Starting phenix.real_space_refine on Sun May 18 19:10:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vhz_43244/05_2025/8vhz_43244.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vhz_43244/05_2025/8vhz_43244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vhz_43244/05_2025/8vhz_43244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vhz_43244/05_2025/8vhz_43244.map" model { file = "/net/cci-nas-00/data/ceres_data/8vhz_43244/05_2025/8vhz_43244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vhz_43244/05_2025/8vhz_43244.cif" } resolution = 3.3 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= 0.001 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 11280 2.51 5 N 2856 2.21 5 O 2985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17208 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5736 Classifications: {'peptide': 714} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 666} Chain breaks: 2 Restraints were copied for chains: C, B Time building chain proxies: 13.56, per 1000 atoms: 0.79 Number of scatterers: 17208 At special positions: 0 Unit cell: (131.76, 135, 104.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 2985 8.00 N 2856 7.00 C 11280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.75 Conformation dependent library (CDL) restraints added in 2.1 seconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4002 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 9 sheets defined 58.8% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 271 through 298 Proline residue: A 277 - end of helix removed outlier: 3.625A pdb=" N PHE A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 292 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLN A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 327 Processing helix chain 'A' and resid 338 through 346 removed outlier: 3.503A pdb=" N LEU A 342 " --> pdb=" O TYR A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 384 removed outlier: 3.781A pdb=" N THR A 375 " --> pdb=" O PRO A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 402 through 427 removed outlier: 3.708A pdb=" N LYS A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Proline residue: A 421 - end of helix Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 452 through 477 removed outlier: 3.598A pdb=" N ARG A 457 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 465 " --> pdb=" O ARG A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 556 Processing helix chain 'A' and resid 574 through 584 removed outlier: 3.633A pdb=" N PHE A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 620 Processing helix chain 'A' and resid 620 through 627 Processing helix chain 'A' and resid 642 through 646 removed outlier: 3.593A pdb=" N TYR A 646 " --> pdb=" O ARG A 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 642 through 646' Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 729 through 737 removed outlier: 3.697A pdb=" N PHE A 737 " --> pdb=" O ILE A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 752 removed outlier: 3.702A pdb=" N THR A 751 " --> pdb=" O ASN A 748 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 752 " --> pdb=" O PRO A 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 748 through 752' Processing helix chain 'A' and resid 753 through 761 removed outlier: 3.506A pdb=" N SER A 761 " --> pdb=" O ILE A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 793 removed outlier: 4.468A pdb=" N LEU A 786 " --> pdb=" O THR A 782 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 787 " --> pdb=" O GLU A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 836 Processing helix chain 'A' and resid 850 through 863 Processing helix chain 'A' and resid 866 through 883 Proline residue: A 877 - end of helix removed outlier: 3.573A pdb=" N THR A 883 " --> pdb=" O PHE A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 918 removed outlier: 4.339A pdb=" N TRP A 898 " --> pdb=" O PHE A 894 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 899 " --> pdb=" O ALA A 895 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER A 910 " --> pdb=" O ILE A 906 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 911 " --> pdb=" O PHE A 907 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 938 removed outlier: 3.519A pdb=" N ALA A 938 " --> pdb=" O GLY A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 953 Processing helix chain 'A' and resid 980 through 982 No H-bonds generated for 'chain 'A' and resid 980 through 982' Processing helix chain 'A' and resid 983 through 1008 removed outlier: 3.755A pdb=" N THR A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1021 removed outlier: 3.879A pdb=" N LEU A1015 " --> pdb=" O SER A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1029 removed outlier: 3.866A pdb=" N ILE A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1037 Processing helix chain 'A' and resid 1044 through 1063 removed outlier: 3.583A pdb=" N ILE A1048 " --> pdb=" O PRO A1044 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A1063 " --> pdb=" O SER A1059 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 298 Proline residue: B 277 - end of helix removed outlier: 3.625A pdb=" N PHE B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLN B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 327 Processing helix chain 'B' and resid 338 through 346 removed outlier: 3.503A pdb=" N LEU B 342 " --> pdb=" O TYR B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 384 removed outlier: 3.780A pdb=" N THR B 375 " --> pdb=" O PRO B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 402 through 427 removed outlier: 3.708A pdb=" N LYS B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Proline residue: B 421 - end of helix Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 452 through 477 removed outlier: 3.598A pdb=" N ARG B 457 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 465 " --> pdb=" O ARG B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 556 Processing helix chain 'B' and resid 574 through 584 removed outlier: 3.634A pdb=" N PHE B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 620 Processing helix chain 'B' and resid 620 through 627 Processing helix chain 'B' and resid 642 through 646 removed outlier: 3.593A pdb=" N TYR B 646 " --> pdb=" O ARG B 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 642 through 646' Processing helix chain 'B' and resid 719 through 726 Processing helix chain 'B' and resid 729 through 737 removed outlier: 3.697A pdb=" N PHE B 737 " --> pdb=" O ILE B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 752 removed outlier: 3.703A pdb=" N THR B 751 " --> pdb=" O ASN B 748 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 752 " --> pdb=" O PRO B 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 748 through 752' Processing helix chain 'B' and resid 753 through 761 removed outlier: 3.506A pdb=" N SER B 761 " --> pdb=" O ILE B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 793 removed outlier: 4.468A pdb=" N LEU B 786 " --> pdb=" O THR B 782 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR B 787 " --> pdb=" O GLU B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 836 Processing helix chain 'B' and resid 850 through 863 Processing helix chain 'B' and resid 866 through 883 Proline residue: B 877 - end of helix removed outlier: 3.574A pdb=" N THR B 883 " --> pdb=" O PHE B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 918 removed outlier: 4.340A pdb=" N TRP B 898 " --> pdb=" O PHE B 894 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE B 899 " --> pdb=" O ALA B 895 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER B 910 " --> pdb=" O ILE B 906 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 911 " --> pdb=" O PHE B 907 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 912 " --> pdb=" O THR B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 938 removed outlier: 3.519A pdb=" N ALA B 938 " --> pdb=" O GLY B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 953 Processing helix chain 'B' and resid 980 through 982 No H-bonds generated for 'chain 'B' and resid 980 through 982' Processing helix chain 'B' and resid 983 through 1008 removed outlier: 3.755A pdb=" N THR B 987 " --> pdb=" O LEU B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1021 removed outlier: 3.879A pdb=" N LEU B1015 " --> pdb=" O SER B1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1029 removed outlier: 3.866A pdb=" N ILE B1026 " --> pdb=" O ALA B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1037 Processing helix chain 'B' and resid 1044 through 1063 removed outlier: 3.583A pdb=" N ILE B1048 " --> pdb=" O PRO B1044 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B1063 " --> pdb=" O SER B1059 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 298 Proline residue: C 277 - end of helix removed outlier: 3.625A pdb=" N PHE C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE C 292 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C 293 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN C 294 " --> pdb=" O GLY C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 327 Processing helix chain 'C' and resid 338 through 346 removed outlier: 3.502A pdb=" N LEU C 342 " --> pdb=" O TYR C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 384 removed outlier: 3.780A pdb=" N THR C 375 " --> pdb=" O PRO C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 402 through 427 removed outlier: 3.708A pdb=" N LYS C 417 " --> pdb=" O ALA C 413 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) Proline residue: C 421 - end of helix Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 452 through 477 removed outlier: 3.598A pdb=" N ARG C 457 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU C 465 " --> pdb=" O ARG C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 556 Processing helix chain 'C' and resid 574 through 584 removed outlier: 3.634A pdb=" N PHE C 582 " --> pdb=" O GLU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 620 Processing helix chain 'C' and resid 620 through 627 Processing helix chain 'C' and resid 642 through 646 removed outlier: 3.593A pdb=" N TYR C 646 " --> pdb=" O ARG C 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 642 through 646' Processing helix chain 'C' and resid 719 through 726 Processing helix chain 'C' and resid 729 through 737 removed outlier: 3.698A pdb=" N PHE C 737 " --> pdb=" O ILE C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 752 removed outlier: 3.703A pdb=" N THR C 751 " --> pdb=" O ASN C 748 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 752 " --> pdb=" O PRO C 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 748 through 752' Processing helix chain 'C' and resid 753 through 761 removed outlier: 3.507A pdb=" N SER C 761 " --> pdb=" O ILE C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 793 removed outlier: 4.467A pdb=" N LEU C 786 " --> pdb=" O THR C 782 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR C 787 " --> pdb=" O GLU C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 836 Processing helix chain 'C' and resid 850 through 863 Processing helix chain 'C' and resid 866 through 883 Proline residue: C 877 - end of helix removed outlier: 3.574A pdb=" N THR C 883 " --> pdb=" O PHE C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 918 removed outlier: 4.339A pdb=" N TRP C 898 " --> pdb=" O PHE C 894 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE C 899 " --> pdb=" O ALA C 895 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER C 910 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE C 911 " --> pdb=" O PHE C 907 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 912 " --> pdb=" O THR C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 938 removed outlier: 3.519A pdb=" N ALA C 938 " --> pdb=" O GLY C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 953 Processing helix chain 'C' and resid 980 through 982 No H-bonds generated for 'chain 'C' and resid 980 through 982' Processing helix chain 'C' and resid 983 through 1008 removed outlier: 3.755A pdb=" N THR C 987 " --> pdb=" O LEU C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1011 through 1021 removed outlier: 3.879A pdb=" N LEU C1015 " --> pdb=" O SER C1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 1022 through 1029 removed outlier: 3.866A pdb=" N ILE C1026 " --> pdb=" O ALA C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1029 through 1037 Processing helix chain 'C' and resid 1044 through 1063 removed outlier: 3.583A pdb=" N ILE C1048 " --> pdb=" O PRO C1044 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C1063 " --> pdb=" O SER C1059 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 269 Processing sheet with id=AA2, first strand: chain 'A' and resid 504 through 507 removed outlier: 4.003A pdb=" N ARG A 524 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL A 358 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N TYR A 395 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL A 360 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N SER A 397 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL A 362 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP A 359 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS A 638 " --> pdb=" O ASN A 563 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N CYS A 593 " --> pdb=" O ASN A 641 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE A 799 " --> pdb=" O CYS A 593 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL A 595 " --> pdb=" O ILE A 799 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 569 through 570 removed outlier: 6.697A pdb=" N ARG A 600 " --> pdb=" O GLY A 810 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 269 Processing sheet with id=AA5, first strand: chain 'B' and resid 504 through 507 removed outlier: 4.003A pdb=" N ARG B 524 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL B 358 " --> pdb=" O SER B 393 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N TYR B 395 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL B 360 " --> pdb=" O TYR B 395 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N SER B 397 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL B 362 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP B 359 " --> pdb=" O LEU B 562 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS B 638 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N CYS B 593 " --> pdb=" O ASN B 641 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ILE B 799 " --> pdb=" O CYS B 593 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL B 595 " --> pdb=" O ILE B 799 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 569 through 570 removed outlier: 6.698A pdb=" N ARG B 600 " --> pdb=" O GLY B 810 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 265 through 269 Processing sheet with id=AA8, first strand: chain 'C' and resid 504 through 507 removed outlier: 4.003A pdb=" N ARG C 524 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL C 358 " --> pdb=" O SER C 393 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N TYR C 395 " --> pdb=" O VAL C 358 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL C 360 " --> pdb=" O TYR C 395 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N SER C 397 " --> pdb=" O VAL C 360 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL C 362 " --> pdb=" O SER C 397 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP C 359 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS C 638 " --> pdb=" O ASN C 563 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N CYS C 593 " --> pdb=" O ASN C 641 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE C 799 " --> pdb=" O CYS C 593 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL C 595 " --> pdb=" O ILE C 799 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 569 through 570 removed outlier: 6.697A pdb=" N ARG C 600 " --> pdb=" O GLY C 810 " (cutoff:3.500A) 858 hydrogen bonds defined for protein. 2556 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: 5.35 Time building geometry restraints manager: 5.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5328 1.34 - 1.46: 4332 1.46 - 1.58: 7929 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 17724 Sorted by residual: bond pdb=" CG PRO B 864 " pdb=" CD PRO B 864 " ideal model delta sigma weight residual 1.503 1.549 -0.046 3.40e-02 8.65e+02 1.83e+00 bond pdb=" CG PRO C 864 " pdb=" CD PRO C 864 " ideal model delta sigma weight residual 1.503 1.549 -0.046 3.40e-02 8.65e+02 1.83e+00 bond pdb=" CG PRO A 864 " pdb=" CD PRO A 864 " ideal model delta sigma weight residual 1.503 1.549 -0.046 3.40e-02 8.65e+02 1.80e+00 bond pdb=" CB LYS B 369 " pdb=" CG LYS B 369 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.04e+00 bond pdb=" CB LYS A 369 " pdb=" CG LYS A 369 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.93e-01 ... (remaining 17719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 23777 1.97 - 3.94: 274 3.94 - 5.91: 48 5.91 - 7.88: 18 7.88 - 9.85: 12 Bond angle restraints: 24129 Sorted by residual: angle pdb=" CA PRO C 864 " pdb=" N PRO C 864 " pdb=" CD PRO C 864 " ideal model delta sigma weight residual 112.00 106.04 5.96 1.40e+00 5.10e-01 1.81e+01 angle pdb=" CA PRO B 864 " pdb=" N PRO B 864 " pdb=" CD PRO B 864 " ideal model delta sigma weight residual 112.00 106.04 5.96 1.40e+00 5.10e-01 1.81e+01 angle pdb=" CA PRO A 864 " pdb=" N PRO A 864 " pdb=" CD PRO A 864 " ideal model delta sigma weight residual 112.00 106.05 5.95 1.40e+00 5.10e-01 1.80e+01 angle pdb=" CB LYS B 369 " pdb=" CG LYS B 369 " pdb=" CD LYS B 369 " ideal model delta sigma weight residual 111.30 119.20 -7.90 2.30e+00 1.89e-01 1.18e+01 angle pdb=" CB LYS A 369 " pdb=" CG LYS A 369 " pdb=" CD LYS A 369 " ideal model delta sigma weight residual 111.30 119.18 -7.88 2.30e+00 1.89e-01 1.18e+01 ... (remaining 24124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 9154 16.59 - 33.18: 930 33.18 - 49.78: 248 49.78 - 66.37: 60 66.37 - 82.96: 15 Dihedral angle restraints: 10407 sinusoidal: 4185 harmonic: 6222 Sorted by residual: dihedral pdb=" CA TYR C 863 " pdb=" C TYR C 863 " pdb=" N PRO C 864 " pdb=" CA PRO C 864 " ideal model delta harmonic sigma weight residual 180.00 160.50 19.50 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA TYR B 863 " pdb=" C TYR B 863 " pdb=" N PRO B 864 " pdb=" CA PRO B 864 " ideal model delta harmonic sigma weight residual 180.00 160.51 19.49 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA TYR A 863 " pdb=" C TYR A 863 " pdb=" N PRO A 864 " pdb=" CA PRO A 864 " ideal model delta harmonic sigma weight residual 180.00 160.53 19.47 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 10404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2140 0.048 - 0.095: 389 0.095 - 0.143: 105 0.143 - 0.190: 0 0.190 - 0.238: 6 Chirality restraints: 2640 Sorted by residual: chirality pdb=" CB THR B 782 " pdb=" CA THR B 782 " pdb=" OG1 THR B 782 " pdb=" CG2 THR B 782 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB THR C 782 " pdb=" CA THR C 782 " pdb=" OG1 THR C 782 " pdb=" CG2 THR C 782 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB THR A 782 " pdb=" CA THR A 782 " pdb=" OG1 THR A 782 " pdb=" CG2 THR A 782 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 2637 not shown) Planarity restraints: 3030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 863 " -0.077 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO B 864 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO B 864 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 864 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 863 " -0.077 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO A 864 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 864 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 864 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 863 " 0.077 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO C 864 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO C 864 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO C 864 " 0.062 5.00e-02 4.00e+02 ... (remaining 3027 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4285 2.80 - 3.32: 16310 3.32 - 3.85: 27873 3.85 - 4.37: 31520 4.37 - 4.90: 54621 Nonbonded interactions: 134609 Sorted by model distance: nonbonded pdb=" O VAL A 904 " pdb=" OG1 THR A 908 " model vdw 2.275 3.040 nonbonded pdb=" O VAL C 904 " pdb=" OG1 THR C 908 " model vdw 2.275 3.040 nonbonded pdb=" O VAL B 904 " pdb=" OG1 THR B 908 " model vdw 2.275 3.040 nonbonded pdb=" OG SER B 867 " pdb=" O GLY B 935 " model vdw 2.279 3.040 nonbonded pdb=" OG SER C 867 " pdb=" O GLY C 935 " model vdw 2.280 3.040 ... (remaining 134604 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 42.830 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 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 : 0.002 0.046 17724 Z= 0.100 Angle : 0.558 9.847 24129 Z= 0.273 Chirality : 0.040 0.238 2640 Planarity : 0.005 0.114 3030 Dihedral : 14.895 82.960 6405 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.16 % Allowed : 12.84 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.54 (0.19), residues: 2124 helix: 1.82 (0.16), residues: 1128 sheet: 2.20 (0.44), residues: 141 loop : -0.24 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 925 HIS 0.001 0.000 HIS C 539 PHE 0.015 0.001 PHE A 903 TYR 0.010 0.001 TYR B 594 ARG 0.006 0.000 ARG B 348 Details of bonding type rmsd hydrogen bonds : bond 0.11641 ( 858) hydrogen bonds : angle 5.34190 ( 2556) covalent geometry : bond 0.00223 (17724) covalent geometry : angle 0.55780 (24129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 227 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 578 GLU cc_start: 0.7446 (tt0) cc_final: 0.7103 (tt0) REVERT: B 403 MET cc_start: 0.8136 (tpt) cc_final: 0.7921 (tpp) REVERT: B 791 MET cc_start: 0.7756 (ttm) cc_final: 0.7308 (mtm) REVERT: C 300 PRO cc_start: 0.6484 (Cg_endo) cc_final: 0.6260 (Cg_exo) REVERT: C 499 ARG cc_start: 0.7355 (mpt-90) cc_final: 0.7099 (mpp80) REVERT: C 825 ARG cc_start: 0.8447 (ttp-110) cc_final: 0.8070 (ttp80) REVERT: C 843 TYR cc_start: 0.7081 (t80) cc_final: 0.4668 (m-10) REVERT: C 845 TYR cc_start: 0.5847 (m-80) cc_final: 0.5624 (m-80) outliers start: 3 outliers final: 1 residues processed: 228 average time/residue: 0.2949 time to fit residues: 100.1553 Evaluate side-chains 185 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 0.1980 chunk 161 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 193 optimal weight: 6.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 ASN ** A 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN ** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.188226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.147736 restraints weight = 22361.465| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 4.14 r_work: 0.3490 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17724 Z= 0.142 Angle : 0.576 9.973 24129 Z= 0.282 Chirality : 0.042 0.178 2640 Planarity : 0.005 0.080 3030 Dihedral : 3.836 50.179 2324 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.68 % Allowed : 10.49 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.55 (0.18), residues: 2124 helix: 1.88 (0.16), residues: 1143 sheet: 2.12 (0.43), residues: 138 loop : -0.33 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 925 HIS 0.003 0.001 HIS B 939 PHE 0.021 0.001 PHE C1032 TYR 0.031 0.001 TYR B 863 ARG 0.005 0.000 ARG C 348 Details of bonding type rmsd hydrogen bonds : bond 0.04159 ( 858) hydrogen bonds : angle 4.10623 ( 2556) covalent geometry : bond 0.00323 (17724) covalent geometry : angle 0.57553 (24129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 208 time to evaluate : 1.996 Fit side-chains REVERT: A 619 ASP cc_start: 0.8367 (t0) cc_final: 0.8112 (m-30) REVERT: A 926 ARG cc_start: 0.7849 (tpp80) cc_final: 0.7166 (mmm-85) REVERT: B 791 MET cc_start: 0.7981 (ttm) cc_final: 0.7681 (mtm) REVERT: B 931 TRP cc_start: 0.7993 (t60) cc_final: 0.7703 (t60) REVERT: C 300 PRO cc_start: 0.6657 (Cg_endo) cc_final: 0.6405 (Cg_exo) REVERT: C 565 ASP cc_start: 0.8386 (t0) cc_final: 0.7845 (t0) REVERT: C 825 ARG cc_start: 0.8581 (ttp-110) cc_final: 0.8183 (ttp80) REVERT: C 843 TYR cc_start: 0.7076 (t80) cc_final: 0.4881 (m-10) REVERT: C 926 ARG cc_start: 0.7546 (tpp80) cc_final: 0.6953 (mmm-85) REVERT: C 927 ASN cc_start: 0.8286 (t0) cc_final: 0.7954 (t0) outliers start: 50 outliers final: 19 residues processed: 244 average time/residue: 0.3043 time to fit residues: 111.0639 Evaluate side-chains 206 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 921 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 870 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 55 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 174 optimal weight: 0.0770 chunk 155 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 0.0070 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 815 ASN ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.189045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.149047 restraints weight = 22346.878| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 4.19 r_work: 0.3504 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17724 Z= 0.110 Angle : 0.539 12.572 24129 Z= 0.261 Chirality : 0.041 0.217 2640 Planarity : 0.004 0.072 3030 Dihedral : 3.749 51.397 2324 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.87 % Allowed : 12.73 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.66 (0.18), residues: 2124 helix: 1.95 (0.16), residues: 1149 sheet: 2.04 (0.43), residues: 138 loop : -0.24 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 925 HIS 0.002 0.000 HIS C1028 PHE 0.016 0.001 PHE A 930 TYR 0.023 0.001 TYR A 863 ARG 0.007 0.000 ARG C 805 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 858) hydrogen bonds : angle 3.84953 ( 2556) covalent geometry : bond 0.00246 (17724) covalent geometry : angle 0.53914 (24129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 201 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 619 ASP cc_start: 0.8440 (t0) cc_final: 0.8159 (m-30) REVERT: B 791 MET cc_start: 0.7926 (ttm) cc_final: 0.7650 (mtm) REVERT: B 902 LEU cc_start: 0.5148 (OUTLIER) cc_final: 0.4734 (tp) REVERT: C 300 PRO cc_start: 0.6592 (Cg_endo) cc_final: 0.6336 (Cg_exo) REVERT: C 565 ASP cc_start: 0.8369 (t0) cc_final: 0.8161 (t0) REVERT: C 825 ARG cc_start: 0.8608 (ttp-110) cc_final: 0.8255 (ttp80) REVERT: C 843 TYR cc_start: 0.7043 (t80) cc_final: 0.4874 (m-10) REVERT: C 927 ASN cc_start: 0.8283 (t0) cc_final: 0.8028 (t0) outliers start: 35 outliers final: 23 residues processed: 232 average time/residue: 0.3161 time to fit residues: 109.6299 Evaluate side-chains 210 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 783 GLU Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 909 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 861 ILE Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 945 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 41 optimal weight: 0.0040 chunk 82 optimal weight: 0.5980 chunk 176 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN ** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.187334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.131798 restraints weight = 22289.350| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.43 r_work: 0.3588 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17724 Z= 0.128 Angle : 0.531 11.817 24129 Z= 0.259 Chirality : 0.041 0.186 2640 Planarity : 0.004 0.066 3030 Dihedral : 3.721 52.511 2324 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.57 % Allowed : 13.06 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.67 (0.18), residues: 2124 helix: 2.03 (0.16), residues: 1149 sheet: 1.83 (0.43), residues: 138 loop : -0.31 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 925 HIS 0.003 0.000 HIS B 511 PHE 0.018 0.001 PHE A 930 TYR 0.034 0.001 TYR B 863 ARG 0.005 0.000 ARG B 348 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 858) hydrogen bonds : angle 3.71478 ( 2556) covalent geometry : bond 0.00296 (17724) covalent geometry : angle 0.53081 (24129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 1.950 Fit side-chains revert: symmetry clash REVERT: A 619 ASP cc_start: 0.8393 (t0) cc_final: 0.8161 (m-30) REVERT: A 926 ARG cc_start: 0.7775 (tpp80) cc_final: 0.7141 (mmm-85) REVERT: B 791 MET cc_start: 0.7865 (ttm) cc_final: 0.7641 (mtm) REVERT: B 879 PHE cc_start: 0.7054 (t80) cc_final: 0.6823 (t80) REVERT: B 902 LEU cc_start: 0.5084 (OUTLIER) cc_final: 0.4781 (tp) REVERT: B 926 ARG cc_start: 0.7868 (tpp80) cc_final: 0.7115 (mmm-85) REVERT: C 300 PRO cc_start: 0.6459 (Cg_endo) cc_final: 0.6153 (Cg_exo) REVERT: C 594 TYR cc_start: 0.8865 (p90) cc_final: 0.8620 (p90) REVERT: C 825 ARG cc_start: 0.8592 (ttp-110) cc_final: 0.8280 (ttp80) REVERT: C 926 ARG cc_start: 0.7448 (tpp80) cc_final: 0.6860 (mmm-85) REVERT: C 927 ASN cc_start: 0.8299 (t0) cc_final: 0.8000 (t0) outliers start: 48 outliers final: 29 residues processed: 246 average time/residue: 0.2868 time to fit residues: 106.0457 Evaluate side-chains 215 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 945 GLN Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 945 GLN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 945 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 210 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 168 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.185691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.129605 restraints weight = 22540.887| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.45 r_work: 0.3558 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17724 Z= 0.150 Angle : 0.553 13.106 24129 Z= 0.269 Chirality : 0.042 0.193 2640 Planarity : 0.004 0.062 3030 Dihedral : 3.790 53.409 2324 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.94 % Allowed : 13.43 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.61 (0.19), residues: 2124 helix: 2.03 (0.16), residues: 1149 sheet: 1.60 (0.44), residues: 138 loop : -0.38 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 925 HIS 0.001 0.000 HIS C 539 PHE 0.018 0.001 PHE A 930 TYR 0.011 0.001 TYR B 463 ARG 0.007 0.000 ARG B 348 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 858) hydrogen bonds : angle 3.73260 ( 2556) covalent geometry : bond 0.00357 (17724) covalent geometry : angle 0.55260 (24129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 209 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 619 ASP cc_start: 0.8393 (t0) cc_final: 0.8156 (m-30) REVERT: B 937 SER cc_start: 0.8916 (m) cc_final: 0.8654 (p) REVERT: C 370 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7373 (pp20) REVERT: C 594 TYR cc_start: 0.8855 (p90) cc_final: 0.8534 (p90) REVERT: C 738 MET cc_start: 0.8756 (tpp) cc_final: 0.8087 (mpp) REVERT: C 825 ARG cc_start: 0.8630 (ttp-110) cc_final: 0.8354 (ttp80) REVERT: C 926 ARG cc_start: 0.7495 (tpp80) cc_final: 0.6972 (tpp80) REVERT: C 927 ASN cc_start: 0.8368 (t0) cc_final: 0.8098 (t0) outliers start: 55 outliers final: 30 residues processed: 256 average time/residue: 0.2862 time to fit residues: 110.2719 Evaluate side-chains 226 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 945 GLN Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 992 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 861 ILE Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 945 GLN Chi-restraints excluded: chain C residue 991 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 85 optimal weight: 0.0980 chunk 174 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 202 optimal weight: 0.7980 chunk 204 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.185989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.133403 restraints weight = 22438.742| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.97 r_work: 0.3552 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17724 Z= 0.126 Angle : 0.547 12.733 24129 Z= 0.265 Chirality : 0.041 0.198 2640 Planarity : 0.004 0.058 3030 Dihedral : 3.754 54.146 2324 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.16 % Allowed : 13.80 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.68 (0.19), residues: 2124 helix: 2.09 (0.16), residues: 1149 sheet: 1.40 (0.44), residues: 135 loop : -0.30 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 925 HIS 0.002 0.000 HIS A1028 PHE 0.017 0.001 PHE A 930 TYR 0.010 0.001 TYR B 463 ARG 0.007 0.000 ARG B 348 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 858) hydrogen bonds : angle 3.64832 ( 2556) covalent geometry : bond 0.00296 (17724) covalent geometry : angle 0.54682 (24129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 198 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 619 ASP cc_start: 0.8395 (t0) cc_final: 0.8171 (m-30) REVERT: A 937 SER cc_start: 0.8916 (m) cc_final: 0.8597 (p) REVERT: B 327 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7079 (t80) REVERT: B 930 PHE cc_start: 0.8283 (t80) cc_final: 0.7965 (t80) REVERT: B 937 SER cc_start: 0.8899 (m) cc_final: 0.8686 (p) REVERT: C 307 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6503 (tt) REVERT: C 594 TYR cc_start: 0.8886 (p90) cc_final: 0.8585 (p90) REVERT: C 825 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.8287 (ttp80) REVERT: C 926 ARG cc_start: 0.7463 (tpp80) cc_final: 0.6966 (mmm-85) REVERT: C 927 ASN cc_start: 0.8431 (t0) cc_final: 0.8135 (t0) outliers start: 59 outliers final: 36 residues processed: 254 average time/residue: 0.2906 time to fit residues: 112.8403 Evaluate side-chains 225 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 GLN Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 909 THR Chi-restraints excluded: chain B residue 992 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 861 ILE Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 945 GLN Chi-restraints excluded: chain C residue 991 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 60 optimal weight: 2.9990 chunk 83 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.184557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.128363 restraints weight = 22526.948| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.44 r_work: 0.3543 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17724 Z= 0.156 Angle : 0.563 13.209 24129 Z= 0.276 Chirality : 0.042 0.198 2640 Planarity : 0.004 0.055 3030 Dihedral : 3.833 54.055 2324 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.53 % Allowed : 13.38 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.62 (0.19), residues: 2124 helix: 2.08 (0.16), residues: 1149 sheet: 1.16 (0.44), residues: 135 loop : -0.33 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 925 HIS 0.002 0.000 HIS C 539 PHE 0.019 0.001 PHE A 930 TYR 0.025 0.001 TYR B 594 ARG 0.009 0.000 ARG C 296 Details of bonding type rmsd hydrogen bonds : bond 0.03677 ( 858) hydrogen bonds : angle 3.69119 ( 2556) covalent geometry : bond 0.00375 (17724) covalent geometry : angle 0.56268 (24129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 195 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 MET cc_start: 0.8384 (tpp) cc_final: 0.8092 (mtp) REVERT: A 619 ASP cc_start: 0.8402 (t0) cc_final: 0.8168 (m-30) REVERT: A 937 SER cc_start: 0.8984 (m) cc_final: 0.8615 (p) REVERT: B 327 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7093 (t80) REVERT: B 925 TRP cc_start: 0.7871 (t-100) cc_final: 0.7634 (t-100) REVERT: C 307 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6443 (tt) REVERT: C 480 MET cc_start: 0.8696 (tpp) cc_final: 0.8355 (tpt) REVERT: C 594 TYR cc_start: 0.8862 (p90) cc_final: 0.8530 (p90) REVERT: C 825 ARG cc_start: 0.8669 (ttp-110) cc_final: 0.8401 (ttp80) REVERT: C 855 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7846 (mp) REVERT: C 926 ARG cc_start: 0.7606 (tpp80) cc_final: 0.7076 (mmm-85) REVERT: C 927 ASN cc_start: 0.8426 (t0) cc_final: 0.8139 (t0) outliers start: 66 outliers final: 44 residues processed: 255 average time/residue: 0.2924 time to fit residues: 112.4686 Evaluate side-chains 236 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 189 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 GLN Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 992 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 839 CYS Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 861 ILE Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 945 GLN Chi-restraints excluded: chain C residue 991 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 210 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 183 optimal weight: 0.0000 chunk 90 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 159 optimal weight: 0.3980 chunk 100 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 929 GLN ** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.185667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.134932 restraints weight = 22330.615| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 3.12 r_work: 0.3543 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17724 Z= 0.128 Angle : 0.559 12.888 24129 Z= 0.271 Chirality : 0.042 0.289 2640 Planarity : 0.004 0.048 3030 Dihedral : 3.808 54.789 2324 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.00 % Allowed : 14.61 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.67 (0.19), residues: 2124 helix: 2.12 (0.16), residues: 1149 sheet: 1.10 (0.44), residues: 135 loop : -0.31 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 925 HIS 0.001 0.000 HIS C 539 PHE 0.015 0.001 PHE A 930 TYR 0.017 0.001 TYR B 594 ARG 0.007 0.000 ARG C 296 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 858) hydrogen bonds : angle 3.61859 ( 2556) covalent geometry : bond 0.00305 (17724) covalent geometry : angle 0.55870 (24129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 196 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 LEU cc_start: 0.7286 (tt) cc_final: 0.7083 (tp) REVERT: A 307 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6310 (tt) REVERT: A 619 ASP cc_start: 0.8387 (t0) cc_final: 0.8181 (m-30) REVERT: A 937 SER cc_start: 0.8977 (m) cc_final: 0.8613 (p) REVERT: B 307 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6405 (tt) REVERT: B 327 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7085 (t80) REVERT: B 925 TRP cc_start: 0.7887 (t-100) cc_final: 0.7664 (t-100) REVERT: C 307 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6486 (tt) REVERT: C 480 MET cc_start: 0.8711 (tpp) cc_final: 0.8297 (tpt) REVERT: C 594 TYR cc_start: 0.8885 (p90) cc_final: 0.8536 (p90) REVERT: C 738 MET cc_start: 0.8822 (tpp) cc_final: 0.8205 (mpp) REVERT: C 825 ARG cc_start: 0.8653 (ttp-110) cc_final: 0.8366 (ttp80) REVERT: C 926 ARG cc_start: 0.7595 (tpp80) cc_final: 0.7036 (mmm-85) REVERT: C 927 ASN cc_start: 0.8471 (t0) cc_final: 0.8191 (t0) outliers start: 56 outliers final: 42 residues processed: 245 average time/residue: 0.2760 time to fit residues: 102.8635 Evaluate side-chains 236 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 190 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 GLN Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 909 THR Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 861 ILE Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 945 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 28 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 184 optimal weight: 0.0770 chunk 22 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 929 GLN ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.185652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.134591 restraints weight = 22549.194| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.82 r_work: 0.3539 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17724 Z= 0.128 Angle : 0.556 12.594 24129 Z= 0.271 Chirality : 0.042 0.263 2640 Planarity : 0.004 0.046 3030 Dihedral : 3.804 55.395 2324 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.68 % Allowed : 14.71 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.70 (0.19), residues: 2124 helix: 2.11 (0.16), residues: 1152 sheet: 0.94 (0.40), residues: 165 loop : -0.25 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 925 HIS 0.002 0.000 HIS C 939 PHE 0.016 0.001 PHE A 930 TYR 0.026 0.001 TYR A 594 ARG 0.007 0.000 ARG B 348 Details of bonding type rmsd hydrogen bonds : bond 0.03388 ( 858) hydrogen bonds : angle 3.59917 ( 2556) covalent geometry : bond 0.00305 (17724) covalent geometry : angle 0.55621 (24129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 197 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.6304 (tt) REVERT: A 619 ASP cc_start: 0.8399 (t0) cc_final: 0.8198 (m-30) REVERT: A 937 SER cc_start: 0.8962 (m) cc_final: 0.8620 (p) REVERT: B 307 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6428 (tt) REVERT: B 327 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7104 (t80) REVERT: B 578 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7658 (tt0) REVERT: B 925 TRP cc_start: 0.7937 (t-100) cc_final: 0.7695 (t-100) REVERT: C 307 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6492 (tt) REVERT: C 480 MET cc_start: 0.8721 (tpp) cc_final: 0.8317 (tpt) REVERT: C 594 TYR cc_start: 0.8904 (p90) cc_final: 0.8602 (p90) REVERT: C 825 ARG cc_start: 0.8659 (ttp-110) cc_final: 0.8398 (ttp80) REVERT: C 926 ARG cc_start: 0.7613 (tpp80) cc_final: 0.7038 (mmm-85) REVERT: C 927 ASN cc_start: 0.8513 (t0) cc_final: 0.8216 (t0) outliers start: 50 outliers final: 41 residues processed: 242 average time/residue: 0.2771 time to fit residues: 101.7655 Evaluate side-chains 238 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 GLN Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 992 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 839 CYS Chi-restraints excluded: chain C residue 861 ILE Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 945 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 172 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 116 optimal weight: 0.0570 chunk 9 optimal weight: 0.7980 chunk 141 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 164 optimal weight: 0.0570 chunk 91 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 929 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.185953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.129879 restraints weight = 22311.773| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.43 r_work: 0.3559 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17724 Z= 0.124 Angle : 0.566 12.597 24129 Z= 0.274 Chirality : 0.042 0.298 2640 Planarity : 0.004 0.045 3030 Dihedral : 3.793 55.868 2324 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.62 % Allowed : 14.98 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.74 (0.19), residues: 2124 helix: 2.14 (0.16), residues: 1152 sheet: 0.97 (0.40), residues: 165 loop : -0.23 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 925 HIS 0.001 0.000 HIS C 539 PHE 0.014 0.001 PHE A 930 TYR 0.019 0.001 TYR A 594 ARG 0.007 0.000 ARG B 348 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 858) hydrogen bonds : angle 3.56681 ( 2556) covalent geometry : bond 0.00296 (17724) covalent geometry : angle 0.56579 (24129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6232 (tt) REVERT: A 937 SER cc_start: 0.8921 (m) cc_final: 0.8597 (p) REVERT: B 307 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6345 (tt) REVERT: B 327 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7120 (t80) REVERT: B 578 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7672 (tt0) REVERT: B 925 TRP cc_start: 0.7893 (t-100) cc_final: 0.7662 (t-100) REVERT: C 307 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6457 (tt) REVERT: C 480 MET cc_start: 0.8693 (tpp) cc_final: 0.8310 (tpt) REVERT: C 594 TYR cc_start: 0.8873 (p90) cc_final: 0.8572 (p90) REVERT: C 825 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8329 (ttp80) REVERT: C 926 ARG cc_start: 0.7541 (tpp80) cc_final: 0.7034 (mmm-85) outliers start: 49 outliers final: 42 residues processed: 235 average time/residue: 0.2871 time to fit residues: 102.2402 Evaluate side-chains 233 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 187 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 GLN Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 992 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 839 CYS Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 861 ILE Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 945 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 134 optimal weight: 0.0040 chunk 156 optimal weight: 0.5980 chunk 130 optimal weight: 6.9990 chunk 157 optimal weight: 0.5980 chunk 163 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 184 optimal weight: 0.0270 chunk 75 optimal weight: 0.2980 chunk 211 optimal weight: 0.9980 chunk 116 optimal weight: 0.0070 overall best weight: 0.1868 ------------------------------------------------------------------------------- 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 = 0.4401 r_free = 0.4401 target = 0.188078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.147524 restraints weight = 22350.436| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 3.98 r_work: 0.3503 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17724 Z= 0.102 Angle : 0.551 12.661 24129 Z= 0.266 Chirality : 0.041 0.292 2640 Planarity : 0.004 0.044 3030 Dihedral : 3.711 56.826 2324 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.98 % Allowed : 15.73 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.89 (0.19), residues: 2124 helix: 2.32 (0.16), residues: 1134 sheet: 1.22 (0.42), residues: 150 loop : -0.21 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP C 925 HIS 0.002 0.000 HIS C 539 PHE 0.013 0.001 PHE A 930 TYR 0.020 0.001 TYR A 594 ARG 0.007 0.000 ARG B 348 Details of bonding type rmsd hydrogen bonds : bond 0.02980 ( 858) hydrogen bonds : angle 3.45882 ( 2556) covalent geometry : bond 0.00231 (17724) covalent geometry : angle 0.55075 (24129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8389.13 seconds wall clock time: 145 minutes 57.92 seconds (8757.92 seconds total)