: 0.0370 chunk 84 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 78 optimal weight: 0.0010 chunk 96 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.8068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN A 524 GLN A 841 ASN ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.153609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.116884 restraints weight = 29085.364| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.98 r_work: 0.3480 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 14532 Z= 0.233 Angle : 0.691 12.416 19822 Z= 0.370 Chirality : 0.047 0.213 2197 Planarity : 0.005 0.061 2370 Dihedral : 14.823 152.411 2271 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.28 % Favored : 95.60 % Rotamer: Outliers : 3.00 % Allowed : 13.08 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.21), residues: 1612 helix: 0.93 (0.22), residues: 573 sheet: 0.29 (0.30), residues: 292 loop : -1.12 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 136 HIS 0.007 0.002 HIS A 839 PHE 0.022 0.002 PHE A 992 TYR 0.020 0.002 TYR C 363 ARG 0.008 0.001 ARG A 692 Details of bonding type rmsd hydrogen bonds : bond 0.05558 ( 602) hydrogen bonds : angle 4.86084 ( 1697) covalent geometry : bond 0.00554 (14532) covalent geometry : angle 0.69117 (19822) *********************** 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 399 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 354 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7929 (pm20) REVERT: A 92 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7772 (mt-10) REVERT: A 105 ASP cc_start: 0.8231 (p0) cc_final: 0.7980 (p0) REVERT: A 144 ASP cc_start: 0.8303 (t0) cc_final: 0.7831 (t0) REVERT: A 230 MET cc_start: 0.7717 (tmm) cc_final: 0.6186 (tmt) REVERT: A 261 THR cc_start: 0.8783 (m) cc_final: 0.8420 (p) REVERT: A 282 GLU cc_start: 0.7876 (tt0) cc_final: 0.7643 (tm-30) REVERT: A 413 ASN cc_start: 0.8596 (p0) cc_final: 0.8172 (p0) REVERT: A 430 LYS cc_start: 0.8120 (ptmt) cc_final: 0.7895 (ptpp) REVERT: A 471 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8250 (mt-10) REVERT: A 742 ARG cc_start: 0.6241 (tpp-160) cc_final: 0.5985 (tpp-160) REVERT: A 794 VAL cc_start: 0.8207 (t) cc_final: 0.7862 (p) REVERT: A 842 MET cc_start: 0.8215 (tpp) cc_final: 0.7874 (tpp) REVERT: A 883 ARG cc_start: 0.8256 (mtp85) cc_final: 0.8051 (mtp85) REVERT: A 895 MET cc_start: 0.7887 (tmt) cc_final: 0.7397 (tmm) REVERT: C 95 MET cc_start: 0.5049 (tpt) cc_final: 0.4432 (tmt) REVERT: C 180 LEU cc_start: 0.8717 (tt) cc_final: 0.8502 (pp) REVERT: C 181 TYR cc_start: 0.8434 (t80) cc_final: 0.8224 (t80) REVERT: C 337 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8270 (pt0) REVERT: C 367 ASP cc_start: 0.8108 (m-30) cc_final: 0.7885 (m-30) REVERT: C 378 LYS cc_start: 0.8298 (ttpp) cc_final: 0.7941 (ttpp) REVERT: C 379 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8729 (pt) REVERT: C 401 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8166 (mt-10) REVERT: B 48 LYS cc_start: 0.8117 (mtpt) cc_final: 0.7852 (mtpp) REVERT: B 114 ASP cc_start: 0.8099 (p0) cc_final: 0.7801 (p0) REVERT: B 153 SER cc_start: 0.8908 (m) cc_final: 0.8577 (t) outliers start: 45 outliers final: 21 residues processed: 369 average time/residue: 1.2520 time to fit residues: 505.6921 Evaluate side-chains 359 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 335 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 45 GLU 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 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 944 LEU Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 964 GLN Chi-restraints excluded: chain C residue 309 SER 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 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 149 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 101 optimal weight: 3.9990 chunk 162 optimal weight: 20.0000 chunk 59 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 841 ASN C 133 ASN B 55 GLN B 199 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.154957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.118458 restraints weight = 29124.991| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.03 r_work: 0.3506 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14532 Z= 0.148 Angle : 0.630 10.039 19822 Z= 0.334 Chirality : 0.043 0.184 2197 Planarity : 0.004 0.054 2370 Dihedral : 14.622 149.774 2267 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.66 % Favored : 96.22 % Rotamer: Outliers : 3.34 % Allowed : 15.94 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1612 helix: 1.05 (0.22), residues: 577 sheet: 0.23 (0.29), residues: 305 loop : -1.14 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 212 HIS 0.004 0.001 HIS B 16 PHE 0.027 0.001 PHE B 29 TYR 0.015 0.001 TYR C 199 ARG 0.008 0.001 ARG C 255 Details of bonding type rmsd hydrogen bonds : bond 0.04524 ( 602) hydrogen bonds : angle 4.55614 ( 1697) covalent geometry : bond 0.00341 (14532) covalent geometry : angle 0.63033 (19822) *********************** 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 386 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 336 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8209 (p0) cc_final: 0.7945 (p0) REVERT: A 144 ASP cc_start: 0.8276 (t0) cc_final: 0.7753 (t0) REVERT: A 261 THR cc_start: 0.8821 (m) cc_final: 0.8582 (p) REVERT: A 282 GLU cc_start: 0.7814 (tt0) cc_final: 0.7611 (tm-30) REVERT: A 413 ASN cc_start: 0.8544 (p0) cc_final: 0.8091 (p0) REVERT: A 427 ASP cc_start: 0.7700 (m-30) cc_final: 0.7098 (t70) REVERT: A 445 LYS cc_start: 0.8569 (tppp) cc_final: 0.8340 (tppt) REVERT: A 643 GLN cc_start: 0.8376 (pp30) cc_final: 0.8054 (pp30) REVERT: A 794 VAL cc_start: 0.8114 (t) cc_final: 0.7754 (p) REVERT: C 95 MET cc_start: 0.5190 (tpt) cc_final: 0.4708 (tmt) REVERT: C 180 LEU cc_start: 0.8730 (tt) cc_final: 0.8525 (pp) REVERT: C 264 VAL cc_start: 0.7262 (p) cc_final: 0.7020 (t) REVERT: C 337 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8298 (pt0) REVERT: C 359 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7539 (mm-30) REVERT: C 367 ASP cc_start: 0.8127 (m-30) cc_final: 0.7905 (m-30) REVERT: C 379 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8728 (pt) REVERT: C 401 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8136 (mt-10) REVERT: C 422 LYS cc_start: 0.8589 (tptt) cc_final: 0.8152 (tppt) REVERT: B 29 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7849 (m-80) REVERT: B 48 LYS cc_start: 0.8113 (mtpt) cc_final: 0.7865 (mtpp) REVERT: B 114 ASP cc_start: 0.8005 (p0) cc_final: 0.7699 (p0) REVERT: B 153 SER cc_start: 0.8878 (m) cc_final: 0.8509 (t) REVERT: B 155 LEU cc_start: 0.8361 (tp) cc_final: 0.8022 (tm) REVERT: B 203 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7855 (mm-30) outliers start: 50 outliers final: 22 residues processed: 357 average time/residue: 1.2708 time to fit residues: 496.1950 Evaluate side-chains 343 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 318 time to evaluate : 1.449 ------------------------------------------------------------------------------- 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 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 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 106 ILE Chi-restraints excluded: chain C residue 309 SER 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 29 PHE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 68 optimal weight: 0.6980 chunk 116 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 84 optimal weight: 0.0770 chunk 53 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 70 optimal weight: 0.0970 chunk 49 optimal weight: 0.7980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 318 GLN ** B 120 ASN ** 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 = 0.4256 r_free = 0.4256 target = 0.156237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.119726 restraints weight = 29131.716| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 3.02 r_work: 0.3531 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14532 Z= 0.127 Angle : 0.637 13.216 19822 Z= 0.330 Chirality : 0.043 0.371 2197 Planarity : 0.004 0.048 2370 Dihedral : 14.588 149.874 2265 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 2.94 % Allowed : 18.68 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1612 helix: 1.12 (0.22), residues: 579 sheet: 0.27 (0.30), residues: 294 loop : -1.01 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 212 HIS 0.003 0.001 HIS B 16 PHE 0.025 0.001 PHE B 29 TYR 0.020 0.001 TYR C 307 ARG 0.009 0.001 ARG A 407 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 602) hydrogen bonds : angle 4.39425 ( 1697) covalent geometry : bond 0.00289 (14532) covalent geometry : angle 0.63657 (19822) *********************** 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 384 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 340 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8158 (p0) cc_final: 0.7898 (p0) REVERT: A 144 ASP cc_start: 0.8288 (t0) cc_final: 0.7668 (t0) REVERT: A 413 ASN cc_start: 0.8541 (p0) cc_final: 0.8102 (p0) REVERT: A 427 ASP cc_start: 0.7670 (m-30) cc_final: 0.7128 (t70) REVERT: A 445 LYS cc_start: 0.8525 (tppp) cc_final: 0.8289 (tppt) REVERT: A 446 ASP cc_start: 0.7813 (p0) cc_final: 0.7529 (p0) REVERT: A 729 ILE cc_start: 0.7977 (pt) cc_final: 0.7663 (pp) REVERT: A 742 ARG cc_start: 0.6313 (tpp-160) cc_final: 0.6106 (tpp-160) REVERT: A 794 VAL cc_start: 0.8059 (t) cc_final: 0.7660 (p) REVERT: A 895 MET cc_start: 0.7803 (tmt) cc_final: 0.7242 (tmm) REVERT: C 95 MET cc_start: 0.5248 (tpt) cc_final: 0.4483 (tmt) REVERT: C 179 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8191 (mp0) REVERT: C 181 TYR cc_start: 0.8622 (t80) cc_final: 0.8402 (t80) REVERT: C 299 ARG cc_start: 0.7784 (mmp80) cc_final: 0.7315 (mmp80) REVERT: C 367 ASP cc_start: 0.8143 (m-30) cc_final: 0.7906 (m-30) REVERT: C 379 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8763 (pt) REVERT: C 422 LYS cc_start: 0.8645 (tptt) cc_final: 0.8208 (tppt) REVERT: B 29 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7916 (m-80) REVERT: B 48 LYS cc_start: 0.8091 (mtpt) cc_final: 0.7817 (mtpp) REVERT: B 155 LEU cc_start: 0.8353 (tp) cc_final: 0.8036 (tm) REVERT: B 203 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7852 (mm-30) outliers start: 44 outliers final: 19 residues processed: 360 average time/residue: 1.3069 time to fit residues: 512.7589 Evaluate side-chains 346 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 325 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 347 ASP 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 824 ILE 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 36 GLU Chi-restraints excluded: chain C residue 309 SER 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 29 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 152 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 138 optimal weight: 0.0970 chunk 152 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.153085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.116375 restraints weight = 29181.225| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.05 r_work: 0.3477 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14532 Z= 0.193 Angle : 0.673 10.807 19822 Z= 0.354 Chirality : 0.044 0.171 2197 Planarity : 0.005 0.050 2370 Dihedral : 14.647 150.854 2265 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.47 % Favored : 95.41 % Rotamer: Outliers : 4.00 % Allowed : 20.15 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1612 helix: 1.00 (0.22), residues: 580 sheet: 0.17 (0.29), residues: 303 loop : -1.00 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 212 HIS 0.007 0.001 HIS A 839 PHE 0.025 0.002 PHE B 29 TYR 0.021 0.001 TYR C 307 ARG 0.010 0.001 ARG A 407 Details of bonding type rmsd hydrogen bonds : bond 0.04861 ( 602) hydrogen bonds : angle 4.48989 ( 1697) covalent geometry : bond 0.00459 (14532) covalent geometry : angle 0.67280 (19822) *********************** 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 405 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 345 time to evaluate : 1.489 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: 0.8247 (p0) cc_final: 0.7705 (OUTLIER) REVERT: A 144 ASP cc_start: 0.8356 (t0) cc_final: 0.7718 (t0) REVERT: A 174 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8670 (ptpt) REVERT: A 413 ASN cc_start: 0.8565 (p0) cc_final: 0.8108 (p0) REVERT: A 427 ASP cc_start: 0.7768 (m-30) cc_final: 0.7189 (t70) REVERT: A 446 ASP cc_start: 0.7926 (p0) cc_final: 0.7665 (p0) REVERT: A 794 VAL cc_start: 0.8157 (t) cc_final: 0.7807 (p) REVERT: A 853 MET cc_start: 0.7661 (ptp) cc_final: 0.7365 (pmm) REVERT: A 895 MET cc_start: 0.7873 (tmt) cc_final: 0.7388 (tmm) REVERT: A 974 ARG cc_start: 0.8824 (mtp180) cc_final: 0.8566 (mtp180) REVERT: A 976 THR cc_start: 0.9028 (t) cc_final: 0.8819 (t) REVERT: A 992 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8630 (t80) REVERT: C 95 MET cc_start: 0.5407 (tpt) cc_final: 0.4637 (tmt) REVERT: C 181 TYR cc_start: 0.8670 (t80) cc_final: 0.8400 (t80) REVERT: C 299 ARG cc_start: 0.7769 (mmp80) cc_final: 0.7294 (mmp80) REVERT: C 322 LYS cc_start: 0.8227 (mtmt) cc_final: 0.7991 (mmmt) REVERT: C 367 ASP cc_start: 0.8174 (m-30) cc_final: 0.7973 (m-30) REVERT: C 379 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8785 (pt) REVERT: C 380 GLU cc_start: 0.8373 (tp30) cc_final: 0.8018 (tm-30) REVERT: C 401 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8194 (mt-10) REVERT: C 422 LYS cc_start: 0.8716 (tptt) cc_final: 0.8124 (tmmt) REVERT: B 48 LYS cc_start: 0.8172 (mtpt) cc_final: 0.7878 (mtpp) REVERT: B 80 GLU cc_start: 0.6562 (tm-30) cc_final: 0.6083 (tm-30) REVERT: B 114 ASP cc_start: 0.8060 (p0) cc_final: 0.7769 (p0) REVERT: B 146 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7862 (mt0) REVERT: B 155 LEU cc_start: 0.8371 (tp) cc_final: 0.8027 (tm) REVERT: B 203 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7858 (mm-30) outliers start: 60 outliers final: 36 residues processed: 373 average time/residue: 1.3121 time to fit residues: 535.3909 Evaluate side-chains 375 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 336 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 LYS 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 696 LEU Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 812 SER 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 A residue 963 ASN Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 992 PHE Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 261 HIS Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 319 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 28 optimal weight: 0.0170 chunk 48 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 127 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN 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 = 0.154643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.118182 restraints weight = 29470.435| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 3.03 r_work: 0.3506 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14532 Z= 0.142 Angle : 0.670 11.652 19822 Z= 0.347 Chirality : 0.043 0.170 2197 Planarity : 0.004 0.048 2370 Dihedral : 14.665 151.656 2265 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.66 % Favored : 96.22 % Rotamer: Outliers : 3.14 % Allowed : 21.35 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1612 helix: 1.07 (0.22), residues: 578 sheet: 0.12 (0.29), residues: 308 loop : -0.99 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 212 HIS 0.004 0.001 HIS A 839 PHE 0.037 0.002 PHE B 29 TYR 0.027 0.001 TYR C 307 ARG 0.014 0.001 ARG C 255 Details of bonding type rmsd hydrogen bonds : bond 0.04177 ( 602) hydrogen bonds : angle 4.38944 ( 1697) covalent geometry : bond 0.00332 (14532) covalent geometry : angle 0.66952 (19822) *********************** 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 390 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 343 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8181 (p0) cc_final: 0.7649 (OUTLIER) REVERT: A 144 ASP cc_start: 0.8306 (t0) cc_final: 0.7697 (t0) REVERT: A 230 MET cc_start: 0.7757 (tmm) cc_final: 0.5767 (tmt) REVERT: A 413 ASN cc_start: 0.8499 (p0) cc_final: 0.8054 (p0) REVERT: A 427 ASP cc_start: 0.7714 (m-30) cc_final: 0.7192 (t70) REVERT: A 445 LYS cc_start: 0.8508 (tppp) cc_final: 0.8268 (tppt) REVERT: A 446 ASP cc_start: 0.7778 (p0) cc_final: 0.7525 (p0) REVERT: A 729 ILE cc_start: 0.7841 (pt) cc_final: 0.7556 (pp) REVERT: A 794 VAL cc_start: 0.8121 (t) cc_final: 0.7761 (p) REVERT: A 895 MET cc_start: 0.7908 (tmt) cc_final: 0.7365 (tmm) REVERT: A 976 THR cc_start: 0.9026 (t) cc_final: 0.8815 (t) REVERT: C 95 MET cc_start: 0.5376 (tpt) cc_final: 0.4902 (tpt) REVERT: C 154 LEU cc_start: 0.8883 (tm) cc_final: 0.8489 (pp) REVERT: C 179 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8169 (mp0) REVERT: C 181 TYR cc_start: 0.8645 (t80) cc_final: 0.8420 (t80) REVERT: C 227 ARG cc_start: 0.7824 (mmm160) cc_final: 0.7604 (mmm160) REVERT: C 299 ARG cc_start: 0.7745 (mmp80) cc_final: 0.7294 (mmp80) REVERT: B 25 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7839 (tm130) REVERT: B 48 LYS cc_start: 0.8075 (mtpt) cc_final: 0.7807 (mtpp) REVERT: B 114 ASP cc_start: 0.8051 (p0) cc_final: 0.7763 (p0) REVERT: B 146 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7845 (mt0) REVERT: B 203 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7834 (mm-30) REVERT: B 206 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8221 (p0) outliers start: 47 outliers final: 26 residues processed: 362 average time/residue: 1.3122 time to fit residues: 518.4331 Evaluate side-chains 354 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 327 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 151 LYS 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 696 LEU Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 812 SER 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 A residue 987 VAL Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 313 ILE 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 64 VAL 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 206 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 108 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 105 optimal weight: 20.0000 chunk 35 optimal weight: 0.0030 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 160 optimal weight: 0.0470 overall best weight: 0.7290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 963 ASN ** 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 = 0.4238 r_free = 0.4238 target = 0.154862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.118275 restraints weight = 29260.013| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.02 r_work: 0.3507 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14532 Z= 0.144 Angle : 0.687 15.114 19822 Z= 0.353 Chirality : 0.044 0.373 2197 Planarity : 0.004 0.050 2370 Dihedral : 14.659 152.435 2265 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.72 % Favored : 96.15 % Rotamer: Outliers : 2.60 % Allowed : 23.62 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.21), residues: 1612 helix: 1.09 (0.22), residues: 578 sheet: 0.31 (0.30), residues: 300 loop : -0.96 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 212 HIS 0.004 0.001 HIS A 839 PHE 0.026 0.001 PHE B 29 TYR 0.028 0.001 TYR C 307 ARG 0.012 0.001 ARG A 407 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 602) hydrogen bonds : angle 4.38016 ( 1697) covalent geometry : bond 0.00338 (14532) covalent geometry : angle 0.68660 (19822) *********************** 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: 39 poor density : 339 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8163 (p0) cc_final: 0.7635 (OUTLIER) REVERT: A 144 ASP cc_start: 0.8317 (t0) cc_final: 0.7702 (t0) REVERT: A 345 LYS cc_start: 0.7186 (mmmt) cc_final: 0.6918 (mmtt) REVERT: A 427 ASP cc_start: 0.7706 (m-30) cc_final: 0.7227 (t70) REVERT: A 445 LYS cc_start: 0.8495 (tppp) cc_final: 0.8188 (tppt) REVERT: A 446 ASP cc_start: 0.7702 (p0) cc_final: 0.7460 (p0) REVERT: A 723 TYR cc_start: 0.7959 (p90) cc_final: 0.7692 (p90) REVERT: A 729 ILE cc_start: 0.7860 (pt) cc_final: 0.7622 (pp) REVERT: A 781 ARG cc_start: 0.8586 (mmm-85) cc_final: 0.7927 (mmm-85) REVERT: A 794 VAL cc_start: 0.8112 (t) cc_final: 0.7748 (p) REVERT: A 834 ASP cc_start: 0.7516 (t0) cc_final: 0.7264 (t0) REVERT: A 859 MET cc_start: 0.5529 (OUTLIER) cc_final: 0.5266 (mmp) REVERT: A 895 MET cc_start: 0.7942 (tmt) cc_final: 0.7408 (tmm) REVERT: A 976 THR cc_start: 0.9029 (t) cc_final: 0.8821 (t) REVERT: C 95 MET cc_start: 0.5434 (tpt) cc_final: 0.4945 (tpt) REVERT: C 131 LEU cc_start: 0.6112 (mt) cc_final: 0.5875 (mt) REVERT: C 154 LEU cc_start: 0.8888 (tm) cc_final: 0.8485 (pp) REVERT: C 179 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8195 (mp0) REVERT: C 218 MET cc_start: 0.5451 (ppp) cc_final: 0.5005 (ppp) REVERT: C 227 ARG cc_start: 0.7819 (mmm160) cc_final: 0.7612 (mmm160) REVERT: C 299 ARG cc_start: 0.7801 (mmp80) cc_final: 0.7335 (mmp80) REVERT: B 48 LYS cc_start: 0.8048 (mtpt) cc_final: 0.7797 (mtpp) REVERT: B 114 ASP cc_start: 0.8023 (p0) cc_final: 0.7748 (p0) REVERT: B 146 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7822 (mt0) REVERT: B 155 LEU cc_start: 0.8384 (tp) cc_final: 0.8079 (tm) outliers start: 39 outliers final: 26 residues processed: 358 average time/residue: 1.3179 time to fit residues: 517.2822 Evaluate side-chains 355 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 328 time to evaluate : 1.833 ------------------------------------------------------------------------------- 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 104 MET Chi-restraints excluded: chain A residue 151 LYS 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 696 LEU Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 812 SER 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 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 313 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 64 VAL 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 201 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 65 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 82 optimal weight: 0.0170 chunk 32 optimal weight: 0.5980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 963 ASN ** 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 = 0.4247 r_free = 0.4247 target = 0.155659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.119104 restraints weight = 29109.110| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 3.03 r_work: 0.3520 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14532 Z= 0.140 Angle : 0.698 13.562 19822 Z= 0.357 Chirality : 0.044 0.381 2197 Planarity : 0.005 0.062 2370 Dihedral : 14.671 153.281 2265 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.54 % Favored : 96.34 % Rotamer: Outliers : 3.14 % Allowed : 23.95 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1612 helix: 1.05 (0.22), residues: 586 sheet: 0.19 (0.28), residues: 335 loop : -0.99 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 212 HIS 0.003 0.001 HIS A 170 PHE 0.027 0.002 PHE C 104 TYR 0.030 0.001 TYR C 307 ARG 0.018 0.001 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 602) hydrogen bonds : angle 4.31072 ( 1697) covalent geometry : bond 0.00329 (14532) covalent geometry : angle 0.69835 (19822) *********************** 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 380 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 333 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8004 (mp0) REVERT: A 105 ASP cc_start: 0.8170 (p0) cc_final: 0.7632 (OUTLIER) REVERT: A 144 ASP cc_start: 0.8310 (t0) cc_final: 0.7639 (t0) REVERT: A 283 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8556 (mptp) REVERT: A 427 ASP cc_start: 0.7742 (m-30) cc_final: 0.7218 (t70) REVERT: A 445 LYS cc_start: 0.8513 (tppp) cc_final: 0.8196 (tppt) REVERT: A 446 ASP cc_start: 0.7670 (p0) cc_final: 0.7441 (p0) REVERT: A 723 TYR cc_start: 0.7970 (p90) cc_final: 0.7714 (p90) REVERT: A 729 ILE cc_start: 0.7896 (pt) cc_final: 0.7644 (pp) REVERT: A 794 VAL cc_start: 0.8050 (t) cc_final: 0.7680 (p) REVERT: A 834 ASP cc_start: 0.7486 (t0) cc_final: 0.7200 (t0) REVERT: A 842 MET cc_start: 0.8371 (tpt) cc_final: 0.8088 (tpt) REVERT: A 859 MET cc_start: 0.5404 (OUTLIER) cc_final: 0.5074 (mmp) REVERT: A 895 MET cc_start: 0.7933 (tmt) cc_final: 0.7395 (tmm) REVERT: C 95 MET cc_start: 0.5420 (tpt) cc_final: 0.4732 (tpt) REVERT: C 154 LEU cc_start: 0.8881 (tm) cc_final: 0.8497 (pp) REVERT: C 179 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8199 (mp0) REVERT: C 208 GLN cc_start: 0.8327 (pm20) cc_final: 0.8118 (pm20) REVERT: C 218 MET cc_start: 0.5340 (ppp) cc_final: 0.4866 (ppp) REVERT: C 224 LYS cc_start: 0.8206 (pttm) cc_final: 0.7921 (pttm) REVERT: C 299 ARG cc_start: 0.7754 (mmp80) cc_final: 0.7320 (mmp80) REVERT: B 16 HIS cc_start: 0.7711 (t70) cc_final: 0.6973 (t-90) REVERT: B 114 ASP cc_start: 0.8071 (p0) cc_final: 0.7782 (p0) REVERT: B 153 SER cc_start: 0.8835 (m) cc_final: 0.8485 (t) REVERT: B 203 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7867 (mm-30) outliers start: 47 outliers final: 26 residues processed: 358 average time/residue: 1.3787 time to fit residues: 544.3968 Evaluate side-chains 353 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 326 time to evaluate : 1.602 ------------------------------------------------------------------------------- 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 104 MET Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 347 ASP 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 859 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 36 GLU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 55 GLN 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 201 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 40 optimal weight: 0.0670 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 158 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 144 optimal weight: 0.2980 chunk 37 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 ASN B 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.156021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.119495 restraints weight = 28908.685| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 3.01 r_work: 0.3527 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14532 Z= 0.141 Angle : 0.719 12.757 19822 Z= 0.368 Chirality : 0.044 0.338 2197 Planarity : 0.005 0.069 2370 Dihedral : 14.692 154.172 2265 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.03 % Favored : 95.84 % Rotamer: Outliers : 2.33 % Allowed : 25.55 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1612 helix: 1.10 (0.22), residues: 580 sheet: 0.15 (0.28), residues: 339 loop : -1.00 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 212 HIS 0.004 0.001 HIS A 839 PHE 0.017 0.001 PHE B 49 TYR 0.033 0.001 TYR C 307 ARG 0.016 0.001 ARG A 870 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 602) hydrogen bonds : angle 4.29147 ( 1697) covalent geometry : bond 0.00333 (14532) covalent geometry : angle 0.71923 (19822) *********************** 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 367 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 332 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8001 (mp0) REVERT: A 105 ASP cc_start: 0.8157 (p0) cc_final: 0.7609 (OUTLIER) REVERT: A 144 ASP cc_start: 0.8336 (t0) cc_final: 0.7673 (t0) REVERT: A 230 MET cc_start: 0.7753 (tmm) cc_final: 0.7241 (tpt) REVERT: A 283 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8536 (mttp) REVERT: A 416 LYS cc_start: 0.8377 (ttpt) cc_final: 0.8133 (tmmt) REVERT: A 427 ASP cc_start: 0.7719 (m-30) cc_final: 0.7255 (t70) REVERT: A 445 LYS cc_start: 0.8542 (tppp) cc_final: 0.8208 (tppt) REVERT: A 446 ASP cc_start: 0.7628 (p0) cc_final: 0.7427 (p0) REVERT: A 455 MET cc_start: 0.8581 (mtp) cc_final: 0.8371 (mtp) REVERT: A 729 ILE cc_start: 0.7932 (pt) cc_final: 0.7700 (pp) REVERT: A 781 ARG cc_start: 0.8529 (mmm-85) cc_final: 0.7822 (mmm-85) REVERT: A 794 VAL cc_start: 0.8027 (t) cc_final: 0.7659 (p) REVERT: A 805 LYS cc_start: 0.8448 (mtpp) cc_final: 0.8248 (mtpt) REVERT: A 832 ARG cc_start: 0.8012 (ttm-80) cc_final: 0.7374 (ttp80) REVERT: A 834 ASP cc_start: 0.7470 (t0) cc_final: 0.7241 (t0) REVERT: A 859 MET cc_start: 0.5210 (OUTLIER) cc_final: 0.4837 (mmp) REVERT: A 895 MET cc_start: 0.7922 (tmt) cc_final: 0.7381 (tmm) REVERT: C 95 MET cc_start: 0.5400 (tpt) cc_final: 0.4558 (tpt) REVERT: C 154 LEU cc_start: 0.8884 (tm) cc_final: 0.8505 (pp) REVERT: C 179 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8206 (mp0) REVERT: C 218 MET cc_start: 0.5290 (ppp) cc_final: 0.4782 (ppp) REVERT: C 299 ARG cc_start: 0.7745 (mmp80) cc_final: 0.7336 (mmp80) REVERT: C 346 ARG cc_start: 0.7223 (pmm-80) cc_final: 0.6979 (pmm-80) REVERT: B 16 HIS cc_start: 0.7750 (t70) cc_final: 0.7038 (t-90) REVERT: B 29 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.8042 (t80) REVERT: B 55 GLN cc_start: 0.6685 (OUTLIER) cc_final: 0.5999 (mm110) REVERT: B 114 ASP cc_start: 0.8090 (p0) cc_final: 0.7795 (p0) REVERT: B 202 LEU cc_start: 0.8312 (tt) cc_final: 0.7908 (pp) REVERT: B 203 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7645 (mm-30) outliers start: 35 outliers final: 26 residues processed: 348 average time/residue: 1.3434 time to fit residues: 511.3632 Evaluate side-chains 350 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 321 time to evaluate : 1.405 ------------------------------------------------------------------------------- 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 104 MET Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 812 SER 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 A residue 944 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 55 GLN 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 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 89 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 92 optimal weight: 0.0000 chunk 30 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.0060 overall best weight: 0.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 ASN B 52 GLN B 206 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.156372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.119957 restraints weight = 28909.557| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 3.02 r_work: 0.3533 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3412 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= 0.142 Angle : 0.746 13.863 19822 Z= 0.378 Chirality : 0.044 0.328 2197 Planarity : 0.005 0.064 2370 Dihedral : 14.717 155.155 2265 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.97 % Favored : 95.91 % Rotamer: Outliers : 2.00 % Allowed : 26.35 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.21), residues: 1612 helix: 1.09 (0.22), residues: 579 sheet: 0.10 (0.28), residues: 341 loop : -1.01 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 212 HIS 0.003 0.001 HIS A 170 PHE 0.025 0.001 PHE A 958 TYR 0.029 0.001 TYR C 307 ARG 0.023 0.001 ARG C 255 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 602) hydrogen bonds : angle 4.28536 ( 1697) covalent geometry : bond 0.00337 (14532) covalent geometry : angle 0.74553 (19822) ********************** 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 354 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 324 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7971 (mp0) REVERT: A 105 ASP cc_start: 0.8156 (p0) cc_final: 0.7901 (p0) REVERT: A 144 ASP cc_start: 0.8295 (t0) cc_final: 0.7610 (t0) REVERT: A 283 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8593 (mttp) REVERT: A 427 ASP cc_start: 0.7701 (m-30) cc_final: 0.7271 (t70) REVERT: A 445 LYS cc_start: 0.8521 (tppp) cc_final: 0.8194 (tppt) REVERT: A 573 VAL cc_start: 0.8799 (m) cc_final: 0.8539 (t) REVERT: A 636 ARG cc_start: 0.8364 (tmm-80) cc_final: 0.8050 (ttt180) REVERT: A 729 ILE cc_start: 0.7915 (pt) cc_final: 0.7658 (pp) REVERT: A 794 VAL cc_start: 0.8014 (t) cc_final: 0.7644 (p) REVERT: A 832 ARG cc_start: 0.8018 (ttm-80) cc_final: 0.7409 (ttp80) REVERT: A 834 ASP cc_start: 0.7434 (t0) cc_final: 0.7109 (t0) REVERT: A 859 MET cc_start: 0.4945 (OUTLIER) cc_final: 0.4542 (mmp) REVERT: A 895 MET cc_start: 0.7915 (tmt) cc_final: 0.7378 (tmm) REVERT: A 976 THR cc_start: 0.8995 (t) cc_final: 0.8785 (t) REVERT: C 95 MET cc_start: 0.5397 (tpt) cc_final: 0.4471 (tpt) REVERT: C 104 PHE cc_start: 0.6846 (t80) cc_final: 0.6531 (p90) REVERT: C 154 LEU cc_start: 0.8915 (tm) cc_final: 0.8535 (pp) REVERT: C 218 MET cc_start: 0.5142 (ppp) cc_final: 0.4789 (ppp) REVERT: C 255 ARG cc_start: 0.8208 (tpt90) cc_final: 0.7930 (ptm-80) REVERT: C 299 ARG cc_start: 0.7748 (mmp80) cc_final: 0.7376 (mmp80) REVERT: C 346 ARG cc_start: 0.7174 (pmm-80) cc_final: 0.6953 (pmm-80) REVERT: C 378 LYS cc_start: 0.8281 (ptmm) cc_final: 0.7717 (ttpp) REVERT: B 16 HIS cc_start: 0.7775 (t70) cc_final: 0.7018 (t-90) REVERT: B 29 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.8090 (t80) REVERT: B 48 LYS cc_start: 0.8160 (mtpt) cc_final: 0.7841 (mtpp) REVERT: B 55 GLN cc_start: 0.6661 (OUTLIER) cc_final: 0.6018 (mm110) REVERT: B 114 ASP cc_start: 0.8088 (p0) cc_final: 0.7798 (p0) REVERT: B 146 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7812 (mt0) REVERT: B 202 LEU cc_start: 0.8225 (tt) cc_final: 0.8001 (pp) outliers start: 30 outliers final: 23 residues processed: 339 average time/residue: 1.4453 time to fit residues: 534.1274 Evaluate side-chains 348 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 320 time to evaluate : 1.573 ------------------------------------------------------------------------------- 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 104 MET Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 812 SER 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 A residue 944 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 64 VAL 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 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 51 optimal weight: 0.7980 chunk 50 optimal weight: 0.0370 chunk 83 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 963 ASN ** B 25 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 = 0.4245 r_free = 0.4245 target = 0.155553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.119038 restraints weight = 29049.547| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 3.03 r_work: 0.3519 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14532 Z= 0.151 Angle : 0.740 12.486 19822 Z= 0.379 Chirality : 0.045 0.300 2197 Planarity : 0.005 0.076 2370 Dihedral : 14.756 156.241 2265 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.22 % Favored : 95.66 % Rotamer: Outliers : 2.60 % Allowed : 25.82 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1612 helix: 1.02 (0.22), residues: 583 sheet: 0.29 (0.29), residues: 315 loop : -0.98 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 212 HIS 0.004 0.001 HIS A 839 PHE 0.028 0.001 PHE A 992 TYR 0.033 0.001 TYR B 156 ARG 0.022 0.001 ARG C 255 Details of bonding type rmsd hydrogen bonds : bond 0.04211 ( 602) hydrogen bonds : angle 4.34035 ( 1697) covalent geometry : bond 0.00361 (14532) covalent geometry : angle 0.73978 (19822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13699.36 seconds wall clock time: 235 minutes 50.32 seconds (14150.32 seconds total)