Starting phenix.real_space_refine on Tue Jan 21 09:44:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bfm_44500/01_2025/9bfm_44500_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bfm_44500/01_2025/9bfm_44500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bfm_44500/01_2025/9bfm_44500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bfm_44500/01_2025/9bfm_44500.map" model { file = "/net/cci-nas-00/data/ceres_data/9bfm_44500/01_2025/9bfm_44500_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bfm_44500/01_2025/9bfm_44500_trim.cif" } resolution = 2.71 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= 0.002 sd= 0.080 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 23530 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: 7 Type Number sf(0) Gaussians S 132 5.16 5 Cl 2 4.86 5 C 15187 2.51 5 N 3891 2.21 5 O 4382 1.98 5 F 3 1.80 5 H 24012 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 47609 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 15877 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1034, 15857 Classifications: {'peptide': 1034} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 988} Conformer: "B" Number of residues, atoms: 1034, 15857 Classifications: {'peptide': 1034} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 988} bond proxies already assigned to first conformer: 15985 Chain: "B" Number of atoms: 15850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 15850 Classifications: {'peptide': 1033} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 987} Chain: "C" Number of atoms: 15849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 15849 Classifications: {'peptide': 1033} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 987} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {'A1AON': 1} Classifications: {'undetermined': 1, 'water': 3} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 617 " occ=0.50 ... (38 atoms not shown) pdb=" HZ BPHE A 617 " occ=0.50 Time building chain proxies: 20.16, per 1000 atoms: 0.42 Number of scatterers: 47609 At special positions: 0 Unit cell: (113.42, 124.12, 146.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 2 17.00 S 132 16.00 F 3 9.00 O 4382 8.00 N 3891 7.00 C 15187 6.00 H 24012 1.00 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: 9.49 Conformation dependent library (CDL) restraints added in 3.9 seconds 6194 Ramachandran restraints generated. 3097 Oldfield, 0 Emsley, 3097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5668 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 24 sheets defined 60.2% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 Processing helix chain 'A' and resid 8 through 30 Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 99 through 115 Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 150 through 169 removed outlier: 4.279A pdb=" N LYS A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA A 165 " --> pdb=" O ASN A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 329 through 360 Processing helix chain 'A' and resid 361 through 386 removed outlier: 3.595A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 424 removed outlier: 4.255A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 454 removed outlier: 5.398A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 461 through 497 removed outlier: 3.668A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 511 through 535 Processing helix chain 'A' and resid 537 through 558 removed outlier: 3.804A pdb=" N TYR A 541 " --> pdb=" O SER A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 601 Processing helix chain 'A' and resid 633 through 637 Processing helix chain 'A' and resid 643 through 656 Processing helix chain 'A' and resid 691 through 708 Processing helix chain 'A' and resid 732 through 739 Processing helix chain 'A' and resid 742 through 755 Processing helix chain 'A' and resid 777 through 780 Processing helix chain 'A' and resid 782 through 788 Processing helix chain 'A' and resid 836 through 849 Processing helix chain 'A' and resid 861 through 869 Processing helix chain 'A' and resid 871 through 893 removed outlier: 4.086A pdb=" N SER A 875 " --> pdb=" O ASN A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 903 removed outlier: 4.220A pdb=" N SER A 900 " --> pdb=" O SER A 896 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 901 " --> pdb=" O ILE A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 919 removed outlier: 3.851A pdb=" N GLY A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 956 Processing helix chain 'A' and resid 959 through 992 removed outlier: 4.801A pdb=" N ARG A 973 " --> pdb=" O ARG A 969 " (cutoff:3.500A) Proline residue: A 974 - end of helix removed outlier: 3.711A pdb=" N ALA A 981 " --> pdb=" O MET A 977 " (cutoff:3.500A) Proline residue: A 988 - end of helix Processing helix chain 'A' and resid 996 through 1033 removed outlier: 4.203A pdb=" N GLY A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A1007 " --> pdb=" O VAL A1003 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE A1020 " --> pdb=" O VAL A1016 " (cutoff:3.500A) Proline residue: A1023 - end of helix Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 8 through 29 Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.617A pdb=" N ASN B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 115 removed outlier: 4.044A pdb=" N LEU B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 298 through 314 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 329 through 360 Processing helix chain 'B' and resid 361 through 387 removed outlier: 3.935A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 424 removed outlier: 4.183A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 454 removed outlier: 5.520A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 459 removed outlier: 3.632A pdb=" N PHE B 459 " --> pdb=" O MET B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 497 removed outlier: 4.446A pdb=" N ILE B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 510 through 535 removed outlier: 3.921A pdb=" N GLY B 514 " --> pdb=" O LYS B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 558 removed outlier: 3.694A pdb=" N TYR B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 558 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 601 removed outlier: 3.537A pdb=" N THR B 587 " --> pdb=" O THR B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 637 Processing helix chain 'B' and resid 643 through 656 Processing helix chain 'B' and resid 691 through 707 Processing helix chain 'B' and resid 732 through 739 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 777 through 780 Processing helix chain 'B' and resid 782 through 788 Processing helix chain 'B' and resid 836 through 849 Processing helix chain 'B' and resid 860 through 869 removed outlier: 3.936A pdb=" N GLN B 865 " --> pdb=" O GLY B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 893 Processing helix chain 'B' and resid 897 through 903 removed outlier: 3.867A pdb=" N VAL B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 920 removed outlier: 3.663A pdb=" N VAL B 909 " --> pdb=" O VAL B 905 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLY B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 957 Processing helix chain 'B' and resid 959 through 992 removed outlier: 4.844A pdb=" N ARG B 973 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Proline residue: B 974 - end of helix Proline residue: B 988 - end of helix Processing helix chain 'B' and resid 998 through 1033 removed outlier: 3.954A pdb=" N ILE B1019 " --> pdb=" O THR B1015 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE B1020 " --> pdb=" O VAL B1016 " (cutoff:3.500A) Proline residue: B1023 - end of helix Processing helix chain 'C' and resid 2 through 7 removed outlier: 3.684A pdb=" N ASP C 7 " --> pdb=" O ASN C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 30 Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 61 through 68 removed outlier: 4.013A pdb=" N ASN C 68 " --> pdb=" O VAL C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 removed outlier: 4.084A pdb=" N LEU C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 298 through 314 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 329 through 360 Processing helix chain 'C' and resid 361 through 370 Proline residue: C 368 - end of helix Processing helix chain 'C' and resid 370 through 386 removed outlier: 3.551A pdb=" N VAL C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 424 removed outlier: 4.251A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASP C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ALA C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 452 removed outlier: 6.121A pdb=" N GLY C 440 " --> pdb=" O GLY C 436 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ALA C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 459 removed outlier: 3.578A pdb=" N PHE C 459 " --> pdb=" O MET C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 496 removed outlier: 3.814A pdb=" N GLN C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 511 through 537 removed outlier: 3.663A pdb=" N TRP C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 537 " --> pdb=" O GLY C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 559 removed outlier: 3.683A pdb=" N VAL C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 544 " --> pdb=" O ARG C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 601 Processing helix chain 'C' and resid 633 through 637 Processing helix chain 'C' and resid 639 through 642 Processing helix chain 'C' and resid 643 through 656 Processing helix chain 'C' and resid 691 through 708 Processing helix chain 'C' and resid 732 through 740 Processing helix chain 'C' and resid 742 through 755 Processing helix chain 'C' and resid 777 through 780 Processing helix chain 'C' and resid 782 through 788 Processing helix chain 'C' and resid 836 through 849 Processing helix chain 'C' and resid 861 through 893 Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 895 through 903 removed outlier: 3.660A pdb=" N PHE C 899 " --> pdb=" O TRP C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 920 removed outlier: 3.631A pdb=" N GLY C 908 " --> pdb=" O VAL C 904 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY C 911 " --> pdb=" O LEU C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 957 removed outlier: 3.832A pdb=" N ILE C 945 " --> pdb=" O ASN C 941 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 991 removed outlier: 5.118A pdb=" N ARG C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Proline residue: C 974 - end of helix Proline residue: C 988 - end of helix Processing helix chain 'C' and resid 996 through 1017 removed outlier: 3.720A pdb=" N GLN C1000 " --> pdb=" O GLY C 996 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL C1007 " --> pdb=" O VAL C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1033 Proline residue: C1023 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.081A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 12.243A pdb=" N ARG A 815 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N GLU A 826 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLU A 826 " --> pdb=" O PRO A 718 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU A 828 " --> pdb=" O VAL A 716 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL A 716 " --> pdb=" O LEU A 828 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.081A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 12.243A pdb=" N ARG A 815 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N GLU A 826 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 178 removed outlier: 3.651A pdb=" N GLY A 288 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL A 139 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 266 through 272 removed outlier: 7.532A pdb=" N TYR A 182 " --> pdb=" O LYS A 770 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N TYR A 772 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N MET A 184 " --> pdb=" O TYR A 772 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N MET A 774 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE A 186 " --> pdb=" O MET A 774 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN A 760 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A 773 " --> pdb=" O TYR A 758 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N TYR A 758 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 218 through 219 removed outlier: 6.635A pdb=" N SER A 233 " --> pdb=" O PHE C 727 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE C 729 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE A 235 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ILE C 731 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 250 through 253 removed outlier: 7.193A pdb=" N VAL A 260 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 278 through 281 removed outlier: 3.503A pdb=" N SER A 608 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 805 through 812 removed outlier: 8.255A pdb=" N ILE B 235 " --> pdb=" O PRO A 725 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE A 727 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 790 through 792 Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 131 removed outlier: 3.672A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 12.185A pdb=" N ARG B 815 " --> pdb=" O GLU B 826 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N GLU B 826 " --> pdb=" O ARG B 815 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLU B 826 " --> pdb=" O PRO B 718 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU B 828 " --> pdb=" O VAL B 716 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL B 716 " --> pdb=" O LEU B 828 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 128 through 131 removed outlier: 3.672A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 12.185A pdb=" N ARG B 815 " --> pdb=" O GLU B 826 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N GLU B 826 " --> pdb=" O ARG B 815 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177 removed outlier: 4.761A pdb=" N ASN B 144 " --> pdb=" O PRO B 285 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL B 139 " --> pdb=" O PRO B 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.930A pdb=" N ALA B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N THR B 624 " --> pdb=" O GLY B 614 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 266 through 272 removed outlier: 7.528A pdb=" N TYR B 182 " --> pdb=" O LYS B 770 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N TYR B 772 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N MET B 184 " --> pdb=" O TYR B 772 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N MET B 774 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ILE B 186 " --> pdb=" O MET B 774 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN B 760 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL B 773 " --> pdb=" O TYR B 758 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N TYR B 758 " --> pdb=" O VAL B 773 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 250 through 253 removed outlier: 6.917A pdb=" N VAL B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 805 through 812 removed outlier: 8.697A pdb=" N ILE C 235 " --> pdb=" O PRO B 725 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE B 727 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLY C 217 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 790 through 792 Processing sheet with id=AB9, first strand: chain 'C' and resid 128 through 132 removed outlier: 4.400A pdb=" N ALA C 42 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 11.983A pdb=" N ARG C 815 " --> pdb=" O GLU C 826 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N GLU C 826 " --> pdb=" O ARG C 815 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU C 817 " --> pdb=" O SER C 824 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN C 830 " --> pdb=" O SER C 715 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N SER C 715 " --> pdb=" O GLN C 830 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 128 through 132 removed outlier: 4.400A pdb=" N ALA C 42 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 11.983A pdb=" N ARG C 815 " --> pdb=" O GLU C 826 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N GLU C 826 " --> pdb=" O ARG C 815 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU C 817 " --> pdb=" O SER C 824 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY C 829 " --> pdb=" O PHE C 680 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 172 through 177 removed outlier: 5.797A pdb=" N LYS C 292 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL C 175 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY C 290 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU C 177 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLY C 288 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN C 144 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET C 138 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL C 139 " --> pdb=" O PRO C 326 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 172 through 177 removed outlier: 5.797A pdb=" N LYS C 292 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL C 175 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY C 290 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU C 177 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLY C 288 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 266 through 270 removed outlier: 5.954A pdb=" N MET C 184 " --> pdb=" O TYR C 772 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N MET C 774 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE C 186 " --> pdb=" O MET C 774 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN C 760 " --> pdb=" O VAL C 771 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C 773 " --> pdb=" O TYR C 758 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N TYR C 758 " --> pdb=" O VAL C 773 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 250 through 253 removed outlier: 7.043A pdb=" N VAL C 260 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 790 through 792 1656 hydrogen bonds defined for protein. 4791 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 18.35 Time building geometry restraints manager: 11.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 24006 1.02 - 1.22: 43 1.22 - 1.41: 9485 1.41 - 1.61: 14266 1.61 - 1.81: 260 Bond restraints: 48060 Sorted by residual: bond pdb=" C13 A1AON A1101 " pdb=" N14 A1AON A1101 " ideal model delta sigma weight residual 1.443 1.216 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" ND2 ASN A 254 " pdb="HD22 ASN A 254 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" ND2 ASN A 254 " pdb="HD21 ASN A 254 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CA GLY A 217 " pdb=" C GLY A 217 " ideal model delta sigma weight residual 1.515 1.451 0.064 1.12e-02 7.97e+03 3.27e+01 bond pdb=" NE ARG A 259 " pdb=" HE ARG A 259 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 48055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 86876 3.01 - 6.02: 267 6.02 - 9.03: 15 9.03 - 12.04: 3 12.04 - 15.05: 2 Bond angle restraints: 87163 Sorted by residual: angle pdb=" N LYS A 510 " pdb=" CA LYS A 510 " pdb=" C LYS A 510 " ideal model delta sigma weight residual 111.36 126.41 -15.05 1.09e+00 8.42e-01 1.91e+02 angle pdb=" N LYS A 226 " pdb=" CA LYS A 226 " pdb=" C LYS A 226 " ideal model delta sigma weight residual 111.28 121.67 -10.39 1.09e+00 8.42e-01 9.09e+01 angle pdb=" N ARG A 620 " pdb=" CA ARG A 620 " pdb=" C ARG A 620 " ideal model delta sigma weight residual 110.80 96.66 14.14 2.13e+00 2.20e-01 4.41e+01 angle pdb=" N GLY A 616 " pdb=" CA GLY A 616 " pdb=" C GLY A 616 " ideal model delta sigma weight residual 111.03 101.50 9.53 1.49e+00 4.50e-01 4.09e+01 angle pdb=" N ALA A 501 " pdb=" CA ALA A 501 " pdb=" C ALA A 501 " ideal model delta sigma weight residual 110.53 118.80 -8.27 1.32e+00 5.74e-01 3.93e+01 ... (remaining 87158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 20527 17.95 - 35.91: 1440 35.91 - 53.86: 478 53.86 - 71.81: 122 71.81 - 89.76: 18 Dihedral angle restraints: 22585 sinusoidal: 12373 harmonic: 10212 Sorted by residual: dihedral pdb=" CA GLN C 437 " pdb=" C GLN C 437 " pdb=" N ILE C 438 " pdb=" CA ILE C 438 " ideal model delta harmonic sigma weight residual -180.00 -161.22 -18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA GLN B 437 " pdb=" C GLN B 437 " pdb=" N ILE B 438 " pdb=" CA ILE B 438 " ideal model delta harmonic sigma weight residual -180.00 -162.39 -17.61 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ASP B 761 " pdb=" CB ASP B 761 " pdb=" CG ASP B 761 " pdb=" OD1 ASP B 761 " ideal model delta sinusoidal sigma weight residual -30.00 -89.69 59.69 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 22582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3675 0.101 - 0.202: 151 0.202 - 0.304: 11 0.304 - 0.405: 2 0.405 - 0.506: 2 Chirality restraints: 3841 Sorted by residual: chirality pdb=" CA LYS A 510 " pdb=" N LYS A 510 " pdb=" C LYS A 510 " pdb=" CB LYS A 510 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.40e+00 chirality pdb=" CB VAL A 225 " pdb=" CA VAL A 225 " pdb=" CG1 VAL A 225 " pdb=" CG2 VAL A 225 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CA GLU B 673 " pdb=" N GLU B 673 " pdb=" C GLU B 673 " pdb=" CB GLU B 673 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.87e+00 ... (remaining 3838 not shown) Planarity restraints: 7139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 255 " 0.194 2.00e-02 2.50e+03 2.28e-01 7.81e+02 pdb=" CD GLN A 255 " -0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN A 255 " -0.191 2.00e-02 2.50e+03 pdb=" NE2 GLN A 255 " 0.003 2.00e-02 2.50e+03 pdb="HE21 GLN A 255 " -0.342 2.00e-02 2.50e+03 pdb="HE22 GLN A 255 " 0.348 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 254 " -0.210 2.00e-02 2.50e+03 2.16e-01 6.98e+02 pdb=" CG ASN A 254 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 254 " 0.205 2.00e-02 2.50e+03 pdb=" ND2 ASN A 254 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN A 254 " 0.307 2.00e-02 2.50e+03 pdb="HD22 ASN A 254 " -0.314 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 213 " -0.123 2.00e-02 2.50e+03 1.38e-01 2.87e+02 pdb=" CD GLN A 213 " -0.000 2.00e-02 2.50e+03 pdb=" OE1 GLN A 213 " 0.126 2.00e-02 2.50e+03 pdb=" NE2 GLN A 213 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN A 213 " 0.205 2.00e-02 2.50e+03 pdb="HE22 GLN A 213 " -0.205 2.00e-02 2.50e+03 ... (remaining 7136 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1311 2.15 - 2.76: 92429 2.76 - 3.38: 141470 3.38 - 3.99: 183511 3.99 - 4.60: 289308 Nonbonded interactions: 708029 Sorted by model distance: nonbonded pdb=" OD2 ASP C 202 " pdb="HH12 ARG C 792 " model vdw 1.539 2.450 nonbonded pdb=" O LYS B 522 " pdb=" HD1 HIS B 526 " model vdw 1.594 2.450 nonbonded pdb=" HH TYR A 527 " pdb=" O ILE A1019 " model vdw 1.601 2.450 nonbonded pdb=" HZ3 LYS C 342 " pdb=" OE2 GLU C 346 " model vdw 1.610 2.450 nonbonded pdb=" O ASN C 361 " pdb=" HG1 THR C 365 " model vdw 1.635 2.450 ... (remaining 708024 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 440 or (resid 441 and (name N or name CA or name \ C or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or resi \ d 442 through 616 or resid 618 through 1033)) selection = (chain 'B' and (resid 1 through 108 or (resid 109 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ )) or resid 110 through 440 or (resid 441 and (name N or name CA or name C or na \ me O or name CB or name HA or name HB1 or name HB2 or name HB3)) or resid 442 th \ rough 616 or resid 618 through 1033)) selection = (chain 'C' and (resid 1 through 108 or (resid 109 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ )) or resid 110 through 616 or resid 618 through 1033)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.320 Construct map_model_manager: 0.610 Extract box with map and model: 1.280 Check model and map are aligned: 0.270 Set scattering table: 0.320 Process input model: 83.770 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.227 24048 Z= 0.288 Angle : 0.583 15.046 32661 Z= 0.339 Chirality : 0.045 0.506 3841 Planarity : 0.004 0.054 4176 Dihedral : 13.662 89.764 8706 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.36 (0.15), residues: 3097 helix: 2.63 (0.12), residues: 1697 sheet: 0.02 (0.25), residues: 407 loop : 0.43 (0.21), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 789 HIS 0.004 0.000 HIS A 505 PHE 0.023 0.001 PHE A 680 TYR 0.024 0.001 TYR B 49 ARG 0.004 0.000 ARG B 239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6194 Ramachandran restraints generated. 3097 Oldfield, 0 Emsley, 3097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6194 Ramachandran restraints generated. 3097 Oldfield, 0 Emsley, 3097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 402 time to evaluate : 2.718 Fit side-chains REVERT: A 522 LYS cc_start: 0.8015 (ttpp) cc_final: 0.7734 (ttpt) REVERT: B 547 ILE cc_start: 0.8606 (mt) cc_final: 0.8310 (mp) REVERT: C 1008 MET cc_start: 0.8677 (ttt) cc_final: 0.8470 (ttt) outliers start: 3 outliers final: 2 residues processed: 405 average time/residue: 2.3440 time to fit residues: 1100.1897 Evaluate side-chains 333 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 331 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 676 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 1.9990 chunk 234 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 180 optimal weight: 0.5980 chunk 280 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.099305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.082705 restraints weight = 86320.918| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.55 r_work: 0.2885 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24048 Z= 0.205 Angle : 0.506 5.487 32661 Z= 0.270 Chirality : 0.040 0.156 3841 Planarity : 0.004 0.049 4176 Dihedral : 4.835 73.981 3320 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.87 % Allowed : 6.87 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.26 (0.15), residues: 3097 helix: 2.56 (0.12), residues: 1712 sheet: 0.07 (0.25), residues: 391 loop : 0.27 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 789 HIS 0.001 0.000 HIS B 526 PHE 0.016 0.001 PHE A 682 TYR 0.016 0.001 TYR A 541 ARG 0.007 0.000 ARG C 558 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6194 Ramachandran restraints generated. 3097 Oldfield, 0 Emsley, 3097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6194 Ramachandran restraints generated. 3097 Oldfield, 0 Emsley, 3097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 341 time to evaluate : 2.717 Fit side-chains REVERT: A 176 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7639 (tm-30) REVERT: A 268 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8581 (mm) REVERT: A 522 LYS cc_start: 0.7865 (ttpp) cc_final: 0.7522 (ttpt) REVERT: A 712 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6889 (mtm) REVERT: A 761 ASP cc_start: 0.8685 (m-30) cc_final: 0.8397 (m-30) REVERT: A 784 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8211 (t0) REVERT: A 966 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.7924 (t0) REVERT: A 1032 ARG cc_start: 0.7338 (mtm-85) cc_final: 0.7045 (ttp-170) REVERT: B 192 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8329 (mm-30) REVERT: B 197 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8368 (mp-120) REVERT: B 547 ILE cc_start: 0.8526 (mt) cc_final: 0.8162 (mp) REVERT: B 962 GLU cc_start: 0.7840 (tt0) cc_final: 0.7634 (tm-30) REVERT: C 620 ARG cc_start: 0.8275 (mtt-85) cc_final: 0.8030 (mtt90) REVERT: C 693 GLU cc_start: 0.7859 (tp30) cc_final: 0.7638 (tp30) outliers start: 21 outliers final: 6 residues processed: 354 average time/residue: 2.4072 time to fit residues: 989.4578 Evaluate side-chains 336 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 324 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain C residue 806 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 71 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 231 optimal weight: 0.8980 chunk 242 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.098338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.081498 restraints weight = 90864.563| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.60 r_work: 0.2865 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24048 Z= 0.234 Angle : 0.496 5.408 32661 Z= 0.264 Chirality : 0.040 0.148 3841 Planarity : 0.004 0.056 4176 Dihedral : 4.743 65.773 3320 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.07 % Allowed : 7.46 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.13 (0.15), residues: 3097 helix: 2.48 (0.12), residues: 1713 sheet: 0.05 (0.25), residues: 382 loop : 0.14 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 789 HIS 0.002 0.000 HIS B 709 PHE 0.015 0.001 PHE A 11 TYR 0.022 0.001 TYR A 49 ARG 0.006 0.000 ARG C 558 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6194 Ramachandran restraints generated. 3097 Oldfield, 0 Emsley, 3097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6194 Ramachandran restraints generated. 3097 Oldfield, 0 Emsley, 3097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 332 time to evaluate : 2.729 Fit side-chains revert: symmetry clash REVERT: A 522 LYS cc_start: 0.7897 (ttpp) cc_final: 0.7558 (ttpt) REVERT: A 662 MET cc_start: 0.8011 (mmt) cc_final: 0.7674 (mmp) REVERT: A 712 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6909 (mtm) REVERT: A 761 ASP cc_start: 0.8698 (m-30) cc_final: 0.8423 (m-30) REVERT: A 784 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8215 (t0) REVERT: A 966 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.7988 (t0) REVERT: A 1032 ARG cc_start: 0.7360 (mtm-85) cc_final: 0.7065 (ttp-170) REVERT: B 130 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7455 (mm-30) REVERT: B 192 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8307 (mm-30) REVERT: B 408 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8101 (t70) REVERT: B 547 ILE cc_start: 0.8555 (mt) cc_final: 0.8198 (mp) REVERT: B 842 GLU cc_start: 0.7772 (tt0) cc_final: 0.7543 (tm-30) REVERT: B 962 GLU cc_start: 0.7837 (tt0) cc_final: 0.7621 (tm-30) REVERT: C 115 MET cc_start: 0.7838 (tpp) cc_final: 0.7462 (tpt) REVERT: C 420 MET cc_start: 0.8742 (mtm) cc_final: 0.8435 (mtm) REVERT: C 620 ARG cc_start: 0.8284 (mtt-85) cc_final: 0.8031 (mtt90) REVERT: C 693 GLU cc_start: 0.7970 (tp30) cc_final: 0.7696 (tp30) outliers start: 26 outliers final: 11 residues processed: 350 average time/residue: 2.3604 time to fit residues: 961.8856 Evaluate side-chains 339 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 323 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 795 ASP Chi-restraints excluded: chain C residue 806 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 79 optimal weight: 0.7980 chunk 252 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 181 optimal weight: 0.7980 chunk 216 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.097302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.080393 restraints weight = 92911.321| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.61 r_work: 0.2843 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24048 Z= 0.275 Angle : 0.509 5.105 32661 Z= 0.271 Chirality : 0.041 0.168 3841 Planarity : 0.004 0.050 4176 Dihedral : 4.742 58.209 3320 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.19 % Allowed : 8.46 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.02 (0.15), residues: 3097 helix: 2.38 (0.12), residues: 1714 sheet: 0.09 (0.25), residues: 377 loop : 0.07 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 789 HIS 0.004 0.001 HIS B 709 PHE 0.020 0.001 PHE A 11 TYR 0.023 0.002 TYR A 49 ARG 0.003 0.000 ARG A 780 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6194 Ramachandran restraints generated. 3097 Oldfield, 0 Emsley, 3097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6194 Ramachandran restraints generated. 3097 Oldfield, 0 Emsley, 3097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 332 time to evaluate : 2.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: A 522 LYS cc_start: 0.7919 (ttpp) cc_final: 0.7555 (ttpt) REVERT: A 662 MET cc_start: 0.8022 (mmt) cc_final: 0.7648 (mmp) REVERT: A 712 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6967 (mtm) REVERT: A 761 ASP cc_start: 0.8676 (m-30) cc_final: 0.8403 (m-30) REVERT: A 784 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8211 (t0) REVERT: B 130 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7541 (mm-30) REVERT: B 192 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8331 (mm-30) REVERT: B 547 ILE cc_start: 0.8521 (mt) cc_final: 0.8165 (mp) REVERT: B 550 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8519 (t) REVERT: B 842 GLU cc_start: 0.7783 (tt0) cc_final: 0.7561 (tm-30) REVERT: C 115 MET cc_start: 0.7899 (tpp) cc_final: 0.7530 (tpt) REVERT: C 620 ARG cc_start: 0.8310 (mtt-85) cc_final: 0.8067 (mtt90) REVERT: C 693 GLU cc_start: 0.8041 (tp30) cc_final: 0.7778 (tp30) outliers start: 29 outliers final: 16 residues processed: 350 average time/residue: 2.3859 time to fit residues: 969.8194 Evaluate side-chains 348 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 327 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 953 MET Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 795 ASP Chi-restraints excluded: chain C residue 806 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 42 optimal weight: 0.2980 chunk 108 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 308 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.099019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.082145 restraints weight = 92178.868| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.61 r_work: 0.2877 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24048 Z= 0.170 Angle : 0.472 5.033 32661 Z= 0.251 Chirality : 0.039 0.146 3841 Planarity : 0.004 0.048 4176 Dihedral : 4.596 55.630 3320 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.91 % Allowed : 9.33 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.21 (0.15), residues: 3097 helix: 2.54 (0.12), residues: 1712 sheet: 0.14 (0.25), residues: 388 loop : 0.16 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 789 HIS 0.004 0.000 HIS B 709 PHE 0.015 0.001 PHE A 11 TYR 0.015 0.001 TYR A 541 ARG 0.005 0.000 ARG C 818 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6194 Ramachandran restraints generated. 3097 Oldfield, 0 Emsley, 3097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6194 Ramachandran restraints generated. 3097 Oldfield, 0 Emsley, 3097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 332 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 LYS cc_start: 0.7855 (ttpp) cc_final: 0.7505 (ttpt) REVERT: A 662 MET cc_start: 0.8020 (mmt) cc_final: 0.7634 (mmp) REVERT: A 681 ASP cc_start: 0.8111 (t0) cc_final: 0.7819 (t0) REVERT: A 761 ASP cc_start: 0.8634 (m-30) cc_final: 0.8350 (m-30) REVERT: A 784 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8231 (t0) REVERT: A 966 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8011 (t0) REVERT: B 130 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7475 (mm-30) REVERT: B 192 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8321 (mm-30) REVERT: B 197 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8393 (mp-120) REVERT: B 408 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8162 (t70) REVERT: B 547 ILE cc_start: 0.8486 (mt) cc_final: 0.8113 (mp) REVERT: B 555 LEU cc_start: 0.8814 (mt) cc_final: 0.8612 (mp) REVERT: B 842 GLU cc_start: 0.7761 (tt0) cc_final: 0.7549 (tm-30) REVERT: B 1011 MET cc_start: 0.8945 (mmm) cc_final: 0.8709 (tpt) REVERT: C 3 ASN cc_start: 0.8972 (m-40) cc_final: 0.8735 (m-40) REVERT: C 115 MET cc_start: 0.7869 (tpp) cc_final: 0.7502 (tpt) REVERT: C 334 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8104 (mtmm) REVERT: C 693 GLU cc_start: 0.8040 (tp30) cc_final: 0.7769 (tp30) REVERT: C 733 GLN cc_start: 0.7778 (mt0) cc_final: 0.7543 (mt0) outliers start: 22 outliers final: 8 residues processed: 347 average time/residue: 2.3963 time to fit residues: 969.0579 Evaluate side-chains 334 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 320 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 953 MET Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 585 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 67 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 209 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.098892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.082358 restraints weight = 85879.382| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.54 r_work: 0.2863 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24048 Z= 0.239 Angle : 0.490 5.310 32661 Z= 0.260 Chirality : 0.040 0.146 3841 Planarity : 0.004 0.048 4176 Dihedral : 4.613 51.073 3320 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.19 % Allowed : 9.33 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.12 (0.15), residues: 3097 helix: 2.47 (0.12), residues: 1715 sheet: 0.15 (0.25), residues: 383 loop : 0.09 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 789 HIS 0.001 0.000 HIS C 709 PHE 0.019 0.001 PHE A 11 TYR 0.019 0.001 TYR B 49 ARG 0.005 0.000 ARG C 818 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6194 Ramachandran restraints generated. 3097 Oldfield, 0 Emsley, 3097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6194 Ramachandran restraints generated. 3097 Oldfield, 0 Emsley, 3097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 334 time to evaluate : 2.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 LYS cc_start: 0.7926 (ttpp) cc_final: 0.7580 (ttpt) REVERT: A 662 MET cc_start: 0.7958 (mmt) cc_final: 0.7586 (mmp) REVERT: A 712 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6997 (mtm) REVERT: A 761 ASP cc_start: 0.8624 (m-30) cc_final: 0.8348 (m-30) REVERT: A 784 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8209 (t0) REVERT: A 966 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8006 (t0) REVERT: B 130 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7519 (mm-30) REVERT: B 192 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8326 (mm-30) REVERT: B 197 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8381 (mp-120) REVERT: B 408 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8175 (t70) REVERT: B 547 ILE cc_start: 0.8490 (mt) cc_final: 0.8121 (mp) REVERT: B 842 GLU cc_start: 0.7776 (tt0) cc_final: 0.7575 (tm-30) REVERT: B 1011 MET cc_start: 0.8951 (mmm) cc_final: 0.8689 (tpt) REVERT: C 3 ASN cc_start: 0.8986 (m-40) cc_final: 0.8688 (m-40) REVERT: C 115 MET cc_start: 0.7897 (tpp) cc_final: 0.7530 (tpt) REVERT: C 334 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8089 (mttm) REVERT: C 620 ARG cc_start: 0.8257 (mtt-85) cc_final: 0.7985 (mtt90) REVERT: C 693 GLU cc_start: 0.8066 (tp30) cc_final: 0.7791 (tp30) REVERT: C 733 GLN cc_start: 0.7785 (mt0) cc_final: 0.7543 (mt0) outliers start: 29 outliers final: 15 residues processed: 351 average time/residue: 2.4271 time to fit residues: 991.7492 Evaluate side-chains 345 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 323 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 953 MET Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 795 ASP Chi-restraints excluded: chain C residue 806 SER Chi-restraints excluded: chain C residue 1008 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 132 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 280 optimal weight: 0.4980 chunk 222 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.098240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.081340 restraints weight = 95312.410| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.63 r_work: 0.2854 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24048 Z= 0.226 Angle : 0.487 5.382 32661 Z= 0.259 Chirality : 0.040 0.147 3841 Planarity : 0.004 0.048 4176 Dihedral : 4.602 50.224 3320 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.07 % Allowed : 9.77 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.11 (0.15), residues: 3097 helix: 2.46 (0.12), residues: 1715 sheet: 0.14 (0.25), residues: 383 loop : 0.08 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 789 HIS 0.002 0.000 HIS C 709 PHE 0.020 0.001 PHE A 11 TYR 0.018 0.001 TYR B 49 ARG 0.004 0.000 ARG C 558 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6194 Ramachandran restraints generated. 3097 Oldfield, 0 Emsley, 3097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6194 Ramachandran restraints generated. 3097 Oldfield, 0 Emsley, 3097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 327 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 LYS cc_start: 0.7920 (ttpp) cc_final: 0.7613 (ttpt) REVERT: A 544 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8198 (mt) REVERT: A 662 MET cc_start: 0.8014 (mmt) cc_final: 0.7654 (mmp) REVERT: A 712 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.7025 (mtm) REVERT: A 761 ASP cc_start: 0.8651 (m-30) cc_final: 0.8372 (m-30) REVERT: A 784 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8220 (t0) REVERT: A 966 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8041 (t0) REVERT: B 130 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7502 (mm-30) REVERT: B 192 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8337 (mm-30) REVERT: B 197 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8400 (mp-120) REVERT: B 408 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8183 (t70) REVERT: B 547 ILE cc_start: 0.8494 (mt) cc_final: 0.8141 (mp) REVERT: B 842 GLU cc_start: 0.7772 (tt0) cc_final: 0.7562 (tm-30) REVERT: B 881 LEU cc_start: 0.8968 (tp) cc_final: 0.8628 (mt) REVERT: B 962 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7573 (tt0) REVERT: B 1011 MET cc_start: 0.8970 (mmm) cc_final: 0.8701 (tpt) REVERT: C 3 ASN cc_start: 0.8998 (m-40) cc_final: 0.8720 (m-40) REVERT: C 115 MET cc_start: 0.7829 (tpp) cc_final: 0.7470 (tpt) REVERT: C 334 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8100 (mtmm) REVERT: C 620 ARG cc_start: 0.8258 (mtt-85) cc_final: 0.7963 (mtt90) REVERT: C 693 GLU cc_start: 0.8086 (tp30) cc_final: 0.7808 (tp30) REVERT: C 733 GLN cc_start: 0.7594 (mt0) cc_final: 0.7344 (mt0) outliers start: 26 outliers final: 13 residues processed: 342 average time/residue: 2.3291 time to fit residues: 924.1092 Evaluate side-chains 345 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 324 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 953 MET Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 795 ASP Chi-restraints excluded: chain C residue 806 SER Chi-restraints excluded: chain C residue 1008 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 4 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 304 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 248 optimal weight: 0.5980 chunk 224 optimal weight: 3.9990 chunk 289 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.097787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.081220 restraints weight = 86564.150| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.55 r_work: 0.2847 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24048 Z= 0.253 Angle : 0.499 6.577 32661 Z= 0.264 Chirality : 0.040 0.147 3841 Planarity : 0.004 0.048 4176 Dihedral : 4.540 43.473 3319 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.07 % Allowed : 10.08 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.06 (0.15), residues: 3097 helix: 2.42 (0.12), residues: 1715 sheet: 0.11 (0.26), residues: 369 loop : 0.07 (0.20), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 789 HIS 0.003 0.000 HIS B 709 PHE 0.023 0.001 PHE A 11 TYR 0.019 0.001 TYR B 49 ARG 0.004 0.000 ARG C 558 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6194 Ramachandran restraints generated. 3097 Oldfield, 0 Emsley, 3097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6194 Ramachandran restraints generated. 3097 Oldfield, 0 Emsley, 3097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 327 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 LYS cc_start: 0.7927 (ttpp) cc_final: 0.7623 (ttpt) REVERT: A 544 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8205 (mt) REVERT: A 662 MET cc_start: 0.7985 (mmt) cc_final: 0.7622 (mmp) REVERT: A 712 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.7016 (mtm) REVERT: A 761 ASP cc_start: 0.8620 (m-30) cc_final: 0.8342 (m-30) REVERT: A 784 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8187 (t0) REVERT: A 966 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.8011 (t0) REVERT: B 130 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7500 (mm-30) REVERT: B 192 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8322 (mm-30) REVERT: B 197 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8402 (mp-120) REVERT: B 408 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8197 (t70) REVERT: B 547 ILE cc_start: 0.8497 (mt) cc_final: 0.8150 (mp) REVERT: B 550 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8602 (t) REVERT: B 881 LEU cc_start: 0.8970 (tp) cc_final: 0.8636 (mt) REVERT: B 1011 MET cc_start: 0.8972 (mmm) cc_final: 0.8696 (tpt) REVERT: C 3 ASN cc_start: 0.9008 (m-40) cc_final: 0.8733 (m-40) REVERT: C 115 MET cc_start: 0.7825 (tpp) cc_final: 0.7474 (tpt) REVERT: C 334 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8089 (mttm) REVERT: C 693 GLU cc_start: 0.8069 (tp30) cc_final: 0.7793 (tp30) REVERT: C 733 GLN cc_start: 0.7571 (mt0) cc_final: 0.7324 (mt0) outliers start: 26 outliers final: 12 residues processed: 340 average time/residue: 2.4113 time to fit residues: 956.2539 Evaluate side-chains 346 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 325 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 953 MET Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 795 ASP Chi-restraints excluded: chain C residue 806 SER Chi-restraints excluded: chain C residue 1008 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 298 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 239 optimal weight: 0.7980 chunk 231 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.097619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.080908 restraints weight = 90166.370| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.58 r_work: 0.2850 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24048 Z= 0.230 Angle : 0.494 5.666 32661 Z= 0.262 Chirality : 0.040 0.147 3841 Planarity : 0.004 0.048 4176 Dihedral : 4.505 41.244 3318 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.99 % Allowed : 10.32 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.09 (0.15), residues: 3097 helix: 2.47 (0.12), residues: 1708 sheet: 0.10 (0.25), residues: 383 loop : 0.07 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 789 HIS 0.002 0.000 HIS B 709 PHE 0.021 0.001 PHE A 11 TYR 0.017 0.001 TYR A 541 ARG 0.004 0.000 ARG C 558 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6194 Ramachandran restraints generated. 3097 Oldfield, 0 Emsley, 3097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6194 Ramachandran restraints generated. 3097 Oldfield, 0 Emsley, 3097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 326 time to evaluate : 2.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 LYS cc_start: 0.7933 (ttpp) cc_final: 0.7632 (ttpt) REVERT: A 544 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8211 (mt) REVERT: A 662 MET cc_start: 0.8000 (mmt) cc_final: 0.7639 (mmp) REVERT: A 712 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.7001 (mtm) REVERT: A 732 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.7029 (m-30) REVERT: A 761 ASP cc_start: 0.8627 (m-30) cc_final: 0.8348 (m-30) REVERT: A 784 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8198 (t0) REVERT: A 966 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8014 (t0) REVERT: B 130 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7510 (mm-30) REVERT: B 192 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8330 (mm-30) REVERT: B 197 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8409 (mp-120) REVERT: B 547 ILE cc_start: 0.8497 (mt) cc_final: 0.8152 (mp) REVERT: B 550 VAL cc_start: 0.8787 (OUTLIER) cc_final: 0.8557 (t) REVERT: B 830 GLN cc_start: 0.8514 (mt0) cc_final: 0.8270 (mt0) REVERT: B 881 LEU cc_start: 0.8974 (tp) cc_final: 0.8632 (mt) REVERT: B 1011 MET cc_start: 0.8978 (mmm) cc_final: 0.8703 (tpt) REVERT: C 3 ASN cc_start: 0.9007 (m-40) cc_final: 0.8745 (m-40) REVERT: C 115 MET cc_start: 0.7804 (tpp) cc_final: 0.7442 (tpt) REVERT: C 334 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8117 (mtmm) REVERT: C 673 GLU cc_start: 0.8255 (tp30) cc_final: 0.7919 (tp30) REVERT: C 693 GLU cc_start: 0.8072 (tp30) cc_final: 0.7798 (tp30) REVERT: C 733 GLN cc_start: 0.7575 (mt0) cc_final: 0.7326 (mt0) outliers start: 24 outliers final: 13 residues processed: 339 average time/residue: 2.4234 time to fit residues: 957.8201 Evaluate side-chains 344 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 322 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 953 MET Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 795 ASP Chi-restraints excluded: chain C residue 806 SER Chi-restraints excluded: chain C residue 1008 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 119 optimal weight: 0.0980 chunk 292 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 308 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 307 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 226 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.098883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.082217 restraints weight = 88316.479| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.58 r_work: 0.2863 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24048 Z= 0.187 Angle : 0.480 5.627 32661 Z= 0.254 Chirality : 0.040 0.146 3841 Planarity : 0.004 0.048 4176 Dihedral : 4.442 40.249 3318 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.99 % Allowed : 10.44 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.19 (0.15), residues: 3097 helix: 2.55 (0.12), residues: 1707 sheet: 0.12 (0.25), residues: 383 loop : 0.12 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 789 HIS 0.004 0.000 HIS B 709 PHE 0.017 0.001 PHE A 11 TYR 0.015 0.001 TYR A 541 ARG 0.006 0.000 ARG C 620 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6194 Ramachandran restraints generated. 3097 Oldfield, 0 Emsley, 3097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6194 Ramachandran restraints generated. 3097 Oldfield, 0 Emsley, 3097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 330 time to evaluate : 2.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 LYS cc_start: 0.7912 (ttpp) cc_final: 0.7617 (ttpt) REVERT: A 662 MET cc_start: 0.7965 (mmt) cc_final: 0.7585 (mmp) REVERT: A 681 ASP cc_start: 0.8110 (t0) cc_final: 0.7806 (t0) REVERT: A 761 ASP cc_start: 0.8583 (m-30) cc_final: 0.8304 (m-30) REVERT: A 784 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8188 (t0) REVERT: A 868 LEU cc_start: 0.7490 (mt) cc_final: 0.7286 (tp) REVERT: B 130 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7481 (mm-30) REVERT: B 182 TYR cc_start: 0.9066 (OUTLIER) cc_final: 0.8604 (m-10) REVERT: B 192 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8297 (mm-30) REVERT: B 197 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8412 (mp-120) REVERT: B 547 ILE cc_start: 0.8482 (mt) cc_final: 0.8137 (mp) REVERT: B 693 GLU cc_start: 0.8038 (mp0) cc_final: 0.7834 (mp0) REVERT: B 842 GLU cc_start: 0.7651 (tt0) cc_final: 0.7415 (tm-30) REVERT: B 881 LEU cc_start: 0.8956 (tp) cc_final: 0.8631 (mt) REVERT: B 1011 MET cc_start: 0.8966 (mmm) cc_final: 0.8706 (tpt) REVERT: C 334 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8100 (mtmm) REVERT: C 673 GLU cc_start: 0.8252 (tp30) cc_final: 0.7945 (tp30) REVERT: C 693 GLU cc_start: 0.8075 (tp30) cc_final: 0.7798 (tp30) REVERT: C 733 GLN cc_start: 0.7563 (mt0) cc_final: 0.7316 (mt0) outliers start: 24 outliers final: 13 residues processed: 346 average time/residue: 2.3881 time to fit residues: 965.7520 Evaluate side-chains 341 residues out of total 2517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 323 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 953 MET Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 566 ASP Chi-restraints excluded: chain C residue 806 SER Chi-restraints excluded: chain C residue 1008 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 41 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 79 optimal weight: 0.0670 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.099835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.083103 restraints weight = 89357.174| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.59 r_work: 0.2882 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24048 Z= 0.156 Angle : 0.469 5.548 32661 Z= 0.247 Chirality : 0.039 0.146 3841 Planarity : 0.004 0.047 4176 Dihedral : 4.373 40.136 3318 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.83 % Allowed : 10.88 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.28 (0.15), residues: 3097 helix: 2.61 (0.12), residues: 1714 sheet: 0.12 (0.25), residues: 388 loop : 0.17 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 789 HIS 0.003 0.000 HIS B 709 PHE 0.014 0.001 PHE A 682 TYR 0.015 0.001 TYR A 541 ARG 0.004 0.000 ARG C 620 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 25818.87 seconds wall clock time: 439 minutes 16.14 seconds (26356.14 seconds total)