Starting phenix.real_space_refine on Sun Jul 5 21:13:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wrc_32722/07_2026/7wrc_32722.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrc_32722/07_2026/7wrc_32722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7wrc_32722/07_2026/7wrc_32722.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wrc_32722/07_2026/7wrc_32722.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wrc_32722/07_2026/7wrc_32722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrc_32722/07_2026/7wrc_32722.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wrc_32722/07_2026/7wrc_32722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrc_32722/07_2026/7wrc_32722.map" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 140 5.16 5 C 19820 2.51 5 N 5052 2.21 5 O 5452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30468 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D Time building chain proxies: 10.10, per 1000 atoms: 0.33 Number of scatterers: 30468 At special positions: 0 Unit cell: (155.142, 155.142, 157.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 140 16.00 O 5452 8.00 N 5052 7.00 C 19820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 929 " - pdb=" SG CYS A 940 " distance=2.01 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 940 " distance=2.01 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.01 Simple disulfide: pdb=" SG CYS D 929 " - pdb=" SG CYS D 940 " distance=2.01 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: 2.60 Conformation dependent library (CDL) restraints added in 1.3 seconds 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7080 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 4 sheets defined 70.5% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 125 through 136 removed outlier: 3.920A pdb=" N LEU A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 176 Processing helix chain 'A' and resid 187 through 204 removed outlier: 3.866A pdb=" N TYR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 removed outlier: 4.625A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.701A pdb=" N LEU A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 341 removed outlier: 3.877A pdb=" N VAL A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 402 through 418 removed outlier: 3.711A pdb=" N TYR A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 438 through 446 removed outlier: 3.566A pdb=" N ALA A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'A' and resid 502 through 516 removed outlier: 3.575A pdb=" N TYR A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 507 " --> pdb=" O THR A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 532 removed outlier: 3.564A pdb=" N ARG A 532 " --> pdb=" O VAL A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.662A pdb=" N ALA A 563 " --> pdb=" O HIS A 559 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 571 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 582 removed outlier: 3.659A pdb=" N VAL A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 602 Processing helix chain 'A' and resid 607 through 636 removed outlier: 3.621A pdb=" N GLU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 644 Processing helix chain 'A' and resid 655 through 663 Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.759A pdb=" N ILE A 669 " --> pdb=" O ASP A 665 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 670 " --> pdb=" O GLN A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 670' Processing helix chain 'A' and resid 671 through 684 Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.538A pdb=" N ILE A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 removed outlier: 3.748A pdb=" N VAL A 705 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY A 706 " --> pdb=" O PRO A 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 702 through 706' Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 733 through 759 removed outlier: 3.682A pdb=" N ASP A 759 " --> pdb=" O VAL A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 790 Processing helix chain 'A' and resid 791 through 795 Processing helix chain 'A' and resid 796 through 817 Processing helix chain 'A' and resid 821 through 842 Processing helix chain 'A' and resid 842 through 847 Processing helix chain 'A' and resid 848 through 850 No H-bonds generated for 'chain 'A' and resid 848 through 850' Processing helix chain 'A' and resid 852 through 861 removed outlier: 4.214A pdb=" N LYS A 856 " --> pdb=" O ASN A 852 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A 861 " --> pdb=" O ILE A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 890 removed outlier: 3.521A pdb=" N ARG A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 904 removed outlier: 4.064A pdb=" N SER A 902 " --> pdb=" O TRP A 898 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 904 " --> pdb=" O PHE A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 910 Processing helix chain 'A' and resid 925 through 929 removed outlier: 4.002A pdb=" N HIS A 928 " --> pdb=" O ASP A 925 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N CYS A 929 " --> pdb=" O PHE A 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 925 through 929' Processing helix chain 'A' and resid 952 through 969 Proline residue: A 958 - end of helix Processing helix chain 'A' and resid 969 through 1007 removed outlier: 3.602A pdb=" N LEU A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N GLU A 988 " --> pdb=" O GLY A 984 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1030 removed outlier: 4.408A pdb=" N VAL A1017 " --> pdb=" O PHE A1013 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N PHE A1018 " --> pdb=" O PRO A1014 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A1019 " --> pdb=" O PHE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1071 removed outlier: 3.862A pdb=" N VAL A1058 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A1059 " --> pdb=" O TRP A1055 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A1071 " --> pdb=" O ILE A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1104 removed outlier: 3.676A pdb=" N MET A1078 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS A1104 " --> pdb=" O ALA A1100 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 136 removed outlier: 3.919A pdb=" N LEU B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 187 through 204 removed outlier: 3.865A pdb=" N TYR B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 287 removed outlier: 4.626A pdb=" N LEU B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 322 removed outlier: 3.701A pdb=" N LEU B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 341 removed outlier: 3.877A pdb=" N VAL B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 402 through 418 removed outlier: 3.712A pdb=" N TYR B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.565A pdb=" N ALA B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 468 Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 489 through 499 Processing helix chain 'B' and resid 502 through 516 removed outlier: 3.576A pdb=" N TYR B 506 " --> pdb=" O SER B 502 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 507 " --> pdb=" O THR B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 532 removed outlier: 3.564A pdb=" N ARG B 532 " --> pdb=" O VAL B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.662A pdb=" N ALA B 563 " --> pdb=" O HIS B 559 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN B 571 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 582 removed outlier: 3.658A pdb=" N VAL B 579 " --> pdb=" O GLU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 602 Processing helix chain 'B' and resid 607 through 636 removed outlier: 3.620A pdb=" N GLU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 655 through 663 Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.761A pdb=" N ILE B 669 " --> pdb=" O ASP B 665 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA B 670 " --> pdb=" O GLN B 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 665 through 670' Processing helix chain 'B' and resid 671 through 684 Processing helix chain 'B' and resid 691 through 701 removed outlier: 3.537A pdb=" N ILE B 695 " --> pdb=" O LYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 706 removed outlier: 3.748A pdb=" N VAL B 705 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY B 706 " --> pdb=" O PRO B 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 702 through 706' Processing helix chain 'B' and resid 723 through 731 Processing helix chain 'B' and resid 733 through 759 removed outlier: 3.682A pdb=" N ASP B 759 " --> pdb=" O VAL B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 790 Processing helix chain 'B' and resid 791 through 795 Processing helix chain 'B' and resid 796 through 817 Processing helix chain 'B' and resid 821 through 842 Processing helix chain 'B' and resid 842 through 847 Processing helix chain 'B' and resid 848 through 850 No H-bonds generated for 'chain 'B' and resid 848 through 850' Processing helix chain 'B' and resid 852 through 861 removed outlier: 4.213A pdb=" N LYS B 856 " --> pdb=" O ASN B 852 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN B 861 " --> pdb=" O ILE B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 890 removed outlier: 3.520A pdb=" N ARG B 890 " --> pdb=" O GLN B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 904 removed outlier: 4.063A pdb=" N SER B 902 " --> pdb=" O TRP B 898 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 904 " --> pdb=" O PHE B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 910 Processing helix chain 'B' and resid 925 through 929 removed outlier: 4.002A pdb=" N HIS B 928 " --> pdb=" O ASP B 925 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N CYS B 929 " --> pdb=" O PHE B 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 925 through 929' Processing helix chain 'B' and resid 952 through 969 Proline residue: B 958 - end of helix Processing helix chain 'B' and resid 969 through 1007 removed outlier: 3.602A pdb=" N LEU B 975 " --> pdb=" O LEU B 971 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N GLU B 988 " --> pdb=" O GLY B 984 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASN B 989 " --> pdb=" O ILE B 985 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR B 999 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B1001 " --> pdb=" O GLN B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1030 removed outlier: 4.419A pdb=" N VAL B1017 " --> pdb=" O PHE B1013 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE B1018 " --> pdb=" O PRO B1014 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B1019 " --> pdb=" O PHE B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1071 removed outlier: 3.861A pdb=" N VAL B1058 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET B1059 " --> pdb=" O TRP B1055 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA B1071 " --> pdb=" O ILE B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1104 removed outlier: 3.676A pdb=" N MET B1078 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B1104 " --> pdb=" O ALA B1100 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 136 removed outlier: 3.919A pdb=" N LEU C 129 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 176 Processing helix chain 'C' and resid 187 through 204 removed outlier: 3.866A pdb=" N TYR C 191 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 4.626A pdb=" N LEU C 277 " --> pdb=" O VAL C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 322 removed outlier: 3.701A pdb=" N LEU C 313 " --> pdb=" O GLY C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 341 removed outlier: 3.877A pdb=" N VAL C 338 " --> pdb=" O GLN C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 402 through 418 removed outlier: 3.711A pdb=" N TYR C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 436 Processing helix chain 'C' and resid 438 through 446 removed outlier: 3.567A pdb=" N ALA C 442 " --> pdb=" O GLN C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 468 Processing helix chain 'C' and resid 470 through 480 Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 489 through 499 Processing helix chain 'C' and resid 502 through 516 removed outlier: 3.576A pdb=" N TYR C 506 " --> pdb=" O SER C 502 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 507 " --> pdb=" O THR C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 532 removed outlier: 3.564A pdb=" N ARG C 532 " --> pdb=" O VAL C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.662A pdb=" N ALA C 563 " --> pdb=" O HIS C 559 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN C 571 " --> pdb=" O TRP C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 582 removed outlier: 3.659A pdb=" N VAL C 579 " --> pdb=" O GLU C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 602 Processing helix chain 'C' and resid 607 through 636 removed outlier: 3.620A pdb=" N GLU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 644 Processing helix chain 'C' and resid 655 through 663 Processing helix chain 'C' and resid 665 through 670 removed outlier: 3.760A pdb=" N ILE C 669 " --> pdb=" O ASP C 665 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA C 670 " --> pdb=" O GLN C 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 665 through 670' Processing helix chain 'C' and resid 671 through 684 Processing helix chain 'C' and resid 691 through 701 removed outlier: 3.538A pdb=" N ILE C 695 " --> pdb=" O LYS C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 706 removed outlier: 3.748A pdb=" N VAL C 705 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY C 706 " --> pdb=" O PRO C 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 702 through 706' Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'C' and resid 733 through 759 removed outlier: 3.682A pdb=" N ASP C 759 " --> pdb=" O VAL C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 765 through 790 Processing helix chain 'C' and resid 791 through 795 Processing helix chain 'C' and resid 796 through 817 Processing helix chain 'C' and resid 821 through 842 Processing helix chain 'C' and resid 842 through 847 Processing helix chain 'C' and resid 848 through 850 No H-bonds generated for 'chain 'C' and resid 848 through 850' Processing helix chain 'C' and resid 852 through 861 removed outlier: 4.214A pdb=" N LYS C 856 " --> pdb=" O ASN C 852 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN C 861 " --> pdb=" O ILE C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 890 removed outlier: 3.520A pdb=" N ARG C 890 " --> pdb=" O GLN C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 904 removed outlier: 4.064A pdb=" N SER C 902 " --> pdb=" O TRP C 898 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 904 " --> pdb=" O PHE C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 910 Processing helix chain 'C' and resid 925 through 929 removed outlier: 4.001A pdb=" N HIS C 928 " --> pdb=" O ASP C 925 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS C 929 " --> pdb=" O PHE C 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 925 through 929' Processing helix chain 'C' and resid 952 through 969 Proline residue: C 958 - end of helix Processing helix chain 'C' and resid 969 through 1007 removed outlier: 3.602A pdb=" N LEU C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N GLU C 988 " --> pdb=" O GLY C 984 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASN C 989 " --> pdb=" O ILE C 985 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR C 999 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU C1001 " --> pdb=" O GLN C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1030 removed outlier: 3.713A pdb=" N ALA C1019 " --> pdb=" O PHE C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1071 removed outlier: 3.862A pdb=" N VAL C1058 " --> pdb=" O ALA C1054 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET C1059 " --> pdb=" O TRP C1055 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA C1071 " --> pdb=" O ILE C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1104 removed outlier: 3.676A pdb=" N MET C1078 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS C1104 " --> pdb=" O ALA C1100 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 136 removed outlier: 3.919A pdb=" N LEU D 129 " --> pdb=" O ASP D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'D' and resid 187 through 204 removed outlier: 3.866A pdb=" N TYR D 191 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 287 removed outlier: 4.625A pdb=" N LEU D 277 " --> pdb=" O VAL D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 322 removed outlier: 3.700A pdb=" N LEU D 313 " --> pdb=" O GLY D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 341 removed outlier: 3.876A pdb=" N VAL D 338 " --> pdb=" O GLN D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 362 Processing helix chain 'D' and resid 365 through 369 Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 402 through 418 removed outlier: 3.711A pdb=" N TYR D 410 " --> pdb=" O ASN D 406 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR D 418 " --> pdb=" O LYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 436 Processing helix chain 'D' and resid 438 through 446 removed outlier: 3.566A pdb=" N ALA D 442 " --> pdb=" O GLN D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 468 Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 489 through 499 Processing helix chain 'D' and resid 502 through 516 removed outlier: 3.576A pdb=" N TYR D 506 " --> pdb=" O SER D 502 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG D 507 " --> pdb=" O THR D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 532 removed outlier: 3.564A pdb=" N ARG D 532 " --> pdb=" O VAL D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.662A pdb=" N ALA D 563 " --> pdb=" O HIS D 559 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN D 571 " --> pdb=" O TRP D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 582 removed outlier: 3.658A pdb=" N VAL D 579 " --> pdb=" O GLU D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 602 Processing helix chain 'D' and resid 607 through 636 removed outlier: 3.619A pdb=" N GLU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 644 Processing helix chain 'D' and resid 655 through 663 Processing helix chain 'D' and resid 665 through 670 removed outlier: 3.760A pdb=" N ILE D 669 " --> pdb=" O ASP D 665 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA D 670 " --> pdb=" O GLN D 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 665 through 670' Processing helix chain 'D' and resid 671 through 684 Processing helix chain 'D' and resid 691 through 701 removed outlier: 3.537A pdb=" N ILE D 695 " --> pdb=" O LYS D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 706 removed outlier: 3.748A pdb=" N VAL D 705 " --> pdb=" O ILE D 702 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY D 706 " --> pdb=" O PRO D 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 702 through 706' Processing helix chain 'D' and resid 723 through 731 Processing helix chain 'D' and resid 733 through 759 removed outlier: 3.682A pdb=" N ASP D 759 " --> pdb=" O VAL D 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 790 Processing helix chain 'D' and resid 791 through 795 Processing helix chain 'D' and resid 796 through 817 Processing helix chain 'D' and resid 821 through 842 Processing helix chain 'D' and resid 842 through 847 Processing helix chain 'D' and resid 848 through 850 No H-bonds generated for 'chain 'D' and resid 848 through 850' Processing helix chain 'D' and resid 852 through 861 removed outlier: 4.213A pdb=" N LYS D 856 " --> pdb=" O ASN D 852 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN D 861 " --> pdb=" O ILE D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 863 through 890 removed outlier: 3.521A pdb=" N ARG D 890 " --> pdb=" O GLN D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 904 removed outlier: 4.064A pdb=" N SER D 902 " --> pdb=" O TRP D 898 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE D 904 " --> pdb=" O PHE D 900 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 910 Processing helix chain 'D' and resid 925 through 929 removed outlier: 4.002A pdb=" N HIS D 928 " --> pdb=" O ASP D 925 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS D 929 " --> pdb=" O PHE D 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 925 through 929' Processing helix chain 'D' and resid 952 through 969 Proline residue: D 958 - end of helix Processing helix chain 'D' and resid 969 through 1007 removed outlier: 3.602A pdb=" N LEU D 975 " --> pdb=" O LEU D 971 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N GLU D 988 " --> pdb=" O GLY D 984 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASN D 989 " --> pdb=" O ILE D 985 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP D 991 " --> pdb=" O GLN D 987 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR D 999 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU D1001 " --> pdb=" O GLN D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1015 through 1030 removed outlier: 3.713A pdb=" N ALA D1019 " --> pdb=" O PHE D1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 1046 through 1071 removed outlier: 3.861A pdb=" N VAL D1058 " --> pdb=" O ALA D1054 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET D1059 " --> pdb=" O TRP D1055 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA D1071 " --> pdb=" O ILE D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1074 through 1104 removed outlier: 3.677A pdb=" N MET D1078 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS D1104 " --> pdb=" O ALA D1100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 121 removed outlier: 6.060A pdb=" N ALA A 211 " --> pdb=" O HIS A 259 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU A 261 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY A 213 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL A 263 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA A 215 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE A 179 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ILE A 214 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR A 181 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU A 144 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE A 304 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A 146 " --> pdb=" O PHE A 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 119 through 121 removed outlier: 6.060A pdb=" N ALA B 211 " --> pdb=" O HIS B 259 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU B 261 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLY B 213 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL B 263 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA B 215 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE B 179 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE B 214 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR B 181 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU B 144 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N PHE B 304 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE B 146 " --> pdb=" O PHE B 304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 119 through 121 removed outlier: 6.061A pdb=" N ALA C 211 " --> pdb=" O HIS C 259 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU C 261 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY C 213 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL C 263 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA C 215 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE C 179 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE C 214 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR C 181 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU C 144 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE C 304 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE C 146 " --> pdb=" O PHE C 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 119 through 121 removed outlier: 6.060A pdb=" N ALA D 211 " --> pdb=" O HIS D 259 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU D 261 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLY D 213 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL D 263 " --> pdb=" O GLY D 213 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA D 215 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE D 179 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE D 214 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR D 181 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU D 144 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N PHE D 304 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE D 146 " --> pdb=" O PHE D 304 " (cutoff:3.500A) 1754 hydrogen bonds defined for protein. 5214 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: 6.64 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4884 1.30 - 1.43: 8745 1.43 - 1.56: 17347 1.56 - 1.69: 0 1.69 - 1.82: 212 Bond restraints: 31188 Sorted by residual: bond pdb=" N21 KX7 D1202 " pdb=" O23 KX7 D1202 " ideal model delta sigma weight residual 1.208 1.399 -0.191 2.00e-02 2.50e+03 9.08e+01 bond pdb=" N21 KX7 A1202 " pdb=" O23 KX7 A1202 " ideal model delta sigma weight residual 1.208 1.398 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" N21 KX7 B1202 " pdb=" O23 KX7 B1202 " ideal model delta sigma weight residual 1.208 1.398 -0.190 2.00e-02 2.50e+03 9.00e+01 bond pdb=" N21 KX7 C1202 " pdb=" O23 KX7 C1202 " ideal model delta sigma weight residual 1.208 1.397 -0.189 2.00e-02 2.50e+03 8.96e+01 bond pdb=" C05 KX7 C1202 " pdb=" N07 KX7 C1202 " ideal model delta sigma weight residual 1.355 1.482 -0.127 2.00e-02 2.50e+03 4.05e+01 ... (remaining 31183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 39342 1.92 - 3.85: 2381 3.85 - 5.77: 385 5.77 - 7.69: 113 7.69 - 9.62: 31 Bond angle restraints: 42252 Sorted by residual: angle pdb=" N PHE D1013 " pdb=" CA PHE D1013 " pdb=" C PHE D1013 " ideal model delta sigma weight residual 113.16 121.60 -8.44 1.42e+00 4.96e-01 3.53e+01 angle pdb=" N PHE C1013 " pdb=" CA PHE C1013 " pdb=" C PHE C1013 " ideal model delta sigma weight residual 113.16 121.29 -8.13 1.42e+00 4.96e-01 3.28e+01 angle pdb=" N PHE A1013 " pdb=" CA PHE A1013 " pdb=" C PHE A1013 " ideal model delta sigma weight residual 113.16 121.23 -8.07 1.42e+00 4.96e-01 3.23e+01 angle pdb=" N PHE B1013 " pdb=" CA PHE B1013 " pdb=" C PHE B1013 " ideal model delta sigma weight residual 113.16 121.17 -8.01 1.42e+00 4.96e-01 3.18e+01 angle pdb=" N ASN B1010 " pdb=" CA ASN B1010 " pdb=" C ASN B1010 " ideal model delta sigma weight residual 109.24 117.84 -8.60 1.63e+00 3.76e-01 2.78e+01 ... (remaining 42247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.20: 17136 15.20 - 30.41: 908 30.41 - 45.61: 216 45.61 - 60.82: 12 60.82 - 76.02: 32 Dihedral angle restraints: 18304 sinusoidal: 7392 harmonic: 10912 Sorted by residual: dihedral pdb=" CA ILE B 985 " pdb=" C ILE B 985 " pdb=" N VAL B 986 " pdb=" CA VAL B 986 " ideal model delta harmonic sigma weight residual -180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA ILE A 985 " pdb=" C ILE A 985 " pdb=" N VAL A 986 " pdb=" CA VAL A 986 " ideal model delta harmonic sigma weight residual 180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA ILE D 985 " pdb=" C ILE D 985 " pdb=" N VAL D 986 " pdb=" CA VAL D 986 " ideal model delta harmonic sigma weight residual -180.00 -154.31 -25.69 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 18301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3442 0.064 - 0.127: 1078 0.127 - 0.191: 167 0.191 - 0.255: 17 0.255 - 0.318: 4 Chirality restraints: 4708 Sorted by residual: chirality pdb=" CA PHE D1013 " pdb=" N PHE D1013 " pdb=" C PHE D1013 " pdb=" CB PHE D1013 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CA PHE A1013 " pdb=" N PHE A1013 " pdb=" C PHE A1013 " pdb=" CB PHE A1013 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA PHE C1013 " pdb=" N PHE C1013 " pdb=" C PHE C1013 " pdb=" CB PHE C1013 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 4705 not shown) Planarity restraints: 5280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C1011 " 0.022 2.00e-02 2.50e+03 4.38e-02 1.92e+01 pdb=" C ILE C1011 " -0.076 2.00e-02 2.50e+03 pdb=" O ILE C1011 " 0.029 2.00e-02 2.50e+03 pdb=" N PRO C1012 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1011 " 0.022 2.00e-02 2.50e+03 4.33e-02 1.87e+01 pdb=" C ILE A1011 " -0.075 2.00e-02 2.50e+03 pdb=" O ILE A1011 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO A1012 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D1011 " 0.022 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C ILE D1011 " -0.074 2.00e-02 2.50e+03 pdb=" O ILE D1011 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO D1012 " 0.025 2.00e-02 2.50e+03 ... (remaining 5277 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6047 2.77 - 3.30: 28815 3.30 - 3.83: 48975 3.83 - 4.37: 57886 4.37 - 4.90: 98089 Nonbonded interactions: 239812 Sorted by model distance: nonbonded pdb=" O ILE A 888 " pdb=" OH TYR B 826 " model vdw 2.235 3.040 nonbonded pdb=" OG SER A 205 " pdb=" OE1 GLU A 206 " model vdw 2.262 3.040 nonbonded pdb=" OG SER C 205 " pdb=" OE1 GLU C 206 " model vdw 2.262 3.040 nonbonded pdb=" OG SER B 205 " pdb=" OE1 GLU B 206 " model vdw 2.262 3.040 nonbonded pdb=" OG SER D 205 " pdb=" OE1 GLU D 206 " model vdw 2.263 3.040 ... (remaining 239807 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.530 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: 0.040 Extract box with map and model: 0.700 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 32.640 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 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 : 0.010 0.191 31192 Z= 0.437 Angle : 1.069 9.619 42260 Z= 0.593 Chirality : 0.060 0.318 4708 Planarity : 0.007 0.064 5280 Dihedral : 10.593 76.021 11212 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.12 % Allowed : 2.82 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.90 (0.11), residues: 3656 helix: -2.12 (0.08), residues: 2436 sheet: -1.76 (0.32), residues: 200 loop : -3.48 (0.15), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 688 TYR 0.040 0.004 TYR D1005 PHE 0.030 0.003 PHE C 832 TRP 0.030 0.004 TRP B 377 HIS 0.008 0.002 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.01000 / 0.44 (31188) covalent geometry : angle 1.06775 / 0.59 (42252) SS BOND : bond 0.01733 / 0.79 ( 4) SS BOND : angle 4.39080 / 2.49 ( 8) hydrogen bonds : bond 0.15042 / 10.13 ( 1754) hydrogen bonds : angle 6.56168 / 4.63 ( 5214) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 802 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ASN cc_start: 0.8449 (m-40) cc_final: 0.8056 (m-40) REVERT: A 306 GLN cc_start: 0.7191 (pp30) cc_final: 0.6667 (tm-30) REVERT: A 330 GLU cc_start: 0.8626 (mp0) cc_final: 0.8330 (mp0) REVERT: A 661 VAL cc_start: 0.9268 (t) cc_final: 0.9040 (p) REVERT: A 723 LEU cc_start: 0.7606 (mm) cc_final: 0.7296 (tt) REVERT: A 859 MET cc_start: 0.8255 (ttp) cc_final: 0.7376 (ttm) REVERT: A 928 HIS cc_start: 0.7720 (m90) cc_final: 0.7440 (m-70) REVERT: B 723 LEU cc_start: 0.7920 (mm) cc_final: 0.7717 (tt) REVERT: B 860 LEU cc_start: 0.9155 (tp) cc_final: 0.8954 (tp) REVERT: B 1023 MET cc_start: 0.5629 (mmm) cc_final: 0.5275 (mmm) REVERT: C 201 ILE cc_start: 0.8316 (tp) cc_final: 0.6637 (tp) REVERT: C 325 PRO cc_start: 0.7692 (Cg_endo) cc_final: 0.7437 (Cg_exo) REVERT: C 723 LEU cc_start: 0.7960 (mm) cc_final: 0.7721 (tt) REVERT: D 146 ILE cc_start: 0.7497 (mt) cc_final: 0.7246 (mt) REVERT: D 252 ILE cc_start: 0.7907 (mm) cc_final: 0.7704 (mm) REVERT: D 325 PRO cc_start: 0.7537 (Cg_endo) cc_final: 0.7274 (Cg_exo) REVERT: D 1023 MET cc_start: 0.5654 (mmm) cc_final: 0.5360 (mmm) outliers start: 4 outliers final: 0 residues processed: 802 average time/residue: 0.2188 time to fit residues: 274.2683 Evaluate side-chains 460 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 460 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 4.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 HIS A 173 GLN A 199 ASN A 257 HIS A 270 HIS A 483 ASN A 609 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 HIS B 257 HIS B 270 HIS B 483 ASN B 572 ASN B 609 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 789 ASN C 136 HIS ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 HIS C 483 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 741 ASN C 789 ASN C 989 ASN D 136 HIS ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 HIS D 294 ASN D 483 ASN ** D 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 675 GLN D 789 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.134489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.099365 restraints weight = 65314.458| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.16 r_work: 0.3255 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 31192 Z= 0.207 Angle : 0.718 9.314 42260 Z= 0.378 Chirality : 0.044 0.188 4708 Planarity : 0.006 0.119 5280 Dihedral : 6.085 44.274 4024 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.37 % Allowed : 9.71 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.13), residues: 3656 helix: -0.28 (0.10), residues: 2456 sheet: -1.66 (0.34), residues: 188 loop : -3.03 (0.16), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1079 TYR 0.019 0.002 TYR D 981 PHE 0.017 0.002 PHE A 752 TRP 0.019 0.002 TRP C 798 HIS 0.006 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (31188) covalent geometry : angle 0.71720 / 0.38 (42252) SS BOND : bond 0.00696 / 0.31 ( 4) SS BOND : angle 1.93818 / 1.12 ( 8) hydrogen bonds : bond 0.05372 / 3.65 ( 1754) hydrogen bonds : angle 4.68172 / 3.27 ( 5214) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 508 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.9041 (t80) cc_final: 0.8677 (t80) REVERT: A 189 MET cc_start: 0.7120 (mpp) cc_final: 0.6852 (mpp) REVERT: A 201 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8449 (tp) REVERT: A 330 GLU cc_start: 0.8749 (mp0) cc_final: 0.8392 (mp0) REVERT: A 507 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.8263 (tpt90) REVERT: A 723 LEU cc_start: 0.7547 (mm) cc_final: 0.7274 (tt) REVERT: A 989 ASN cc_start: 0.7992 (t0) cc_final: 0.7761 (t0) REVERT: B 161 MET cc_start: 0.7964 (mmm) cc_final: 0.7732 (mmm) REVERT: B 201 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8107 (tp) REVERT: B 364 ARG cc_start: 0.8055 (mtm180) cc_final: 0.7813 (tmt170) REVERT: B 396 MET cc_start: 0.7478 (mmp) cc_final: 0.7265 (mmp) REVERT: B 445 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8471 (mp0) REVERT: B 723 LEU cc_start: 0.7938 (mm) cc_final: 0.7694 (tt) REVERT: B 740 TRP cc_start: 0.8222 (t-100) cc_final: 0.7758 (t-100) REVERT: B 788 MET cc_start: 0.7744 (tmm) cc_final: 0.7449 (tmm) REVERT: B 789 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.8012 (t0) REVERT: B 801 MET cc_start: 0.8636 (ptm) cc_final: 0.8354 (ptt) REVERT: B 860 LEU cc_start: 0.9283 (tp) cc_final: 0.9059 (tp) REVERT: B 918 ASP cc_start: 0.8287 (p0) cc_final: 0.8067 (p0) REVERT: B 935 GLU cc_start: 0.7955 (pt0) cc_final: 0.7674 (pm20) REVERT: B 937 LYS cc_start: 0.7747 (mtmm) cc_final: 0.7323 (mtmt) REVERT: B 989 ASN cc_start: 0.8091 (t0) cc_final: 0.7855 (t0) REVERT: C 201 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7554 (tp) REVERT: C 306 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7550 (tp-100) REVERT: C 325 PRO cc_start: 0.7795 (Cg_endo) cc_final: 0.7569 (Cg_exo) REVERT: C 364 ARG cc_start: 0.8178 (mtm-85) cc_final: 0.7488 (mtm180) REVERT: C 431 LYS cc_start: 0.9125 (mttm) cc_final: 0.8877 (mttp) REVERT: C 451 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6416 (ptt-90) REVERT: C 496 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8764 (mp) REVERT: C 723 LEU cc_start: 0.7908 (mm) cc_final: 0.7686 (tt) REVERT: C 740 TRP cc_start: 0.8202 (t-100) cc_final: 0.7650 (t-100) REVERT: C 789 ASN cc_start: 0.8261 (OUTLIER) cc_final: 0.7791 (t0) REVERT: C 801 MET cc_start: 0.8372 (ppp) cc_final: 0.8087 (ptp) REVERT: C 863 MET cc_start: 0.8584 (mmt) cc_final: 0.8209 (mmt) REVERT: C 989 ASN cc_start: 0.7949 (t0) cc_final: 0.7709 (t0) REVERT: C 1007 ASN cc_start: 0.7277 (OUTLIER) cc_final: 0.7054 (p0) REVERT: C 1059 MET cc_start: 0.9071 (mpp) cc_final: 0.8847 (mmm) REVERT: C 1078 MET cc_start: 0.6604 (mmt) cc_final: 0.6080 (mmt) REVERT: D 252 ILE cc_start: 0.8059 (mm) cc_final: 0.7706 (tt) REVERT: D 306 GLN cc_start: 0.7541 (tm-30) cc_final: 0.7022 (tp-100) REVERT: D 325 PRO cc_start: 0.7782 (Cg_endo) cc_final: 0.7578 (Cg_exo) REVERT: D 431 LYS cc_start: 0.9106 (mttm) cc_final: 0.8863 (mttp) REVERT: D 740 TRP cc_start: 0.8210 (t-100) cc_final: 0.7750 (t-100) REVERT: D 788 MET cc_start: 0.7825 (tmm) cc_final: 0.7623 (tmm) REVERT: D 789 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7879 (t0) REVERT: D 801 MET cc_start: 0.8507 (ptm) cc_final: 0.8221 (ptt) REVERT: D 863 MET cc_start: 0.8641 (mmt) cc_final: 0.8372 (mmt) REVERT: D 989 ASN cc_start: 0.7998 (t0) cc_final: 0.7770 (t0) outliers start: 79 outliers final: 40 residues processed: 564 average time/residue: 0.2069 time to fit residues: 186.7402 Evaluate side-chains 483 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 434 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 787 TYR Chi-restraints excluded: chain B residue 789 ASN Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 787 TYR Chi-restraints excluded: chain C residue 789 ASN Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 1007 ASN Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 787 TYR Chi-restraints excluded: chain D residue 789 ASN Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 985 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 64 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 278 optimal weight: 7.9990 chunk 223 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 217 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 255 optimal weight: 0.7980 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 572 ASN A 671 GLN A 741 ASN A 990 ASN B 199 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 ASN ** D 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 990 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.133187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.097918 restraints weight = 65160.141| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.17 r_work: 0.3222 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31192 Z= 0.172 Angle : 0.627 8.256 42260 Z= 0.329 Chirality : 0.042 0.179 4708 Planarity : 0.004 0.088 5280 Dihedral : 5.664 46.802 4024 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.19 % Allowed : 12.80 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.13), residues: 3656 helix: 0.49 (0.10), residues: 2484 sheet: -1.31 (0.36), residues: 184 loop : -2.86 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1079 TYR 0.016 0.002 TYR D 787 PHE 0.016 0.001 PHE B 779 TRP 0.017 0.002 TRP B 898 HIS 0.004 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (31188) covalent geometry : angle 0.62715 / 0.33 (42252) SS BOND : bond 0.00554 / 0.25 ( 4) SS BOND : angle 1.16409 / 0.68 ( 8) hydrogen bonds : bond 0.04703 / 3.19 ( 1754) hydrogen bonds : angle 4.37923 / 3.05 ( 5214) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 457 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.9076 (t80) cc_final: 0.8678 (t80) REVERT: A 189 MET cc_start: 0.7282 (mpp) cc_final: 0.7046 (mpp) REVERT: A 197 ARG cc_start: 0.8642 (ttp-110) cc_final: 0.8414 (ttp-110) REVERT: A 201 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8376 (tp) REVERT: A 304 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.7936 (m-80) REVERT: A 330 GLU cc_start: 0.8707 (mp0) cc_final: 0.8490 (mp0) REVERT: A 393 VAL cc_start: 0.9134 (p) cc_final: 0.8858 (t) REVERT: A 507 ARG cc_start: 0.8631 (mmm-85) cc_final: 0.8426 (tpt170) REVERT: A 723 LEU cc_start: 0.7702 (mm) cc_final: 0.7420 (tt) REVERT: A 801 MET cc_start: 0.8708 (ptm) cc_final: 0.8470 (ptp) REVERT: A 931 PHE cc_start: 0.8440 (m-80) cc_final: 0.8017 (m-80) REVERT: A 955 ILE cc_start: 0.8816 (tp) cc_final: 0.8556 (tt) REVERT: A 989 ASN cc_start: 0.8070 (t0) cc_final: 0.7823 (t0) REVERT: A 1023 MET cc_start: 0.5066 (mmt) cc_final: 0.4846 (mtt) REVERT: B 189 MET cc_start: 0.7507 (mpp) cc_final: 0.7295 (mpp) REVERT: B 197 ARG cc_start: 0.8747 (ttp-110) cc_final: 0.8502 (ttp-110) REVERT: B 201 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8156 (tp) REVERT: B 364 ARG cc_start: 0.8018 (mtm180) cc_final: 0.7739 (tmt170) REVERT: B 496 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8849 (mp) REVERT: B 723 LEU cc_start: 0.7986 (mm) cc_final: 0.7754 (tt) REVERT: B 801 MET cc_start: 0.8676 (ptm) cc_final: 0.8391 (ptp) REVERT: B 860 LEU cc_start: 0.9319 (tp) cc_final: 0.9104 (tp) REVERT: B 874 PHE cc_start: 0.8898 (t80) cc_final: 0.8606 (t80) REVERT: B 918 ASP cc_start: 0.8353 (p0) cc_final: 0.8070 (p0) REVERT: B 989 ASN cc_start: 0.8103 (t0) cc_final: 0.7858 (t0) REVERT: C 186 TYR cc_start: 0.7845 (m-80) cc_final: 0.7595 (m-80) REVERT: C 189 MET cc_start: 0.7867 (mpp) cc_final: 0.7632 (mpp) REVERT: C 190 LYS cc_start: 0.8541 (ttmm) cc_final: 0.8304 (mtpt) REVERT: C 364 ARG cc_start: 0.8145 (mtm-85) cc_final: 0.7503 (mtm180) REVERT: C 723 LEU cc_start: 0.7975 (mm) cc_final: 0.7752 (tt) REVERT: C 740 TRP cc_start: 0.8309 (t-100) cc_final: 0.8020 (t-100) REVERT: C 863 MET cc_start: 0.8618 (mmt) cc_final: 0.8324 (mmt) REVERT: C 989 ASN cc_start: 0.7975 (t0) cc_final: 0.7739 (t0) REVERT: D 186 TYR cc_start: 0.7877 (m-80) cc_final: 0.7520 (m-80) REVERT: D 189 MET cc_start: 0.7864 (mpp) cc_final: 0.7620 (mpp) REVERT: D 201 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8179 (tp) REVERT: D 740 TRP cc_start: 0.8270 (t-100) cc_final: 0.7783 (t-100) REVERT: D 801 MET cc_start: 0.8581 (ptm) cc_final: 0.8293 (ptp) REVERT: D 863 MET cc_start: 0.8658 (mmt) cc_final: 0.8403 (mmt) REVERT: D 989 ASN cc_start: 0.7990 (t0) cc_final: 0.7722 (t0) outliers start: 73 outliers final: 33 residues processed: 498 average time/residue: 0.2014 time to fit residues: 161.5654 Evaluate side-chains 440 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 402 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 990 ASN Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 787 TYR Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 878 MET Chi-restraints excluded: chain D residue 990 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 13 optimal weight: 10.0000 chunk 371 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 333 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 271 optimal weight: 6.9990 chunk 297 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 ASN A 204 ASN A 789 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN B 741 ASN B 789 ASN B 990 ASN C 204 ASN C 257 HIS C 483 ASN C 485 GLN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 ASN D 485 GLN D 609 ASN D 789 ASN D 990 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.130204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.094233 restraints weight = 65278.700| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.19 r_work: 0.3167 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 31192 Z= 0.212 Angle : 0.648 7.244 42260 Z= 0.339 Chirality : 0.043 0.194 4708 Planarity : 0.004 0.090 5280 Dihedral : 5.485 59.730 4024 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.82 % Allowed : 13.13 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.14), residues: 3656 helix: 0.87 (0.10), residues: 2460 sheet: -1.21 (0.36), residues: 180 loop : -2.62 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C1083 TYR 0.021 0.002 TYR C 787 PHE 0.025 0.002 PHE A 155 TRP 0.019 0.002 TRP B 898 HIS 0.009 0.001 HIS C 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (31188) covalent geometry : angle 0.64635 / 0.34 (42252) SS BOND : bond 0.00599 / 0.28 ( 4) SS BOND : angle 3.36593 / 1.88 ( 8) hydrogen bonds : bond 0.04898 / 3.34 ( 1754) hydrogen bonds : angle 4.36199 / 3.04 ( 5214) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 429 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.9037 (t80) cc_final: 0.8793 (t80) REVERT: A 201 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8464 (tp) REVERT: A 304 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: A 393 VAL cc_start: 0.9170 (p) cc_final: 0.8937 (t) REVERT: A 507 ARG cc_start: 0.8708 (mmm-85) cc_final: 0.8478 (tpt90) REVERT: A 723 LEU cc_start: 0.7861 (mm) cc_final: 0.7579 (tt) REVERT: A 725 TRP cc_start: 0.7921 (t60) cc_final: 0.7451 (t60) REVERT: A 801 MET cc_start: 0.8790 (ptm) cc_final: 0.8556 (ptp) REVERT: A 918 ASP cc_start: 0.8480 (p0) cc_final: 0.8144 (p0) REVERT: A 989 ASN cc_start: 0.8139 (t0) cc_final: 0.7880 (t0) REVERT: B 197 ARG cc_start: 0.8785 (ttp-110) cc_final: 0.8465 (ttp-110) REVERT: B 201 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.7882 (tp) REVERT: B 304 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8379 (m-80) REVERT: B 364 ARG cc_start: 0.7983 (mtm180) cc_final: 0.7751 (tmt170) REVERT: B 723 LEU cc_start: 0.8057 (mm) cc_final: 0.7831 (tt) REVERT: B 801 MET cc_start: 0.8765 (ptm) cc_final: 0.8554 (ptp) REVERT: B 817 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8122 (mm) REVERT: B 918 ASP cc_start: 0.8429 (p0) cc_final: 0.8160 (p0) REVERT: B 1007 ASN cc_start: 0.7430 (p0) cc_final: 0.6582 (p0) REVERT: C 186 TYR cc_start: 0.7875 (m-80) cc_final: 0.7525 (m-80) REVERT: C 201 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7424 (tp) REVERT: C 364 ARG cc_start: 0.8217 (mtm-85) cc_final: 0.7835 (tmm160) REVERT: C 646 TYR cc_start: 0.7532 (t80) cc_final: 0.7261 (t80) REVERT: C 723 LEU cc_start: 0.7985 (mm) cc_final: 0.7782 (tt) REVERT: C 863 MET cc_start: 0.8654 (mmt) cc_final: 0.8308 (mmt) REVERT: C 989 ASN cc_start: 0.8049 (t0) cc_final: 0.7732 (t0) REVERT: C 1051 GLU cc_start: 0.8925 (tp30) cc_final: 0.8432 (tp30) REVERT: D 186 TYR cc_start: 0.7835 (m-80) cc_final: 0.7620 (m-80) REVERT: D 201 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8094 (tp) REVERT: D 396 MET cc_start: 0.6498 (mpp) cc_final: 0.5788 (mmt) REVERT: D 801 MET cc_start: 0.8677 (ptm) cc_final: 0.8445 (ptp) REVERT: D 817 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8150 (mm) REVERT: D 863 MET cc_start: 0.8727 (mmt) cc_final: 0.8515 (mmt) REVERT: D 874 PHE cc_start: 0.8908 (t80) cc_final: 0.8698 (t80) REVERT: D 918 ASP cc_start: 0.8399 (p0) cc_final: 0.7971 (p0) REVERT: D 989 ASN cc_start: 0.8044 (t0) cc_final: 0.7843 (t0) REVERT: D 1007 ASN cc_start: 0.7725 (p0) cc_final: 0.7490 (p0) outliers start: 94 outliers final: 50 residues processed: 490 average time/residue: 0.2024 time to fit residues: 160.5229 Evaluate side-chains 452 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 394 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 787 TYR Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 990 ASN Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 787 TYR Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 787 TYR Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 967 THR Chi-restraints excluded: chain D residue 990 ASN Chi-restraints excluded: chain D residue 1069 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 134 optimal weight: 0.9980 chunk 349 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 348 optimal weight: 0.9990 chunk 340 optimal weight: 1.9990 chunk 252 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 336 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 789 ASN B 572 ASN B 671 GLN B 990 ASN ** B1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 ASN C 485 GLN C 609 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 GLN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 485 GLN D 671 GLN D 990 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.132550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.096891 restraints weight = 65279.209| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.22 r_work: 0.3212 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31192 Z= 0.126 Angle : 0.587 8.009 42260 Z= 0.304 Chirality : 0.040 0.170 4708 Planarity : 0.004 0.050 5280 Dihedral : 5.258 58.767 4024 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.37 % Allowed : 14.00 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.14), residues: 3656 helix: 1.20 (0.11), residues: 2448 sheet: -1.17 (0.36), residues: 180 loop : -2.51 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D1079 TYR 0.018 0.001 TYR C 787 PHE 0.026 0.001 PHE A 155 TRP 0.019 0.001 TRP B 740 HIS 0.003 0.000 HIS D 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (31188) covalent geometry : angle 0.58655 / 0.30 (42252) SS BOND : bond 0.00536 / 0.25 ( 4) SS BOND : angle 1.54027 / 0.87 ( 8) hydrogen bonds : bond 0.04109 / 2.79 ( 1754) hydrogen bonds : angle 4.12337 / 2.87 ( 5214) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 462 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ARG cc_start: 0.8624 (tpp80) cc_final: 0.8395 (tpp80) REVERT: A 170 TYR cc_start: 0.9038 (t80) cc_final: 0.8777 (t80) REVERT: A 201 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8391 (tp) REVERT: A 304 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.8091 (m-80) REVERT: A 364 ARG cc_start: 0.7723 (tmt170) cc_final: 0.7244 (ttp-170) REVERT: A 393 VAL cc_start: 0.9188 (p) cc_final: 0.8968 (t) REVERT: A 485 GLN cc_start: 0.8320 (pm20) cc_final: 0.7868 (mm-40) REVERT: A 723 LEU cc_start: 0.7864 (mm) cc_final: 0.7605 (tt) REVERT: A 725 TRP cc_start: 0.7857 (t60) cc_final: 0.7460 (t60) REVERT: A 801 MET cc_start: 0.8753 (ptm) cc_final: 0.8519 (ptp) REVERT: A 859 MET cc_start: 0.9087 (ptp) cc_final: 0.8785 (ptp) REVERT: A 918 ASP cc_start: 0.8401 (p0) cc_final: 0.8041 (p0) REVERT: B 197 ARG cc_start: 0.8820 (ttp-110) cc_final: 0.8497 (ttp-110) REVERT: B 201 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8012 (tp) REVERT: B 304 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8331 (m-80) REVERT: B 364 ARG cc_start: 0.8037 (mtm180) cc_final: 0.7815 (tmt170) REVERT: B 485 GLN cc_start: 0.8288 (pm20) cc_final: 0.7837 (mm-40) REVERT: B 713 ARG cc_start: 0.7567 (tpm170) cc_final: 0.7061 (tpm170) REVERT: B 723 LEU cc_start: 0.8001 (mm) cc_final: 0.7789 (tt) REVERT: B 801 MET cc_start: 0.8782 (ptm) cc_final: 0.8524 (ptp) REVERT: B 817 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8045 (mm) REVERT: B 860 LEU cc_start: 0.9343 (tp) cc_final: 0.9111 (tp) REVERT: B 918 ASP cc_start: 0.8320 (p0) cc_final: 0.7997 (p0) REVERT: B 978 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8022 (mpp) REVERT: C 186 TYR cc_start: 0.7796 (m-80) cc_final: 0.7326 (m-80) REVERT: C 201 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7369 (tp) REVERT: C 364 ARG cc_start: 0.8219 (mtm-85) cc_final: 0.7842 (tmm160) REVERT: C 697 LEU cc_start: 0.8664 (tt) cc_final: 0.8429 (tt) REVERT: C 713 ARG cc_start: 0.7516 (tpm170) cc_final: 0.7035 (tpm170) REVERT: C 740 TRP cc_start: 0.8296 (t-100) cc_final: 0.7981 (t-100) REVERT: C 801 MET cc_start: 0.8688 (ptm) cc_final: 0.8476 (ptp) REVERT: C 817 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8031 (mm) REVERT: C 840 THR cc_start: 0.9239 (m) cc_final: 0.9028 (m) REVERT: C 863 MET cc_start: 0.8711 (mmt) cc_final: 0.8366 (mmt) REVERT: C 989 ASN cc_start: 0.7940 (t0) cc_final: 0.7630 (t0) REVERT: C 1051 GLU cc_start: 0.8967 (tp30) cc_final: 0.8590 (tp30) REVERT: D 186 TYR cc_start: 0.7844 (m-80) cc_final: 0.7552 (m-80) REVERT: D 201 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8076 (tp) REVERT: D 304 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8197 (m-80) REVERT: D 364 ARG cc_start: 0.7649 (tmm160) cc_final: 0.7043 (tmm-80) REVERT: D 713 ARG cc_start: 0.7549 (tpm170) cc_final: 0.7082 (tpm170) REVERT: D 801 MET cc_start: 0.8687 (ptm) cc_final: 0.8451 (ptp) REVERT: D 817 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8070 (mm) REVERT: D 822 LYS cc_start: 0.8579 (mmmt) cc_final: 0.8191 (mtmt) REVERT: D 863 MET cc_start: 0.8680 (mmt) cc_final: 0.8366 (mmt) REVERT: D 918 ASP cc_start: 0.8336 (p0) cc_final: 0.7920 (p0) outliers start: 79 outliers final: 45 residues processed: 506 average time/residue: 0.1930 time to fit residues: 156.5293 Evaluate side-chains 459 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 403 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 978 MET Chi-restraints excluded: chain B residue 990 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 967 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 990 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 323 optimal weight: 6.9990 chunk 344 optimal weight: 0.0980 chunk 182 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 303 optimal weight: 10.0000 chunk 360 optimal weight: 0.9980 chunk 187 optimal weight: 20.0000 chunk 214 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 239 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 990 ASN ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS B 572 ASN ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1062 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 ASN ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 HIS ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 990 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.131371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.095672 restraints weight = 65491.720| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.22 r_work: 0.3193 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31192 Z= 0.156 Angle : 0.601 8.266 42260 Z= 0.311 Chirality : 0.041 0.189 4708 Planarity : 0.004 0.066 5280 Dihedral : 5.167 58.314 4024 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.61 % Allowed : 14.39 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.14), residues: 3656 helix: 1.32 (0.11), residues: 2456 sheet: -1.16 (0.36), residues: 180 loop : -2.42 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 452 TYR 0.018 0.001 TYR C 787 PHE 0.023 0.001 PHE B 155 TRP 0.024 0.001 TRP B 898 HIS 0.003 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (31188) covalent geometry : angle 0.60053 / 0.31 (42252) SS BOND : bond 0.00575 / 0.26 ( 4) SS BOND : angle 1.45216 / 0.82 ( 8) hydrogen bonds : bond 0.04225 / 2.87 ( 1754) hydrogen bonds : angle 4.14418 / 2.89 ( 5214) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 430 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.9057 (t80) cc_final: 0.8752 (t80) REVERT: A 201 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8439 (tp) REVERT: A 304 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8067 (m-80) REVERT: A 364 ARG cc_start: 0.7816 (tmt170) cc_final: 0.7361 (ttp-170) REVERT: A 393 VAL cc_start: 0.9206 (p) cc_final: 0.8993 (t) REVERT: A 485 GLN cc_start: 0.8359 (pm20) cc_final: 0.8062 (mm-40) REVERT: A 496 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8949 (mp) REVERT: A 665 ASP cc_start: 0.8971 (t0) cc_final: 0.8756 (t0) REVERT: A 723 LEU cc_start: 0.7899 (mm) cc_final: 0.7633 (tt) REVERT: A 725 TRP cc_start: 0.7915 (t60) cc_final: 0.7545 (t60) REVERT: A 801 MET cc_start: 0.8797 (ptm) cc_final: 0.8576 (ptp) REVERT: A 918 ASP cc_start: 0.8375 (p0) cc_final: 0.8014 (p0) REVERT: B 197 ARG cc_start: 0.8786 (ttp-110) cc_final: 0.8444 (ttp-110) REVERT: B 201 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.7986 (tp) REVERT: B 304 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8313 (m-80) REVERT: B 364 ARG cc_start: 0.8006 (mtm180) cc_final: 0.7797 (tmt170) REVERT: B 485 GLN cc_start: 0.8337 (pm20) cc_final: 0.8088 (mm-40) REVERT: B 713 ARG cc_start: 0.7497 (tpm170) cc_final: 0.6924 (tpm170) REVERT: B 817 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7998 (mm) REVERT: B 822 LYS cc_start: 0.8596 (mmmt) cc_final: 0.8186 (mtmt) REVERT: B 918 ASP cc_start: 0.8302 (p0) cc_final: 0.7983 (p0) REVERT: B 974 LEU cc_start: 0.8745 (tp) cc_final: 0.8185 (tp) REVERT: B 978 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8191 (mpp) REVERT: C 186 TYR cc_start: 0.7760 (m-80) cc_final: 0.7272 (m-80) REVERT: C 201 ILE cc_start: 0.7429 (OUTLIER) cc_final: 0.7202 (tp) REVERT: C 364 ARG cc_start: 0.8211 (mtm-85) cc_final: 0.7917 (tmm160) REVERT: C 697 LEU cc_start: 0.8699 (tt) cc_final: 0.8441 (tt) REVERT: C 713 ARG cc_start: 0.7547 (tpm170) cc_final: 0.6942 (tpm170) REVERT: C 740 TRP cc_start: 0.8319 (t-100) cc_final: 0.7990 (t-100) REVERT: C 817 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8041 (mm) REVERT: C 863 MET cc_start: 0.8683 (mmt) cc_final: 0.8336 (mmt) REVERT: C 989 ASN cc_start: 0.7891 (t0) cc_final: 0.7624 (t0) REVERT: C 1051 GLU cc_start: 0.8916 (tp30) cc_final: 0.8494 (tp30) REVERT: D 186 TYR cc_start: 0.7825 (m-80) cc_final: 0.7524 (m-80) REVERT: D 201 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8080 (tp) REVERT: D 304 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8192 (m-80) REVERT: D 364 ARG cc_start: 0.7784 (tmm160) cc_final: 0.7457 (ttp-170) REVERT: D 396 MET cc_start: 0.6670 (mpp) cc_final: 0.5963 (mmt) REVERT: D 713 ARG cc_start: 0.7528 (tpm170) cc_final: 0.6939 (tpm170) REVERT: D 740 TRP cc_start: 0.8454 (t-100) cc_final: 0.8196 (t-100) REVERT: D 817 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8045 (mm) REVERT: D 863 MET cc_start: 0.8677 (mmt) cc_final: 0.8373 (mmt) REVERT: D 918 ASP cc_start: 0.8290 (p0) cc_final: 0.7873 (p0) outliers start: 87 outliers final: 52 residues processed: 482 average time/residue: 0.1859 time to fit residues: 145.3803 Evaluate side-chains 450 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 386 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 978 MET Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1067 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 967 THR Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 990 ASN Chi-restraints excluded: chain D residue 1001 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 98 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 351 optimal weight: 4.9990 chunk 246 optimal weight: 10.0000 chunk 341 optimal weight: 7.9990 chunk 153 optimal weight: 10.0000 chunk 51 optimal weight: 0.0030 chunk 11 optimal weight: 30.0000 chunk 242 optimal weight: 6.9990 chunk 295 optimal weight: 10.0000 overall best weight: 5.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 559 HIS B 204 ASN B 268 HIS B 671 GLN B 990 ASN C 572 ASN D 204 ASN D 483 ASN D 572 ASN ** D1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.126523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.091386 restraints weight = 65215.531| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.98 r_work: 0.3119 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.6073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 31192 Z= 0.279 Angle : 0.701 8.471 42260 Z= 0.364 Chirality : 0.045 0.228 4708 Planarity : 0.004 0.057 5280 Dihedral : 5.394 55.843 4024 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.43 % Allowed : 13.97 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.14), residues: 3656 helix: 1.16 (0.10), residues: 2460 sheet: -1.33 (0.36), residues: 184 loop : -2.39 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 452 TYR 0.019 0.002 TYR C 787 PHE 0.023 0.002 PHE B 155 TRP 0.027 0.002 TRP B 898 HIS 0.005 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.28 (31188) covalent geometry : angle 0.69959 / 0.36 (42252) SS BOND : bond 0.01005 / 0.44 ( 4) SS BOND : angle 3.34634 / 1.96 ( 8) hydrogen bonds : bond 0.05319 / 3.62 ( 1754) hydrogen bonds : angle 4.46947 / 3.12 ( 5214) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 391 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.9057 (t80) cc_final: 0.8706 (t80) REVERT: A 201 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8454 (tp) REVERT: A 304 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.8220 (m-80) REVERT: A 364 ARG cc_start: 0.7823 (tmt170) cc_final: 0.7354 (ttp-170) REVERT: A 393 VAL cc_start: 0.9215 (p) cc_final: 0.9005 (t) REVERT: A 445 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8583 (mp0) REVERT: A 496 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9048 (mp) REVERT: A 723 LEU cc_start: 0.7940 (mm) cc_final: 0.7706 (tt) REVERT: A 725 TRP cc_start: 0.7972 (t60) cc_final: 0.7649 (t60) REVERT: A 788 MET cc_start: 0.8061 (tmm) cc_final: 0.7658 (tmm) REVERT: A 817 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8209 (mm) REVERT: A 859 MET cc_start: 0.9061 (ptp) cc_final: 0.8547 (ptp) REVERT: A 918 ASP cc_start: 0.8300 (p0) cc_final: 0.7954 (p0) REVERT: B 197 ARG cc_start: 0.8823 (ttp-110) cc_final: 0.8614 (ttp-110) REVERT: B 201 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.7963 (tp) REVERT: B 304 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8301 (m-80) REVERT: B 646 TYR cc_start: 0.8007 (t80) cc_final: 0.7649 (t80) REVERT: B 788 MET cc_start: 0.8123 (tmm) cc_final: 0.7708 (tmm) REVERT: B 817 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8127 (mm) REVERT: B 822 LYS cc_start: 0.8644 (mmmt) cc_final: 0.8249 (mtmt) REVERT: B 918 ASP cc_start: 0.8266 (p0) cc_final: 0.7810 (p0) REVERT: B 978 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8393 (mpp) REVERT: B 1003 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8518 (tm-30) REVERT: C 186 TYR cc_start: 0.7823 (m-80) cc_final: 0.7248 (m-80) REVERT: C 697 LEU cc_start: 0.8937 (tt) cc_final: 0.8728 (tt) REVERT: C 817 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8180 (mm) REVERT: C 863 MET cc_start: 0.8729 (mmt) cc_final: 0.8366 (mmt) REVERT: C 918 ASP cc_start: 0.8072 (p0) cc_final: 0.7577 (p0) REVERT: C 1051 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8357 (tp30) REVERT: D 186 TYR cc_start: 0.7664 (m-80) cc_final: 0.7256 (m-80) REVERT: D 201 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8105 (tp) REVERT: D 364 ARG cc_start: 0.7686 (tmm160) cc_final: 0.7470 (tmm160) REVERT: D 445 GLU cc_start: 0.8579 (mp0) cc_final: 0.8224 (mp0) REVERT: D 740 TRP cc_start: 0.8472 (t-100) cc_final: 0.8220 (t-100) REVERT: D 817 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8124 (mm) REVERT: D 822 LYS cc_start: 0.8684 (mmmt) cc_final: 0.8283 (mtmt) REVERT: D 863 MET cc_start: 0.8738 (mmt) cc_final: 0.8387 (mmt) REVERT: D 918 ASP cc_start: 0.8195 (p0) cc_final: 0.7780 (p0) REVERT: D 1003 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8556 (tm-30) outliers start: 114 outliers final: 78 residues processed: 464 average time/residue: 0.1941 time to fit residues: 146.8269 Evaluate side-chains 459 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 369 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1067 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 978 MET Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 990 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1022 TYR Chi-restraints excluded: chain C residue 1051 GLU Chi-restraints excluded: chain C residue 1067 ILE Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 878 MET Chi-restraints excluded: chain D residue 967 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1067 ILE Chi-restraints excluded: chain D residue 1069 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 339 optimal weight: 0.0980 chunk 241 optimal weight: 1.9990 chunk 197 optimal weight: 10.0000 chunk 326 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 265 optimal weight: 0.0010 chunk 255 optimal weight: 0.9980 chunk 295 optimal weight: 8.9990 chunk 201 optimal weight: 5.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 990 ASN A1062 ASN B 268 HIS ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 ASN C 671 GLN C1062 ASN ** D1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.131310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.095775 restraints weight = 65293.790| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.12 r_work: 0.3205 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.6215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31192 Z= 0.122 Angle : 0.595 9.577 42260 Z= 0.307 Chirality : 0.040 0.195 4708 Planarity : 0.004 0.062 5280 Dihedral : 5.040 54.506 4024 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.74 % Allowed : 15.93 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.14), residues: 3656 helix: 1.49 (0.11), residues: 2472 sheet: -1.13 (0.37), residues: 180 loop : -2.32 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 452 TYR 0.015 0.001 TYR C 787 PHE 0.023 0.001 PHE B 155 TRP 0.020 0.001 TRP D 798 HIS 0.004 0.000 HIS A1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (31188) covalent geometry : angle 0.59457 / 0.31 (42252) SS BOND : bond 0.00515 / 0.23 ( 4) SS BOND : angle 1.87627 / 1.09 ( 8) hydrogen bonds : bond 0.03899 / 2.64 ( 1754) hydrogen bonds : angle 4.05699 / 2.83 ( 5214) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 433 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.8981 (t80) cc_final: 0.8610 (t80) REVERT: A 201 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.7927 (tp) REVERT: A 304 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8115 (m-80) REVERT: A 364 ARG cc_start: 0.7882 (tmt170) cc_final: 0.7467 (ttp-170) REVERT: A 496 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9006 (mp) REVERT: A 665 ASP cc_start: 0.8775 (t0) cc_final: 0.8534 (t70) REVERT: A 723 LEU cc_start: 0.8022 (mm) cc_final: 0.7782 (tt) REVERT: A 725 TRP cc_start: 0.7943 (t60) cc_final: 0.7667 (t60) REVERT: A 788 MET cc_start: 0.7961 (tmm) cc_final: 0.7614 (tmm) REVERT: A 817 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8142 (mm) REVERT: A 918 ASP cc_start: 0.8131 (p0) cc_final: 0.7757 (p0) REVERT: A 928 HIS cc_start: 0.8314 (m-70) cc_final: 0.8100 (m-70) REVERT: B 197 ARG cc_start: 0.8828 (ttp-110) cc_final: 0.8514 (ttp-110) REVERT: B 201 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8013 (tp) REVERT: B 304 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8140 (m-80) REVERT: B 364 ARG cc_start: 0.7903 (tmt170) cc_final: 0.7456 (tmm160) REVERT: B 646 TYR cc_start: 0.7872 (t80) cc_final: 0.7531 (t80) REVERT: B 788 MET cc_start: 0.8070 (tmm) cc_final: 0.7673 (tmm) REVERT: B 817 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8025 (mm) REVERT: B 860 LEU cc_start: 0.9386 (tp) cc_final: 0.9155 (tp) REVERT: B 918 ASP cc_start: 0.8132 (p0) cc_final: 0.7684 (p0) REVERT: B 1003 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8389 (tm-30) REVERT: B 1051 GLU cc_start: 0.8778 (tp30) cc_final: 0.8533 (tp30) REVERT: C 186 TYR cc_start: 0.7702 (m-80) cc_final: 0.7248 (m-80) REVERT: C 304 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8203 (m-80) REVERT: C 364 ARG cc_start: 0.8118 (tmt170) cc_final: 0.7786 (mtt180) REVERT: C 402 GLU cc_start: 0.8622 (pp20) cc_final: 0.8072 (pp20) REVERT: C 697 LEU cc_start: 0.8814 (tt) cc_final: 0.8541 (tt) REVERT: C 817 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8039 (mm) REVERT: C 822 LYS cc_start: 0.8601 (mmmt) cc_final: 0.8166 (mmtp) REVERT: C 863 MET cc_start: 0.8630 (mmt) cc_final: 0.8280 (mmt) REVERT: C 1051 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8409 (tp30) REVERT: D 186 TYR cc_start: 0.7576 (m-80) cc_final: 0.7257 (m-80) REVERT: D 201 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.8074 (tp) REVERT: D 364 ARG cc_start: 0.7884 (tmm160) cc_final: 0.7537 (ttp80) REVERT: D 396 MET cc_start: 0.6682 (mpp) cc_final: 0.6009 (mmt) REVERT: D 445 GLU cc_start: 0.8567 (mp0) cc_final: 0.8200 (mp0) REVERT: D 740 TRP cc_start: 0.8482 (t-100) cc_final: 0.8254 (t-100) REVERT: D 817 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8113 (mm) REVERT: D 863 MET cc_start: 0.8586 (mmt) cc_final: 0.8230 (mmt) REVERT: D 918 ASP cc_start: 0.8139 (p0) cc_final: 0.7736 (p0) REVERT: D 1003 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8405 (tm-30) outliers start: 58 outliers final: 33 residues processed: 463 average time/residue: 0.1770 time to fit residues: 133.7647 Evaluate side-chains 430 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 385 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1067 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 990 ASN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain C residue 1051 GLU Chi-restraints excluded: chain C residue 1067 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 878 MET Chi-restraints excluded: chain D residue 967 THR Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1067 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 24 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 279 optimal weight: 20.0000 chunk 356 optimal weight: 7.9990 chunk 216 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 227 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 79 optimal weight: 0.0050 chunk 159 optimal weight: 8.9990 chunk 179 optimal weight: 7.9990 overall best weight: 2.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS B 990 ASN ** C 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 ASN ** D1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.130278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.094328 restraints weight = 65626.157| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.15 r_work: 0.3181 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.6344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31192 Z= 0.149 Angle : 0.622 10.198 42260 Z= 0.316 Chirality : 0.041 0.208 4708 Planarity : 0.004 0.055 5280 Dihedral : 4.970 54.806 4024 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.10 % Allowed : 16.05 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.14), residues: 3656 helix: 1.53 (0.11), residues: 2472 sheet: -0.82 (0.38), residues: 172 loop : -2.27 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 452 TYR 0.015 0.001 TYR C 787 PHE 0.031 0.001 PHE B 155 TRP 0.024 0.002 TRP D 898 HIS 0.002 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (31188) covalent geometry : angle 0.62084 / 0.32 (42252) SS BOND : bond 0.00573 / 0.26 ( 4) SS BOND : angle 2.50381 / 1.54 ( 8) hydrogen bonds : bond 0.04118 / 2.80 ( 1754) hydrogen bonds : angle 4.08820 / 2.86 ( 5214) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 396 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.9012 (t80) cc_final: 0.8672 (t80) REVERT: A 201 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.7917 (tp) REVERT: A 304 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8131 (m-80) REVERT: A 364 ARG cc_start: 0.7863 (tmt170) cc_final: 0.7441 (ttp-170) REVERT: A 445 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8440 (mp0) REVERT: A 496 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9039 (mp) REVERT: A 665 ASP cc_start: 0.8775 (t0) cc_final: 0.8544 (t70) REVERT: A 723 LEU cc_start: 0.8072 (mm) cc_final: 0.7857 (tt) REVERT: A 725 TRP cc_start: 0.8001 (t60) cc_final: 0.7680 (t60) REVERT: A 788 MET cc_start: 0.7948 (tmm) cc_final: 0.7555 (tmm) REVERT: A 817 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8170 (mm) REVERT: A 918 ASP cc_start: 0.8217 (p0) cc_final: 0.7899 (p0) REVERT: A 928 HIS cc_start: 0.8355 (m-70) cc_final: 0.8133 (m-70) REVERT: B 197 ARG cc_start: 0.8836 (ttp-110) cc_final: 0.8613 (ttp-110) REVERT: B 201 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.7912 (tp) REVERT: B 304 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8167 (m-80) REVERT: B 518 ASP cc_start: 0.8792 (t0) cc_final: 0.8513 (t0) REVERT: B 646 TYR cc_start: 0.7945 (t80) cc_final: 0.7629 (t80) REVERT: B 788 MET cc_start: 0.8068 (tmm) cc_final: 0.7673 (tmm) REVERT: B 817 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8073 (mm) REVERT: B 822 LYS cc_start: 0.8583 (mmmt) cc_final: 0.8202 (mtmt) REVERT: B 918 ASP cc_start: 0.8135 (p0) cc_final: 0.7688 (p0) REVERT: B 1003 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8407 (tm-30) REVERT: B 1051 GLU cc_start: 0.8782 (tp30) cc_final: 0.8532 (tp30) REVERT: C 186 TYR cc_start: 0.7771 (m-80) cc_final: 0.7289 (m-80) REVERT: C 304 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8176 (m-80) REVERT: C 697 LEU cc_start: 0.8840 (tt) cc_final: 0.8559 (tt) REVERT: C 817 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8078 (mm) REVERT: C 822 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8157 (mmtp) REVERT: C 863 MET cc_start: 0.8658 (mmt) cc_final: 0.8317 (mmt) REVERT: C 1051 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8382 (tp30) REVERT: D 186 TYR cc_start: 0.7605 (m-80) cc_final: 0.7272 (m-80) REVERT: D 201 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8108 (tp) REVERT: D 304 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.8295 (m-80) REVERT: D 364 ARG cc_start: 0.7892 (tmm160) cc_final: 0.7334 (tmm-80) REVERT: D 396 MET cc_start: 0.6709 (mpp) cc_final: 0.6084 (mmp) REVERT: D 445 GLU cc_start: 0.8515 (mp0) cc_final: 0.8287 (mp0) REVERT: D 801 MET cc_start: 0.8440 (ptt) cc_final: 0.8147 (ptt) REVERT: D 817 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8106 (mm) REVERT: D 863 MET cc_start: 0.8638 (mmt) cc_final: 0.8297 (mmt) REVERT: D 918 ASP cc_start: 0.8139 (p0) cc_final: 0.7739 (p0) REVERT: D 1003 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8471 (tm-30) outliers start: 70 outliers final: 51 residues processed: 436 average time/residue: 0.1771 time to fit residues: 126.5464 Evaluate side-chains 451 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 387 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1067 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 990 ASN Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain C residue 1051 GLU Chi-restraints excluded: chain C residue 1067 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 878 MET Chi-restraints excluded: chain D residue 967 THR Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1013 PHE Chi-restraints excluded: chain D residue 1067 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 147 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 204 optimal weight: 20.0000 chunk 183 optimal weight: 7.9990 chunk 304 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 338 optimal weight: 0.9990 chunk 212 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 265 optimal weight: 0.0470 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** C 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1047 ASN ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 973 ASN ** D1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.130810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.094946 restraints weight = 65245.980| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.15 r_work: 0.3193 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.6461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31192 Z= 0.136 Angle : 0.614 9.508 42260 Z= 0.312 Chirality : 0.040 0.196 4708 Planarity : 0.004 0.056 5280 Dihedral : 4.902 54.674 4024 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.01 % Allowed : 16.29 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.14), residues: 3656 helix: 1.60 (0.11), residues: 2468 sheet: -0.78 (0.39), residues: 172 loop : -2.18 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 197 TYR 0.016 0.001 TYR A 646 PHE 0.020 0.001 PHE C1021 TRP 0.021 0.001 TRP A 898 HIS 0.002 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (31188) covalent geometry : angle 0.61277 / 0.31 (42252) SS BOND : bond 0.00600 / 0.28 ( 4) SS BOND : angle 2.63332 / 1.50 ( 8) hydrogen bonds : bond 0.03925 / 2.67 ( 1754) hydrogen bonds : angle 4.02112 / 2.81 ( 5214) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 405 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.7902 (tp) REVERT: A 304 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.8085 (m-80) REVERT: A 364 ARG cc_start: 0.7946 (tmt170) cc_final: 0.7555 (ttp-170) REVERT: A 445 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8516 (mp0) REVERT: A 496 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9058 (mp) REVERT: A 665 ASP cc_start: 0.8812 (t0) cc_final: 0.8585 (t70) REVERT: A 725 TRP cc_start: 0.7993 (t60) cc_final: 0.7709 (t60) REVERT: A 788 MET cc_start: 0.8011 (tmm) cc_final: 0.7646 (tmm) REVERT: A 817 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8156 (mm) REVERT: A 918 ASP cc_start: 0.8115 (p0) cc_final: 0.7734 (p0) REVERT: A 1051 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8526 (tm-30) REVERT: B 197 ARG cc_start: 0.8839 (ttp-110) cc_final: 0.8611 (ttp-110) REVERT: B 201 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.7835 (tp) REVERT: B 304 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8154 (m-80) REVERT: B 518 ASP cc_start: 0.8718 (t0) cc_final: 0.8451 (t0) REVERT: B 646 TYR cc_start: 0.7913 (t80) cc_final: 0.7656 (t80) REVERT: B 740 TRP cc_start: 0.8479 (t-100) cc_final: 0.8149 (t-100) REVERT: B 788 MET cc_start: 0.8078 (tmm) cc_final: 0.7678 (tmm) REVERT: B 817 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8003 (mm) REVERT: B 822 LYS cc_start: 0.8565 (mmmt) cc_final: 0.8147 (mtmt) REVERT: B 860 LEU cc_start: 0.9380 (tp) cc_final: 0.9133 (tp) REVERT: B 918 ASP cc_start: 0.8119 (p0) cc_final: 0.7773 (p0) REVERT: B 1003 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8400 (tm-30) REVERT: B 1051 GLU cc_start: 0.8739 (tp30) cc_final: 0.8481 (tp30) REVERT: C 186 TYR cc_start: 0.7789 (m-80) cc_final: 0.7305 (m-80) REVERT: C 199 ASN cc_start: 0.8235 (m-40) cc_final: 0.7900 (t0) REVERT: C 304 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8225 (m-80) REVERT: C 697 LEU cc_start: 0.8849 (tt) cc_final: 0.8566 (tt) REVERT: C 817 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8098 (mm) REVERT: C 822 LYS cc_start: 0.8552 (mmmt) cc_final: 0.8145 (mmtp) REVERT: C 863 MET cc_start: 0.8601 (mmt) cc_final: 0.8228 (mmt) REVERT: C 1051 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8344 (tp30) REVERT: D 186 TYR cc_start: 0.7560 (m-80) cc_final: 0.7218 (m-80) REVERT: D 201 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.7991 (tp) REVERT: D 304 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8321 (m-80) REVERT: D 364 ARG cc_start: 0.7881 (tmm160) cc_final: 0.7371 (tmm-80) REVERT: D 396 MET cc_start: 0.6658 (mpp) cc_final: 0.6079 (mmt) REVERT: D 801 MET cc_start: 0.8632 (ptt) cc_final: 0.8303 (ptt) REVERT: D 817 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8023 (mm) REVERT: D 863 MET cc_start: 0.8583 (mmt) cc_final: 0.8213 (mmt) REVERT: D 918 ASP cc_start: 0.8178 (p0) cc_final: 0.7760 (p0) REVERT: D 1003 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8378 (tm-30) outliers start: 67 outliers final: 53 residues processed: 445 average time/residue: 0.1808 time to fit residues: 132.7570 Evaluate side-chains 452 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 386 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1067 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain C residue 1051 GLU Chi-restraints excluded: chain C residue 1067 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 878 MET Chi-restraints excluded: chain D residue 967 THR Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1067 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 167 optimal weight: 0.8980 chunk 325 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 353 optimal weight: 0.8980 chunk 364 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 203 optimal weight: 0.4980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 GLN ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1003 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 = 0.3935 r_free = 0.3935 target = 0.132220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.096711 restraints weight = 65707.495| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.08 r_work: 0.3219 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.6558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31192 Z= 0.118 Angle : 0.605 9.755 42260 Z= 0.306 Chirality : 0.039 0.173 4708 Planarity : 0.004 0.056 5280 Dihedral : 4.768 54.812 4024 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.10 % Allowed : 16.41 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.14), residues: 3656 helix: 1.67 (0.11), residues: 2480 sheet: -0.70 (0.39), residues: 172 loop : -2.16 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 452 TYR 0.014 0.001 TYR C 787 PHE 0.021 0.001 PHE D1021 TRP 0.020 0.001 TRP B 798 HIS 0.006 0.000 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (31188) covalent geometry : angle 0.60399 / 0.31 (42252) SS BOND : bond 0.00567 / 0.26 ( 4) SS BOND : angle 2.43778 / 1.35 ( 8) hydrogen bonds : bond 0.03632 / 2.47 ( 1754) hydrogen bonds : angle 3.92906 / 2.74 ( 5214) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7875.89 seconds wall clock time: 135 minutes 40.53 seconds (8140.53 seconds total)