Starting phenix.real_space_refine on Sun Oct 13 16:41:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bfm_44500/10_2024/9bfm_44500_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bfm_44500/10_2024/9bfm_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bfm_44500/10_2024/9bfm_44500.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bfm_44500/10_2024/9bfm_44500.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bfm_44500/10_2024/9bfm_44500_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bfm_44500/10_2024/9bfm_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-5477/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: 20.23, 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: 9.33 Conformation dependent library (CDL) restraints added in 3.8 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: 3.14 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: 17.47 Time building geometry restraints manager: 11.29 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: 2.070 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: 1.240 Check model and map are aligned: 0.270 Set scattering table: 0.330 Process input model: 82.380 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.120 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:8.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.290 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 402 time to evaluate : 2.671 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: 2.3623 time to fit residues: 1105.3376 Evaluate side-chains 333 residues out of total 2517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 331 time to evaluate : 2.695 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 fitting. rotamer outliers: 21 poor density : 341 time to evaluate : 2.692 Fit side-chains REVERT: A 176 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7502 (tm-30) REVERT: A 268 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8592 (mm) REVERT: A 522 LYS cc_start: 0.8018 (ttpp) cc_final: 0.7747 (ttpt) REVERT: A 712 MET cc_start: 0.7256 (OUTLIER) cc_final: 0.6991 (mtm) REVERT: A 761 ASP cc_start: 0.8330 (m-30) cc_final: 0.8027 (m-30) REVERT: A 784 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7405 (t0) REVERT: A 966 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7330 (t0) REVERT: A 1032 ARG cc_start: 0.7227 (mtm-85) cc_final: 0.6969 (ttp-170) REVERT: B 197 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8277 (mp-120) REVERT: B 547 ILE cc_start: 0.8613 (mt) cc_final: 0.8317 (mp) outliers start: 21 outliers final: 6 residues processed: 354 average time/residue: 2.4577 time to fit residues: 1011.7697 Evaluate side-chains 335 residues out of total 2517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 323 time to evaluate : 2.659 ------------------------------------------------------------------------------- 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 155 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 281 optimal weight: 4.9990 chunk 303 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 278 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 225 optimal weight: 0.6980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.0990 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= 0.189 Angle : 0.482 5.475 32661 Z= 0.256 Chirality : 0.040 0.147 3841 Planarity : 0.004 0.054 4176 Dihedral : 4.686 67.356 3320 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.03 % Allowed : 7.58 % Favored : 91.39 % 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: 2.22 (0.15), residues: 3097 helix: 2.55 (0.12), residues: 1715 sheet: 0.06 (0.25), residues: 382 loop : 0.18 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 789 HIS 0.002 0.000 HIS B 709 PHE 0.014 0.001 PHE A 682 TYR 0.017 0.001 TYR A 49 ARG 0.007 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 357 residues out of total 2517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 332 time to evaluate : 2.681 Fit side-chains revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: A 522 LYS cc_start: 0.8029 (ttpp) cc_final: 0.7763 (ttpt) REVERT: A 662 MET cc_start: 0.6878 (mmt) cc_final: 0.6544 (mmp) REVERT: A 761 ASP cc_start: 0.8341 (m-30) cc_final: 0.8043 (m-30) REVERT: A 784 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7390 (t0) REVERT: A 1032 ARG cc_start: 0.7227 (mtm-85) cc_final: 0.6966 (ttp-170) REVERT: B 130 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6800 (mm-30) REVERT: B 408 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7635 (t70) REVERT: B 547 ILE cc_start: 0.8624 (mt) cc_final: 0.8338 (mp) REVERT: C 115 MET cc_start: 0.7208 (tpp) cc_final: 0.6832 (tpt) REVERT: C 130 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7858 (pm20) outliers start: 25 outliers final: 9 residues processed: 349 average time/residue: 2.3783 time to fit residues: 960.8762 Evaluate side-chains 333 residues out of total 2517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 319 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU 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 732 ASP Chi-restraints excluded: chain A residue 784 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 806 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 145 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 282 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 267 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24048 Z= 0.279 Angle : 0.509 5.237 32661 Z= 0.271 Chirality : 0.041 0.182 3841 Planarity : 0.004 0.049 4176 Dihedral : 4.722 59.708 3320 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.03 % Allowed : 8.81 % Favored : 90.15 % 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: 2.41 (0.12), residues: 1714 sheet: 0.11 (0.25), residues: 377 loop : 0.09 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 789 HIS 0.005 0.001 HIS B 709 PHE 0.018 0.001 PHE A 11 TYR 0.023 0.002 TYR A 49 ARG 0.005 0.000 ARG C 620 *********************** 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 354 residues out of total 2517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 329 time to evaluate : 2.684 Fit side-chains revert: symmetry clash REVERT: A 176 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: A 522 LYS cc_start: 0.8061 (ttpp) cc_final: 0.7767 (ttpt) REVERT: A 662 MET cc_start: 0.6902 (mmt) cc_final: 0.6544 (mmp) REVERT: A 712 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.7046 (mtm) REVERT: A 761 ASP cc_start: 0.8337 (m-30) cc_final: 0.8040 (m-30) REVERT: A 784 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7441 (t0) REVERT: A 966 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7378 (t0) REVERT: B 130 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6881 (mm-30) REVERT: B 197 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8316 (mp-120) REVERT: B 547 ILE cc_start: 0.8626 (mt) cc_final: 0.8339 (mp) REVERT: C 115 MET cc_start: 0.7335 (tpp) cc_final: 0.6966 (tpt) REVERT: C 276 ASP cc_start: 0.7713 (m-30) cc_final: 0.7473 (m-30) outliers start: 25 outliers final: 13 residues processed: 344 average time/residue: 2.4017 time to fit residues: 958.8590 Evaluate side-chains 343 residues out of total 2517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 324 time to evaluate : 2.676 ------------------------------------------------------------------------------- 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 495 THR 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 197 GLN Chi-restraints excluded: chain B residue 330 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 123 optimal weight: 0.0980 chunk 254 optimal weight: 2.9990 chunk 206 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 152 optimal weight: 0.0670 chunk 268 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24048 Z= 0.155 Angle : 0.467 5.033 32661 Z= 0.247 Chirality : 0.039 0.146 3841 Planarity : 0.004 0.047 4176 Dihedral : 4.564 57.639 3320 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.91 % Allowed : 9.17 % Favored : 89.92 % 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: 2.27 (0.15), residues: 3097 helix: 2.59 (0.12), residues: 1713 sheet: 0.14 (0.25), residues: 388 loop : 0.18 (0.20), residues: 996 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 0.014 0.001 PHE A 11 TYR 0.014 0.001 TYR A 541 ARG 0.006 0.000 ARG C 620 *********************** 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 362 residues out of total 2517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 340 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 LYS cc_start: 0.8033 (ttpp) cc_final: 0.7771 (ttpt) REVERT: A 662 MET cc_start: 0.6916 (mmt) cc_final: 0.6542 (mmp) REVERT: A 681 ASP cc_start: 0.7745 (t0) cc_final: 0.7435 (t0) REVERT: A 712 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.7055 (mtm) REVERT: A 761 ASP cc_start: 0.8259 (m-30) cc_final: 0.7956 (m-30) REVERT: A 966 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7379 (t0) REVERT: B 130 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6841 (mm-30) REVERT: B 408 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7670 (t70) REVERT: B 547 ILE cc_start: 0.8599 (mt) cc_final: 0.8301 (mp) REVERT: C 3 ASN cc_start: 0.8885 (m-40) cc_final: 0.8614 (m-40) REVERT: C 115 MET cc_start: 0.7238 (tpp) cc_final: 0.6875 (tpt) REVERT: C 334 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7784 (mttt) outliers start: 22 outliers final: 9 residues processed: 354 average time/residue: 2.3525 time to fit residues: 968.5125 Evaluate side-chains 336 residues out of total 2517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 322 time to evaluate : 2.688 ------------------------------------------------------------------------------- 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 825 MET 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 408 ASP Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 334 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 4.9990 chunk 268 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 298 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 156 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24048 Z= 0.230 Angle : 0.487 5.425 32661 Z= 0.258 Chirality : 0.040 0.146 3841 Planarity : 0.004 0.047 4176 Dihedral : 4.585 53.207 3320 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.19 % Allowed : 9.41 % Favored : 89.40 % 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: 2.17 (0.15), residues: 3097 helix: 2.51 (0.12), residues: 1716 sheet: 0.09 (0.25), residues: 382 loop : 0.14 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 789 HIS 0.001 0.000 HIS C 709 PHE 0.018 0.001 PHE A 11 TYR 0.019 0.001 TYR B 49 ARG 0.004 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 360 residues out of total 2517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 331 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 LYS cc_start: 0.8093 (ttpp) cc_final: 0.7830 (ttpt) REVERT: A 662 MET cc_start: 0.6971 (mmt) cc_final: 0.6602 (mmp) REVERT: A 712 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.7058 (mtm) REVERT: A 761 ASP cc_start: 0.8284 (m-30) cc_final: 0.8003 (m-30) REVERT: A 784 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7433 (t0) REVERT: A 966 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7391 (t0) REVERT: B 130 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6875 (mm-30) REVERT: B 197 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8319 (mp-120) REVERT: B 408 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7687 (t70) REVERT: B 547 ILE cc_start: 0.8580 (mt) cc_final: 0.8291 (mp) REVERT: C 3 ASN cc_start: 0.8906 (m-40) cc_final: 0.8654 (m-40) REVERT: C 115 MET cc_start: 0.7325 (tpp) cc_final: 0.6964 (tpt) REVERT: C 334 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7904 (mttm) outliers start: 29 outliers final: 13 residues processed: 346 average time/residue: 2.3384 time to fit residues: 936.7877 Evaluate side-chains 341 residues out of total 2517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 321 time to evaluate : 2.623 ------------------------------------------------------------------------------- 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 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 825 MET 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 1011 MET Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 733 GLN Chi-restraints excluded: chain C residue 795 ASP 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 288 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 170 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 251 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 297 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1336 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= 0.183 Angle : 0.476 6.499 32661 Z= 0.251 Chirality : 0.039 0.145 3841 Planarity : 0.004 0.047 4176 Dihedral : 4.456 50.865 3319 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.03 % Allowed : 9.88 % Favored : 89.08 % 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: 2.22 (0.15), residues: 3097 helix: 2.56 (0.12), residues: 1716 sheet: 0.13 (0.25), residues: 388 loop : 0.14 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 789 HIS 0.001 0.000 HIS B 709 PHE 0.017 0.001 PHE A 11 TYR 0.016 0.001 TYR A 541 ARG 0.008 0.000 ARG C 620 *********************** 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 352 residues out of total 2517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 327 time to evaluate : 2.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 LYS cc_start: 0.8080 (ttpp) cc_final: 0.7826 (ttpt) REVERT: A 662 MET cc_start: 0.6960 (mmt) cc_final: 0.6589 (mmp) REVERT: A 681 ASP cc_start: 0.7792 (t0) cc_final: 0.7480 (t0) REVERT: A 761 ASP cc_start: 0.8245 (m-30) cc_final: 0.7959 (m-30) REVERT: A 784 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7423 (t0) REVERT: A 966 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7408 (t0) REVERT: B 130 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6870 (mm-30) REVERT: B 197 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8308 (mp-120) REVERT: B 408 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7672 (t70) REVERT: B 547 ILE cc_start: 0.8560 (mt) cc_final: 0.8279 (mp) REVERT: B 881 LEU cc_start: 0.8993 (tp) cc_final: 0.8716 (mt) REVERT: C 3 ASN cc_start: 0.8913 (m-40) cc_final: 0.8654 (m-40) REVERT: C 115 MET cc_start: 0.7305 (tpp) cc_final: 0.6948 (tpt) REVERT: C 334 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7922 (mtmm) outliers start: 25 outliers final: 16 residues processed: 342 average time/residue: 2.4064 time to fit residues: 959.2305 Evaluate side-chains 342 residues out of total 2517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 320 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 732 ASP 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 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 620 ARG Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 355 MET 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 184 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 189 optimal weight: 0.7980 chunk 202 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24048 Z= 0.237 Angle : 0.495 5.526 32661 Z= 0.262 Chirality : 0.040 0.146 3841 Planarity : 0.004 0.047 4176 Dihedral : 4.496 46.681 3319 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.07 % Allowed : 10.16 % Favored : 88.77 % 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: 2.14 (0.15), residues: 3097 helix: 2.49 (0.12), residues: 1714 sheet: 0.11 (0.25), residues: 377 loop : 0.11 (0.20), residues: 1006 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 0.021 0.001 PHE A 11 TYR 0.020 0.001 TYR B 49 ARG 0.007 0.000 ARG C 620 *********************** 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 355 residues out of total 2517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 329 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 LYS cc_start: 0.8092 (ttpp) cc_final: 0.7842 (ttpt) REVERT: A 662 MET cc_start: 0.6926 (mmt) cc_final: 0.6572 (mmp) REVERT: A 761 ASP cc_start: 0.8290 (m-30) cc_final: 0.8004 (m-30) REVERT: A 784 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7408 (t0) REVERT: A 966 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7405 (t0) REVERT: B 130 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6873 (mm-30) REVERT: B 197 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8317 (mp-120) REVERT: B 408 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7691 (t70) REVERT: B 547 ILE cc_start: 0.8588 (mt) cc_final: 0.8310 (mp) REVERT: B 881 LEU cc_start: 0.8999 (tp) cc_final: 0.8718 (mt) REVERT: C 3 ASN cc_start: 0.8924 (m-40) cc_final: 0.8668 (m-40) REVERT: C 115 MET cc_start: 0.7355 (tpp) cc_final: 0.7000 (tpt) REVERT: C 334 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7922 (mtmm) outliers start: 26 outliers final: 14 residues processed: 345 average time/residue: 2.3988 time to fit residues: 961.5117 Evaluate side-chains 345 residues out of total 2517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 325 time to evaluate : 2.627 ------------------------------------------------------------------------------- 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 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 B residue 1011 MET Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 566 ASP Chi-restraints excluded: chain C residue 733 GLN 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 270 optimal weight: 2.9990 chunk 285 optimal weight: 4.9990 chunk 260 optimal weight: 1.9990 chunk 277 optimal weight: 1.9990 chunk 167 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 217 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 262 optimal weight: 0.7980 chunk 276 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24048 Z= 0.204 Angle : 0.485 5.942 32661 Z= 0.256 Chirality : 0.040 0.146 3841 Planarity : 0.004 0.047 4176 Dihedral : 4.446 44.456 3318 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.91 % Allowed : 10.28 % Favored : 88.81 % 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: 2.17 (0.15), residues: 3097 helix: 2.52 (0.12), residues: 1714 sheet: 0.10 (0.25), residues: 377 loop : 0.13 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 789 HIS 0.002 0.000 HIS B 709 PHE 0.019 0.001 PHE A 11 TYR 0.016 0.001 TYR A 541 ARG 0.007 0.000 ARG C 620 *********************** 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 349 residues out of total 2517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 327 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 LYS cc_start: 0.8084 (ttpp) cc_final: 0.7839 (ttpt) REVERT: A 662 MET cc_start: 0.6927 (mmt) cc_final: 0.6543 (mmp) REVERT: A 681 ASP cc_start: 0.7807 (t0) cc_final: 0.7525 (t0) REVERT: A 761 ASP cc_start: 0.8294 (m-30) cc_final: 0.8011 (m-30) REVERT: A 784 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7403 (t0) REVERT: A 966 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7396 (t0) REVERT: B 130 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6871 (mm-30) REVERT: B 197 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8309 (mp-120) REVERT: B 408 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7671 (t70) REVERT: B 547 ILE cc_start: 0.8543 (mt) cc_final: 0.8260 (mp) REVERT: B 693 GLU cc_start: 0.7673 (mp0) cc_final: 0.7450 (mp0) REVERT: B 881 LEU cc_start: 0.8995 (tp) cc_final: 0.8715 (mt) REVERT: C 115 MET cc_start: 0.7238 (tpp) cc_final: 0.6888 (tpt) REVERT: C 334 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7922 (mtmm) outliers start: 22 outliers final: 10 residues processed: 342 average time/residue: 2.4763 time to fit residues: 991.4437 Evaluate side-chains 338 residues out of total 2517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 322 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR 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 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 B residue 1011 MET Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 566 ASP Chi-restraints excluded: chain C residue 733 GLN 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 182 optimal weight: 3.9990 chunk 293 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 204 optimal weight: 0.6980 chunk 307 optimal weight: 0.9990 chunk 283 optimal weight: 2.9990 chunk 245 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24048 Z= 0.212 Angle : 0.488 5.632 32661 Z= 0.258 Chirality : 0.040 0.147 3841 Planarity : 0.004 0.047 4176 Dihedral : 4.443 42.358 3318 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.79 % Allowed : 10.56 % Favored : 88.65 % 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: 2.17 (0.15), residues: 3097 helix: 2.52 (0.12), residues: 1714 sheet: 0.06 (0.25), residues: 382 loop : 0.14 (0.20), residues: 1001 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 0.019 0.001 PHE A 11 TYR 0.017 0.001 TYR B 49 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 345 residues out of total 2517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 326 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 LYS cc_start: 0.8085 (ttpp) cc_final: 0.7839 (ttpt) REVERT: A 662 MET cc_start: 0.6925 (mmt) cc_final: 0.6549 (mmp) REVERT: A 681 ASP cc_start: 0.7814 (t0) cc_final: 0.7530 (t0) REVERT: A 761 ASP cc_start: 0.8283 (m-30) cc_final: 0.7992 (m-30) REVERT: A 784 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7404 (t0) REVERT: A 966 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7394 (t0) REVERT: B 130 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6872 (mm-30) REVERT: B 197 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8308 (mp-120) REVERT: B 408 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7672 (t70) REVERT: B 547 ILE cc_start: 0.8541 (mt) cc_final: 0.8260 (mp) REVERT: B 881 LEU cc_start: 0.8993 (tp) cc_final: 0.8716 (mt) REVERT: C 3 ASN cc_start: 0.8911 (m-40) cc_final: 0.8659 (m-40) REVERT: C 115 MET cc_start: 0.7251 (tpp) cc_final: 0.6902 (tpt) REVERT: C 334 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7929 (mtmm) outliers start: 19 outliers final: 11 residues processed: 336 average time/residue: 2.4319 time to fit residues: 950.7689 Evaluate side-chains 336 residues out of total 2517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 319 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 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 B residue 562 SER Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 566 ASP Chi-restraints excluded: chain C residue 733 GLN 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 194 optimal weight: 0.2980 chunk 261 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 245 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 252 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3068 r_free = 0.3068 target = 0.099613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.082898 restraints weight = 90858.800| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.59 r_work: 0.2886 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 24048 Z= 0.153 Angle : 0.469 5.493 32661 Z= 0.248 Chirality : 0.039 0.146 3841 Planarity : 0.004 0.046 4176 Dihedral : 4.356 42.123 3318 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.79 % Allowed : 10.56 % Favored : 88.65 % 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: 2.31 (0.15), residues: 3097 helix: 2.64 (0.12), residues: 1715 sheet: 0.14 (0.25), residues: 388 loop : 0.18 (0.20), residues: 994 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 11 TYR 0.017 0.001 TYR B 554 ARG 0.006 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: 14429.20 seconds wall clock time: 246 minutes 46.79 seconds (14806.79 seconds total)