Starting phenix.real_space_refine on Thu Nov 20 04:16:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wrc_32722/11_2025/7wrc_32722.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrc_32722/11_2025/7wrc_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wrc_32722/11_2025/7wrc_32722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrc_32722/11_2025/7wrc_32722.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wrc_32722/11_2025/7wrc_32722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrc_32722/11_2025/7wrc_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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: 8.90, per 1000 atoms: 0.29 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: 2.62 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: 1.15 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: 6.27 Time building geometry restraints manager: 3.47 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: 0.05 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: 1.280 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.140 Find NCS groups from input model: 0.200 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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 covalent geometry : bond 0.01000 (31188) covalent geometry : angle 1.06775 (42252) SS BOND : bond 0.01733 ( 4) SS BOND : angle 4.39080 ( 8) hydrogen bonds : bond 0.15042 ( 1754) hydrogen bonds : angle 6.56168 ( 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 : 1.141 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: 0.8627 (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: 0.7693 (Cg_endo) cc_final: 0.7437 (Cg_exo) REVERT: C 622 GLU cc_start: 0.7923 (pp20) cc_final: 0.7723 (pt0) 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: 0.2225 time to fit residues: 277.5146 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 : 1.095 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 136 HIS A 173 GLN A 257 HIS A 270 HIS A 483 ASN A 572 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 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: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.134247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.098880 restraints weight = 65821.984| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.18 r_work: 0.3251 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 31192 Z= 0.208 Angle : 0.711 8.931 42260 Z= 0.375 Chirality : 0.044 0.205 4708 Planarity : 0.006 0.131 5280 Dihedral : 6.077 44.606 4024 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.46 % Allowed : 9.28 % Favored : 88.25 % 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: -1.66 (0.13), residues: 3656 helix: -0.23 (0.10), residues: 2456 sheet: -1.64 (0.35), residues: 184 loop : -3.02 (0.16), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1079 TYR 0.019 0.002 TYR D 981 PHE 0.019 0.002 PHE A1013 TRP 0.019 0.002 TRP C 798 HIS 0.007 0.001 HIS D1080 Details of bonding type rmsd covalent geometry : bond 0.00472 (31188) covalent geometry : angle 0.71085 (42252) SS BOND : bond 0.00782 ( 4) SS BOND : angle 1.89686 ( 8) hydrogen bonds : bond 0.05267 ( 1754) hydrogen bonds : angle 4.65467 ( 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 591 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 509 time to evaluate : 1.274 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: 0.9045 (t80) cc_final: 0.8682 (t80) REVERT: A 189 MET cc_start: 0.7118 (mpp) cc_final: 0.6861 (mpp) REVERT: A 201 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8459 (tp) REVERT: A 330 GLU cc_start: 0.8745 (mp0) cc_final: 0.8383 (mp0) REVERT: A 445 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8401 (mp0) REVERT: A 507 ARG cc_start: 0.8478 (mmm-85) cc_final: 0.8272 (tpt90) REVERT: A 723 LEU cc_start: 0.7571 (mm) cc_final: 0.7305 (tt) REVERT: A 989 ASN cc_start: 0.7982 (t0) cc_final: 0.7746 (t0) REVERT: B 201 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8095 (tp) REVERT: B 396 MET cc_start: 0.7472 (mmp) cc_final: 0.7241 (mmp) REVERT: B 445 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8457 (mp0) REVERT: B 740 TRP cc_start: 0.8223 (t-100) cc_final: 0.7761 (t-100) REVERT: B 788 MET cc_start: 0.7719 (tmm) cc_final: 0.7485 (tmm) REVERT: B 789 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.8019 (t0) REVERT: B 801 MET cc_start: 0.8647 (ptm) cc_final: 0.8386 (ptt) REVERT: B 860 LEU cc_start: 0.9285 (tp) cc_final: 0.9062 (tp) REVERT: B 918 ASP cc_start: 0.8257 (p0) cc_final: 0.8037 (p0) REVERT: B 935 GLU cc_start: 0.7947 (pt0) cc_final: 0.7658 (pm20) REVERT: B 937 LYS cc_start: 0.7740 (mtmm) cc_final: 0.7318 (mtmt) REVERT: B 989 ASN cc_start: 0.8061 (t0) cc_final: 0.7830 (t0) REVERT: B 1079 ARG cc_start: 0.8269 (ttp80) cc_final: 0.8041 (ttp80) REVERT: C 201 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7612 (tp) REVERT: C 306 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7588 (tp-100) REVERT: C 325 PRO cc_start: 0.7801 (Cg_endo) cc_final: 0.7577 (Cg_exo) REVERT: C 364 ARG cc_start: 0.8204 (mtm-85) cc_final: 0.7568 (mtm180) REVERT: C 431 LYS cc_start: 0.9122 (mttm) cc_final: 0.8870 (mttp) REVERT: C 451 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6401 (ptt-90) REVERT: C 496 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8777 (mp) REVERT: C 622 GLU cc_start: 0.8697 (pp20) cc_final: 0.8497 (pt0) REVERT: C 723 LEU cc_start: 0.7988 (mm) cc_final: 0.7726 (tt) REVERT: C 740 TRP cc_start: 0.8192 (t-100) cc_final: 0.7648 (t-100) REVERT: C 789 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7986 (t0) REVERT: C 863 MET cc_start: 0.8584 (mmt) cc_final: 0.8255 (mmt) REVERT: C 989 ASN cc_start: 0.7924 (t0) cc_final: 0.7679 (t0) REVERT: C 1007 ASN cc_start: 0.7281 (OUTLIER) cc_final: 0.7063 (p0) REVERT: C 1059 MET cc_start: 0.9079 (mpp) cc_final: 0.8863 (mmm) REVERT: C 1078 MET cc_start: 0.6607 (mmt) cc_final: 0.5998 (mmt) REVERT: D 306 GLN cc_start: 0.7568 (tm-30) cc_final: 0.7066 (tp-100) REVERT: D 325 PRO cc_start: 0.7788 (Cg_endo) cc_final: 0.7586 (Cg_exo) REVERT: D 431 LYS cc_start: 0.9103 (mttm) cc_final: 0.8862 (mttp) REVERT: D 740 TRP cc_start: 0.8213 (t-100) cc_final: 0.7753 (t-100) REVERT: D 789 ASN cc_start: 0.8226 (OUTLIER) cc_final: 0.7923 (t0) REVERT: D 801 MET cc_start: 0.8516 (ptm) cc_final: 0.8231 (ptt) REVERT: D 863 MET cc_start: 0.8637 (mmt) cc_final: 0.8385 (mmt) REVERT: D 989 ASN cc_start: 0.7968 (t0) cc_final: 0.7720 (t0) outliers start: 82 outliers final: 36 residues processed: 566 average time/residue: 0.1996 time to fit residues: 180.3830 Evaluate side-chains 482 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 437 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 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 756 LEU 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 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 353 MET 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 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 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 723 LEU Chi-restraints excluded: chain D residue 783 VAL 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: 10.0000 chunk 223 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 chunk 217 optimal weight: 8.9990 chunk 23 optimal weight: 20.0000 chunk 244 optimal weight: 3.9990 chunk 255 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 741 ASN A 990 ASN B 199 ASN B 990 ASN C 204 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 ASN D 572 ASN D 609 ASN D 990 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.129543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.093685 restraints weight = 65244.498| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.18 r_work: 0.3156 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 31192 Z= 0.253 Angle : 0.715 10.273 42260 Z= 0.374 Chirality : 0.045 0.198 4708 Planarity : 0.005 0.109 5280 Dihedral : 5.849 47.581 4024 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.40 % Allowed : 11.39 % Favored : 85.22 % 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: -0.79 (0.13), residues: 3656 helix: 0.48 (0.10), residues: 2456 sheet: -1.37 (0.35), residues: 180 loop : -2.81 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1081 TYR 0.020 0.002 TYR C 646 PHE 0.023 0.002 PHE D 752 TRP 0.020 0.002 TRP C 798 HIS 0.006 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00584 (31188) covalent geometry : angle 0.71522 (42252) SS BOND : bond 0.00673 ( 4) SS BOND : angle 1.56270 ( 8) hydrogen bonds : bond 0.05509 ( 1754) hydrogen bonds : angle 4.58306 ( 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 561 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 448 time to evaluate : 1.251 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 201 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8437 (tp) REVERT: A 304 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.8040 (m-80) REVERT: A 393 VAL cc_start: 0.9183 (p) cc_final: 0.8913 (t) REVERT: A 507 ARG cc_start: 0.8693 (mmm-85) cc_final: 0.8470 (tpt90) REVERT: A 723 LEU cc_start: 0.7811 (mm) cc_final: 0.7508 (tt) REVERT: A 725 TRP cc_start: 0.7951 (t60) cc_final: 0.7454 (t60) REVERT: A 801 MET cc_start: 0.8838 (ptm) cc_final: 0.8604 (ptp) REVERT: A 955 ILE cc_start: 0.8974 (tp) cc_final: 0.8698 (tt) REVERT: A 989 ASN cc_start: 0.8167 (t0) cc_final: 0.7878 (t0) REVERT: B 197 ARG cc_start: 0.8775 (ttp-110) cc_final: 0.8496 (ttp-110) REVERT: B 201 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8185 (tp) REVERT: B 304 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: B 364 ARG cc_start: 0.7895 (tmt170) cc_final: 0.7305 (tmm160) REVERT: B 801 MET cc_start: 0.8777 (ptm) cc_final: 0.8569 (ptp) REVERT: B 918 ASP cc_start: 0.8494 (p0) cc_final: 0.8243 (p0) REVERT: B 935 GLU cc_start: 0.8152 (pt0) cc_final: 0.7869 (pm20) REVERT: B 1083 ARG cc_start: 0.8457 (tmm-80) cc_final: 0.8141 (ptt180) REVERT: C 186 TYR cc_start: 0.8032 (m-80) cc_final: 0.7710 (m-80) REVERT: C 189 MET cc_start: 0.7934 (mpp) cc_final: 0.7684 (mpp) REVERT: C 251 TYR cc_start: 0.7389 (m-10) cc_final: 0.7053 (m-10) REVERT: C 364 ARG cc_start: 0.8221 (mtm-85) cc_final: 0.7831 (tmm160) REVERT: C 521 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9034 (tp) REVERT: C 723 LEU cc_start: 0.8072 (mm) cc_final: 0.7812 (tt) REVERT: C 863 MET cc_start: 0.8711 (mmt) cc_final: 0.8419 (mmt) REVERT: C 989 ASN cc_start: 0.8095 (t0) cc_final: 0.7818 (t0) REVERT: C 1078 MET cc_start: 0.6412 (mmt) cc_final: 0.6159 (mmt) REVERT: D 186 TYR cc_start: 0.7989 (m-80) cc_final: 0.7637 (m-80) REVERT: D 189 MET cc_start: 0.7925 (mpp) cc_final: 0.7678 (mpp) REVERT: D 201 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8149 (tp) REVERT: D 330 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.8014 (pm20) REVERT: D 521 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9057 (tp) REVERT: D 801 MET cc_start: 0.8667 (ptm) cc_final: 0.8438 (ptp) REVERT: D 863 MET cc_start: 0.8757 (mmt) cc_final: 0.8511 (mmt) REVERT: D 918 ASP cc_start: 0.8394 (p0) cc_final: 0.7965 (p0) REVERT: D 989 ASN cc_start: 0.8108 (t0) cc_final: 0.7869 (t0) outliers start: 113 outliers final: 50 residues processed: 518 average time/residue: 0.2022 time to fit residues: 167.8651 Evaluate side-chains 444 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 386 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 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 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 941 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1069 THR 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 392 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 723 LEU 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 990 ASN Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 521 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 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 292 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 521 LEU 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 878 MET Chi-restraints excluded: chain D residue 990 ASN Chi-restraints excluded: chain D residue 1069 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 13 optimal weight: 9.9990 chunk 371 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 134 optimal weight: 0.8980 chunk 333 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 271 optimal weight: 5.9990 chunk 297 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 GLN A 789 ASN B 671 GLN B 990 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 ASN C 609 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 D 990 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.132674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.096721 restraints weight = 65007.488| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.22 r_work: 0.3213 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31192 Z= 0.129 Angle : 0.593 7.615 42260 Z= 0.307 Chirality : 0.040 0.196 4708 Planarity : 0.004 0.101 5280 Dihedral : 5.379 55.170 4024 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.95 % Allowed : 13.70 % Favored : 84.34 % 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: -0.14 (0.14), residues: 3656 helix: 0.97 (0.10), residues: 2460 sheet: -1.18 (0.36), residues: 184 loop : -2.57 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1079 TYR 0.019 0.001 TYR C 787 PHE 0.025 0.001 PHE A 155 TRP 0.018 0.002 TRP B 898 HIS 0.006 0.001 HIS A1080 Details of bonding type rmsd covalent geometry : bond 0.00288 (31188) covalent geometry : angle 0.59139 (42252) SS BOND : bond 0.00713 ( 4) SS BOND : angle 2.70513 ( 8) hydrogen bonds : bond 0.04203 ( 1754) hydrogen bonds : angle 4.21153 ( 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 541 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 476 time to evaluate : 1.184 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: A 201 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8468 (tp) REVERT: A 393 VAL cc_start: 0.9174 (p) cc_final: 0.8950 (t) REVERT: A 507 ARG cc_start: 0.8696 (mmm-85) cc_final: 0.8483 (tpt90) REVERT: A 723 LEU cc_start: 0.7782 (mm) cc_final: 0.7514 (tt) REVERT: A 725 TRP cc_start: 0.7891 (t60) cc_final: 0.7441 (t60) REVERT: A 797 LEU cc_start: 0.6581 (pt) cc_final: 0.6314 (pp) REVERT: A 801 MET cc_start: 0.8770 (ptm) cc_final: 0.8558 (ptp) REVERT: A 918 ASP cc_start: 0.8447 (p0) cc_final: 0.8115 (p0) REVERT: B 197 ARG cc_start: 0.8811 (ttp-110) cc_final: 0.8504 (ttp-110) REVERT: B 201 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.7995 (tp) REVERT: B 304 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.8297 (m-80) REVERT: B 364 ARG cc_start: 0.7907 (tmt170) cc_final: 0.7347 (tmm160) REVERT: B 801 MET cc_start: 0.8757 (ptm) cc_final: 0.8510 (ptp) REVERT: B 817 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8062 (mm) REVERT: B 822 LYS cc_start: 0.8559 (mmmt) cc_final: 0.8209 (mtmt) REVERT: B 860 LEU cc_start: 0.9344 (tp) cc_final: 0.9126 (tp) REVERT: B 918 ASP cc_start: 0.8383 (p0) cc_final: 0.8113 (p0) REVERT: B 1007 ASN cc_start: 0.7251 (p0) cc_final: 0.6882 (p0) REVERT: C 186 TYR cc_start: 0.7946 (m-80) cc_final: 0.7615 (m-80) REVERT: C 364 ARG cc_start: 0.8237 (mtm-85) cc_final: 0.7850 (tmm160) REVERT: C 697 LEU cc_start: 0.8704 (tt) cc_final: 0.8476 (tt) REVERT: C 740 TRP cc_start: 0.8286 (t-100) cc_final: 0.7984 (t-100) REVERT: C 817 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8076 (mm) REVERT: C 863 MET cc_start: 0.8623 (mmt) cc_final: 0.8274 (mmt) REVERT: C 989 ASN cc_start: 0.7987 (t0) cc_final: 0.7742 (t0) REVERT: C 1051 GLU cc_start: 0.8985 (tp30) cc_final: 0.8622 (tp30) REVERT: D 201 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8206 (tp) REVERT: D 330 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7850 (pm20) REVERT: D 396 MET cc_start: 0.6617 (mpp) cc_final: 0.6018 (mmt) REVERT: D 801 MET cc_start: 0.8684 (ptm) cc_final: 0.8464 (ptp) REVERT: D 817 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8091 (mm) REVERT: D 822 LYS cc_start: 0.8604 (mmmt) cc_final: 0.8207 (mtmt) REVERT: D 863 MET cc_start: 0.8654 (mmt) cc_final: 0.8328 (mmt) REVERT: D 918 ASP cc_start: 0.8366 (p0) cc_final: 0.7927 (p0) REVERT: D 1007 ASN cc_start: 0.7337 (p0) cc_final: 0.6835 (p0) outliers start: 65 outliers final: 29 residues processed: 520 average time/residue: 0.2032 time to fit residues: 168.4511 Evaluate side-chains 451 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 414 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 791 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 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 516 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 C residue 338 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 441 LEU 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 330 GLU Chi-restraints excluded: chain D residue 338 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 976 VAL Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 990 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 134 optimal weight: 5.9990 chunk 349 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 348 optimal weight: 0.6980 chunk 340 optimal weight: 9.9990 chunk 252 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 336 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 789 ASN A 990 ASN A1062 ASN B 268 HIS B 990 ASN B1062 ASN C 257 HIS C 306 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 GLN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 990 ASN ** D1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.130775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.094931 restraints weight = 65531.402| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.21 r_work: 0.3176 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.5646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31192 Z= 0.166 Angle : 0.606 8.624 42260 Z= 0.315 Chirality : 0.041 0.183 4708 Planarity : 0.004 0.083 5280 Dihedral : 5.255 58.628 4024 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.70 % Allowed : 13.46 % Favored : 83.83 % 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: 0.09 (0.14), residues: 3656 helix: 1.20 (0.10), residues: 2448 sheet: -1.19 (0.36), residues: 184 loop : -2.56 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 452 TYR 0.021 0.001 TYR D 646 PHE 0.027 0.001 PHE A 155 TRP 0.026 0.002 TRP B 898 HIS 0.003 0.001 HIS C 138 Details of bonding type rmsd covalent geometry : bond 0.00386 (31188) covalent geometry : angle 0.60552 (42252) SS BOND : bond 0.00671 ( 4) SS BOND : angle 1.90775 ( 8) hydrogen bonds : bond 0.04390 ( 1754) hydrogen bonds : angle 4.20459 ( 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 519 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 429 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8445 (tp) REVERT: A 304 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8078 (m-80) REVERT: A 393 VAL cc_start: 0.9200 (p) cc_final: 0.8987 (t) REVERT: A 469 ASP cc_start: 0.8603 (t70) cc_final: 0.8362 (t70) REVERT: A 496 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8989 (mp) REVERT: A 723 LEU cc_start: 0.7854 (mm) cc_final: 0.7588 (tt) REVERT: A 725 TRP cc_start: 0.7918 (t60) cc_final: 0.7516 (t60) REVERT: A 801 MET cc_start: 0.8830 (ptm) cc_final: 0.8598 (ptp) REVERT: A 918 ASP cc_start: 0.8413 (p0) cc_final: 0.8058 (p0) REVERT: B 197 ARG cc_start: 0.8784 (ttp-110) cc_final: 0.8459 (ttp-110) REVERT: B 201 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.7909 (tp) REVERT: B 304 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8315 (m-80) REVERT: B 364 ARG cc_start: 0.7929 (tmt170) cc_final: 0.7575 (ttp-170) REVERT: B 485 GLN cc_start: 0.8356 (pm20) cc_final: 0.7933 (mm-40) REVERT: B 646 TYR cc_start: 0.7526 (t80) cc_final: 0.7205 (t80) REVERT: B 817 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8017 (mm) REVERT: B 860 LEU cc_start: 0.9346 (tp) cc_final: 0.9113 (tp) REVERT: B 918 ASP cc_start: 0.8333 (p0) cc_final: 0.8014 (p0) REVERT: B 978 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8135 (mpp) REVERT: C 186 TYR cc_start: 0.7884 (m-80) cc_final: 0.7485 (m-80) REVERT: C 364 ARG cc_start: 0.8234 (mtm-85) cc_final: 0.7975 (tmm160) REVERT: C 697 LEU cc_start: 0.8713 (tt) cc_final: 0.8475 (tt) REVERT: C 817 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8107 (mm) REVERT: C 863 MET cc_start: 0.8711 (mmt) cc_final: 0.8351 (mmt) REVERT: C 989 ASN cc_start: 0.7964 (t0) cc_final: 0.7698 (t0) REVERT: C 1051 GLU cc_start: 0.8921 (tp30) cc_final: 0.8486 (tp30) REVERT: D 201 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.8079 (tp) REVERT: D 330 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7909 (pm20) REVERT: D 364 ARG cc_start: 0.7725 (tmm160) cc_final: 0.7161 (tmm-80) REVERT: D 646 TYR cc_start: 0.7422 (t80) cc_final: 0.7194 (t80) REVERT: D 713 ARG cc_start: 0.7617 (tpm170) cc_final: 0.7156 (tpm170) REVERT: D 817 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8081 (mm) REVERT: D 863 MET cc_start: 0.8672 (mmt) cc_final: 0.8386 (mmt) REVERT: D 918 ASP cc_start: 0.8293 (p0) cc_final: 0.7874 (p0) REVERT: D 1048 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8687 (pm20) outliers start: 90 outliers final: 55 residues processed: 485 average time/residue: 0.2004 time to fit residues: 155.9055 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 : 1.186 ------------------------------------------------------------------------------- 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 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 392 THR 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 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 990 ASN 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 329 VAL 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 661 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 942 GLU 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 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 358 LEU 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 967 THR Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain C residue 1083 ARG Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 392 THR 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 967 THR Chi-restraints excluded: chain D residue 1069 THR 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: 5.9990 chunk 182 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 303 optimal weight: 9.9990 chunk 360 optimal weight: 0.8980 chunk 187 optimal weight: 0.0870 chunk 214 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 239 optimal weight: 9.9990 overall best weight: 3.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 HIS ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS B 572 ASN B 990 ASN D 257 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.129524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.093606 restraints weight = 65495.688| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.19 r_work: 0.3151 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.5984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 31192 Z= 0.201 Angle : 0.629 8.868 42260 Z= 0.328 Chirality : 0.042 0.223 4708 Planarity : 0.004 0.052 5280 Dihedral : 5.240 56.580 4024 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.09 % Allowed : 14.21 % Favored : 82.69 % 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: 0.27 (0.14), residues: 3656 helix: 1.32 (0.11), residues: 2448 sheet: -1.23 (0.36), residues: 184 loop : -2.40 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 452 TYR 0.023 0.001 TYR A 646 PHE 0.029 0.002 PHE A 155 TRP 0.023 0.002 TRP D 898 HIS 0.003 0.001 HIS C 138 Details of bonding type rmsd covalent geometry : bond 0.00471 (31188) covalent geometry : angle 0.62856 (42252) SS BOND : bond 0.00613 ( 4) SS BOND : angle 1.72746 ( 8) hydrogen bonds : bond 0.04632 ( 1754) hydrogen bonds : angle 4.26542 ( 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 507 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 404 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8453 (tp) REVERT: A 304 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.8115 (m-80) REVERT: A 364 ARG cc_start: 0.7846 (tmt170) cc_final: 0.6987 (ttp-170) REVERT: A 393 VAL cc_start: 0.9216 (p) cc_final: 0.9001 (t) REVERT: A 496 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8988 (mp) REVERT: A 723 LEU cc_start: 0.7894 (mm) cc_final: 0.7630 (tt) REVERT: A 725 TRP cc_start: 0.7942 (t60) cc_final: 0.7553 (t60) REVERT: A 801 MET cc_start: 0.8903 (ptm) cc_final: 0.8696 (ptp) REVERT: A 918 ASP cc_start: 0.8339 (p0) cc_final: 0.7989 (p0) REVERT: B 197 ARG cc_start: 0.8786 (ttp-110) cc_final: 0.8456 (ttp-110) REVERT: B 201 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.7896 (tp) REVERT: B 304 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.8241 (m-80) REVERT: B 364 ARG cc_start: 0.8022 (tmt170) cc_final: 0.7501 (tmm160) REVERT: B 485 GLN cc_start: 0.8402 (pm20) cc_final: 0.8061 (mm-40) REVERT: B 646 TYR cc_start: 0.7723 (t80) cc_final: 0.7394 (t80) REVERT: B 817 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8049 (mm) REVERT: B 822 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8222 (mtmt) REVERT: B 918 ASP cc_start: 0.8320 (p0) cc_final: 0.7831 (p0) REVERT: B 978 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8152 (mpp) REVERT: C 186 TYR cc_start: 0.7783 (m-80) cc_final: 0.7236 (m-80) REVERT: C 364 ARG cc_start: 0.8264 (mtm-85) cc_final: 0.7508 (mtm180) REVERT: C 597 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9160 (tt) REVERT: C 646 TYR cc_start: 0.7644 (t80) cc_final: 0.7290 (t80) REVERT: C 697 LEU cc_start: 0.8733 (tt) cc_final: 0.8500 (tt) REVERT: C 817 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8123 (mm) REVERT: C 863 MET cc_start: 0.8711 (mmt) cc_final: 0.8342 (mmt) REVERT: C 989 ASN cc_start: 0.7975 (t0) cc_final: 0.7749 (t0) REVERT: C 1051 GLU cc_start: 0.8935 (tp30) cc_final: 0.8446 (tp30) REVERT: C 1066 LYS cc_start: 0.9187 (mttp) cc_final: 0.8960 (mttt) REVERT: D 201 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8076 (tp) REVERT: D 364 ARG cc_start: 0.7786 (tmm160) cc_final: 0.7488 (ttp-170) REVERT: D 396 MET cc_start: 0.6676 (mpp) cc_final: 0.6101 (mmt) REVERT: D 646 TYR cc_start: 0.7608 (t80) cc_final: 0.7404 (t80) REVERT: D 713 ARG cc_start: 0.7600 (tpm170) cc_final: 0.6949 (tpm170) REVERT: D 740 TRP cc_start: 0.8543 (t-100) cc_final: 0.8249 (t-100) REVERT: D 817 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8068 (mm) REVERT: D 822 LYS cc_start: 0.8613 (mmmt) cc_final: 0.8197 (mtmt) REVERT: D 863 MET cc_start: 0.8661 (mmt) cc_final: 0.8300 (mmt) REVERT: D 918 ASP cc_start: 0.8239 (p0) cc_final: 0.7804 (p0) REVERT: D 1048 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8737 (pm20) outliers start: 103 outliers final: 68 residues processed: 469 average time/residue: 0.1995 time to fit residues: 150.8174 Evaluate side-chains 456 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 377 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 440 ASP 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 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 849 VAL Chi-restraints excluded: chain A residue 864 LEU 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 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 392 THR Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 661 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 942 GLU 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 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 358 LEU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 597 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 849 VAL Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain C residue 985 ILE 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 302 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 353 MET 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 849 VAL Chi-restraints excluded: chain D residue 878 MET Chi-restraints excluded: chain D residue 967 THR Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1022 TYR Chi-restraints excluded: chain D residue 1067 ILE Chi-restraints excluded: chain D residue 1069 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 98 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 chunk 351 optimal weight: 2.9990 chunk 246 optimal weight: 9.9990 chunk 341 optimal weight: 8.9990 chunk 153 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 30.0000 chunk 242 optimal weight: 20.0000 chunk 295 optimal weight: 9.9990 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 ASN B 268 HIS B 559 HIS B 572 ASN B 765 HIS ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 GLN C 559 HIS C 572 ASN D 559 HIS ** 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 = 0.3864 r_free = 0.3864 target = 0.127208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.091231 restraints weight = 65712.627| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.12 r_work: 0.3119 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.6254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 31192 Z= 0.242 Angle : 0.657 8.937 42260 Z= 0.343 Chirality : 0.044 0.248 4708 Planarity : 0.004 0.095 5280 Dihedral : 5.297 55.946 4024 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.49 % Allowed : 13.94 % Favored : 82.57 % 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: 0.27 (0.14), residues: 3656 helix: 1.29 (0.11), residues: 2456 sheet: -1.23 (0.37), residues: 184 loop : -2.35 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 452 TYR 0.017 0.002 TYR C 787 PHE 0.029 0.002 PHE A 155 TRP 0.025 0.002 TRP D 426 HIS 0.005 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00569 (31188) covalent geometry : angle 0.65633 (42252) SS BOND : bond 0.00742 ( 4) SS BOND : angle 2.20913 ( 8) hydrogen bonds : bond 0.04929 ( 1754) hydrogen bonds : angle 4.36270 ( 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 506 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 390 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8465 (tp) REVERT: A 304 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.8164 (m-80) REVERT: A 393 VAL cc_start: 0.9216 (p) cc_final: 0.9004 (t) REVERT: A 597 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9209 (tt) REVERT: A 646 TYR cc_start: 0.7744 (t80) cc_final: 0.7433 (t80) REVERT: A 723 LEU cc_start: 0.8100 (mm) cc_final: 0.7850 (tt) REVERT: A 725 TRP cc_start: 0.8006 (t60) cc_final: 0.7633 (t60) REVERT: A 788 MET cc_start: 0.8029 (tmm) cc_final: 0.7624 (tmm) REVERT: A 801 MET cc_start: 0.8972 (ptm) cc_final: 0.8771 (ptp) REVERT: A 817 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8231 (mm) REVERT: A 918 ASP cc_start: 0.8303 (p0) cc_final: 0.7964 (p0) REVERT: B 197 ARG cc_start: 0.8820 (ttp-110) cc_final: 0.8619 (ttp-110) REVERT: B 201 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8014 (tp) REVERT: B 304 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.8183 (m-80) REVERT: B 364 ARG cc_start: 0.7995 (tmt170) cc_final: 0.7582 (tmm160) REVERT: B 451 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7436 (ptt180) REVERT: B 452 ARG cc_start: 0.6740 (ptt90) cc_final: 0.6522 (ptt90) REVERT: B 646 TYR cc_start: 0.7932 (t80) cc_final: 0.7573 (t80) REVERT: B 817 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8155 (mm) REVERT: B 918 ASP cc_start: 0.8286 (p0) cc_final: 0.7826 (p0) REVERT: B 978 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8343 (mpp) REVERT: B 1003 GLN cc_start: 0.8848 (tm130) cc_final: 0.8517 (tm-30) REVERT: C 186 TYR cc_start: 0.7844 (m-80) cc_final: 0.7478 (m-80) REVERT: C 646 TYR cc_start: 0.7821 (t80) cc_final: 0.7559 (t80) REVERT: C 697 LEU cc_start: 0.8889 (tt) cc_final: 0.8671 (tt) REVERT: C 817 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8087 (mm) REVERT: C 863 MET cc_start: 0.8721 (mmt) cc_final: 0.8326 (mmt) REVERT: C 918 ASP cc_start: 0.8067 (p0) cc_final: 0.7576 (p0) REVERT: C 1003 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8514 (tm-30) REVERT: C 1051 GLU cc_start: 0.8922 (tp30) cc_final: 0.8465 (tp30) REVERT: C 1066 LYS cc_start: 0.9153 (mttp) cc_final: 0.8902 (mtmm) REVERT: D 201 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8104 (tp) REVERT: D 364 ARG cc_start: 0.7829 (tmm160) cc_final: 0.7426 (tmm-80) REVERT: D 646 TYR cc_start: 0.7855 (t80) cc_final: 0.7618 (t80) REVERT: D 740 TRP cc_start: 0.8507 (t-100) cc_final: 0.8194 (t-100) REVERT: D 817 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8082 (mm) REVERT: D 863 MET cc_start: 0.8709 (mmt) cc_final: 0.8354 (mmt) REVERT: D 918 ASP cc_start: 0.8159 (p0) cc_final: 0.7748 (p0) REVERT: D 1048 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8793 (pm20) outliers start: 116 outliers final: 86 residues processed: 469 average time/residue: 0.1929 time to fit residues: 145.7906 Evaluate side-chains 467 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 369 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 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 755 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 990 ASN Chi-restraints excluded: chain A residue 1001 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 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 392 THR Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 484 LEU 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 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 864 LEU Chi-restraints excluded: chain B residue 942 GLU 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 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 755 VAL Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 787 TYR 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 864 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 1001 LEU 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 353 MET Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 605 LYS Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 755 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 942 GLU Chi-restraints excluded: chain D residue 967 THR Chi-restraints excluded: chain D residue 989 ASN Chi-restraints excluded: chain D residue 990 ASN 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: 6.9990 chunk 241 optimal weight: 0.3980 chunk 197 optimal weight: 20.0000 chunk 326 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 265 optimal weight: 0.6980 chunk 255 optimal weight: 0.0770 chunk 295 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 990 ASN B 268 HIS B 572 ASN B 990 ASN C 671 GLN D1003 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.131103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.096222 restraints weight = 64644.359| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.99 r_work: 0.3205 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.6374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31192 Z= 0.125 Angle : 0.597 10.874 42260 Z= 0.308 Chirality : 0.040 0.208 4708 Planarity : 0.004 0.113 5280 Dihedral : 5.044 54.133 4024 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.22 % Allowed : 15.35 % Favored : 82.42 % 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: 0.62 (0.14), residues: 3656 helix: 1.55 (0.11), residues: 2464 sheet: -0.85 (0.38), residues: 172 loop : -2.25 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 364 TYR 0.015 0.001 TYR C 186 PHE 0.033 0.001 PHE B 155 TRP 0.022 0.001 TRP A 453 HIS 0.009 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00272 (31188) covalent geometry : angle 0.59606 (42252) SS BOND : bond 0.00749 ( 4) SS BOND : angle 2.76341 ( 8) hydrogen bonds : bond 0.03874 ( 1754) hydrogen bonds : angle 4.04889 ( 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 509 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 435 time to evaluate : 1.172 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 201 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.7881 (tp) REVERT: A 304 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.8077 (m-80) REVERT: A 393 VAL cc_start: 0.9209 (p) cc_final: 0.9007 (t) REVERT: A 646 TYR cc_start: 0.7660 (t80) cc_final: 0.7402 (t80) REVERT: A 723 LEU cc_start: 0.8064 (mm) cc_final: 0.7826 (tt) REVERT: A 725 TRP cc_start: 0.7975 (t60) cc_final: 0.7693 (t60) REVERT: A 788 MET cc_start: 0.7997 (tmm) cc_final: 0.7689 (tmm) REVERT: A 789 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8283 (t0) REVERT: A 817 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8149 (mm) REVERT: A 918 ASP cc_start: 0.8099 (p0) cc_final: 0.7732 (p0) REVERT: A 928 HIS cc_start: 0.8318 (m-70) cc_final: 0.8104 (m-70) REVERT: A 1066 LYS cc_start: 0.9047 (mmtp) cc_final: 0.8845 (mttp) REVERT: B 197 ARG cc_start: 0.8821 (ttp-110) cc_final: 0.8611 (ttp-110) REVERT: B 201 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.7968 (tp) REVERT: B 364 ARG cc_start: 0.8053 (tmt170) cc_final: 0.7732 (ttp-170) REVERT: B 817 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8045 (mm) REVERT: B 822 LYS cc_start: 0.8558 (mmmt) cc_final: 0.8154 (mmtp) REVERT: B 860 LEU cc_start: 0.9387 (tp) cc_final: 0.9174 (tp) REVERT: B 918 ASP cc_start: 0.8159 (p0) cc_final: 0.7710 (p0) REVERT: B 974 LEU cc_start: 0.8737 (tp) cc_final: 0.8499 (tp) REVERT: B 978 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8330 (mpp) REVERT: B 1003 GLN cc_start: 0.8746 (tm130) cc_final: 0.8398 (tm-30) REVERT: B 1051 GLU cc_start: 0.8739 (tp30) cc_final: 0.8465 (tp30) REVERT: C 186 TYR cc_start: 0.7600 (m-80) cc_final: 0.7327 (m-80) REVERT: C 199 ASN cc_start: 0.8228 (m-40) cc_final: 0.7898 (t0) REVERT: C 646 TYR cc_start: 0.7794 (t80) cc_final: 0.7564 (t80) REVERT: C 665 ASP cc_start: 0.8768 (t0) cc_final: 0.8556 (t70) REVERT: C 697 LEU cc_start: 0.8846 (tt) cc_final: 0.8576 (tt) REVERT: C 740 TRP cc_start: 0.8318 (t-100) cc_final: 0.8026 (t-100) REVERT: C 817 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8100 (mm) REVERT: C 863 MET cc_start: 0.8579 (mmt) cc_final: 0.8205 (mmt) REVERT: C 1003 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8415 (tm-30) REVERT: C 1051 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8413 (tp30) REVERT: C 1066 LYS cc_start: 0.9100 (mttp) cc_final: 0.8894 (mttt) REVERT: D 201 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.8089 (tp) REVERT: D 396 MET cc_start: 0.6726 (mpp) cc_final: 0.6099 (mmp) REVERT: D 740 TRP cc_start: 0.8453 (t-100) cc_final: 0.8162 (t-100) REVERT: D 817 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8077 (mm) REVERT: D 822 LYS cc_start: 0.8548 (mmmt) cc_final: 0.8160 (mtmt) REVERT: D 863 MET cc_start: 0.8590 (mmt) cc_final: 0.8196 (mmt) REVERT: D 918 ASP cc_start: 0.8107 (p0) cc_final: 0.7706 (p0) REVERT: D 1003 GLN cc_start: 0.8796 (tm130) cc_final: 0.8484 (tm-30) REVERT: D 1048 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8736 (pm20) outliers start: 74 outliers final: 44 residues processed: 476 average time/residue: 0.2002 time to fit residues: 152.5155 Evaluate side-chains 454 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 399 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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 404 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 789 ASN 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 990 ASN Chi-restraints excluded: chain A residue 1001 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 338 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 779 PHE 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 978 MET Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 990 ASN Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 392 THR 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 846 ILE Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain C residue 985 ILE 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 329 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 392 THR 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 846 ILE Chi-restraints excluded: chain D residue 967 THR 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: 0.3980 chunk 174 optimal weight: 0.9980 chunk 279 optimal weight: 20.0000 chunk 356 optimal weight: 7.9990 chunk 216 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 79 optimal weight: 0.0010 chunk 159 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 overall best weight: 1.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN B 268 HIS B 572 ASN B 990 ASN ** C 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 990 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 = 0.130385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.095376 restraints weight = 64619.341| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.99 r_work: 0.3191 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.6469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31192 Z= 0.140 Angle : 0.611 10.049 42260 Z= 0.312 Chirality : 0.041 0.207 4708 Planarity : 0.004 0.062 5280 Dihedral : 4.981 55.347 4024 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.92 % Allowed : 16.20 % Favored : 81.88 % 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: 0.70 (0.14), residues: 3656 helix: 1.60 (0.11), residues: 2456 sheet: -0.90 (0.38), residues: 172 loop : -2.16 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 452 TYR 0.022 0.001 TYR B 646 PHE 0.025 0.001 PHE B1082 TRP 0.024 0.001 TRP A 898 HIS 0.009 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00326 (31188) covalent geometry : angle 0.61023 (42252) SS BOND : bond 0.00631 ( 4) SS BOND : angle 2.84270 ( 8) hydrogen bonds : bond 0.03983 ( 1754) hydrogen bonds : angle 4.05841 ( 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 472 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 408 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.7859 (tp) REVERT: A 304 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8064 (m-80) REVERT: A 646 TYR cc_start: 0.7700 (t80) cc_final: 0.7465 (t80) REVERT: A 723 LEU cc_start: 0.8112 (mm) cc_final: 0.7885 (tt) REVERT: A 725 TRP cc_start: 0.7977 (t60) cc_final: 0.7667 (t60) REVERT: A 788 MET cc_start: 0.7994 (tmm) cc_final: 0.7668 (tmm) REVERT: A 789 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8244 (t0) REVERT: A 817 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8141 (mm) REVERT: A 918 ASP cc_start: 0.8178 (p0) cc_final: 0.7829 (p0) REVERT: A 1051 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8496 (tm-30) REVERT: B 197 ARG cc_start: 0.8820 (ttp-110) cc_final: 0.8608 (ttp-110) REVERT: B 201 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.7930 (tp) REVERT: B 364 ARG cc_start: 0.8087 (tmt170) cc_final: 0.7758 (ttp-170) REVERT: B 445 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8429 (mp0) REVERT: B 817 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8016 (mm) REVERT: B 822 LYS cc_start: 0.8556 (mmmt) cc_final: 0.8191 (mtmt) REVERT: B 860 LEU cc_start: 0.9389 (tp) cc_final: 0.9179 (tp) REVERT: B 918 ASP cc_start: 0.8122 (p0) cc_final: 0.7676 (p0) REVERT: B 974 LEU cc_start: 0.8750 (tp) cc_final: 0.8498 (tp) REVERT: B 978 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8367 (mpp) REVERT: B 1003 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8423 (tm-30) REVERT: B 1051 GLU cc_start: 0.8700 (tp30) cc_final: 0.8354 (tp30) REVERT: C 186 TYR cc_start: 0.7761 (m-80) cc_final: 0.7412 (m-80) REVERT: C 646 TYR cc_start: 0.7831 (t80) cc_final: 0.7621 (t80) REVERT: C 665 ASP cc_start: 0.8797 (t0) cc_final: 0.8563 (t70) REVERT: C 697 LEU cc_start: 0.8832 (tt) cc_final: 0.8562 (tt) REVERT: C 740 TRP cc_start: 0.8338 (t-100) cc_final: 0.8056 (t-100) REVERT: C 817 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8030 (mm) REVERT: C 863 MET cc_start: 0.8622 (mmt) cc_final: 0.8258 (mmt) REVERT: C 1003 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8419 (tm-30) REVERT: C 1051 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8418 (tp30) REVERT: C 1066 LYS cc_start: 0.9120 (mttp) cc_final: 0.8912 (mttt) REVERT: D 201 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7956 (tp) REVERT: D 364 ARG cc_start: 0.7873 (tmm160) cc_final: 0.7367 (ttt-90) REVERT: D 396 MET cc_start: 0.6733 (mpp) cc_final: 0.6106 (mmp) REVERT: D 740 TRP cc_start: 0.8417 (t-100) cc_final: 0.8096 (t-100) REVERT: D 817 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8063 (mm) REVERT: D 822 LYS cc_start: 0.8508 (mmmt) cc_final: 0.8113 (mtmt) REVERT: D 863 MET cc_start: 0.8596 (mmt) cc_final: 0.8281 (mmt) REVERT: D 918 ASP cc_start: 0.8166 (p0) cc_final: 0.7762 (p0) REVERT: D 1003 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8451 (tm-30) outliers start: 64 outliers final: 46 residues processed: 445 average time/residue: 0.1903 time to fit residues: 138.4198 Evaluate side-chains 449 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 390 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 404 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 789 ASN 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 990 ASN Chi-restraints excluded: chain A residue 1001 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 338 VAL 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 849 VAL Chi-restraints excluded: chain B residue 878 MET 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 1003 GLN 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 392 THR 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 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 329 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 392 THR 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 1003 GLN 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: 0.9990 chunk 188 optimal weight: 9.9990 chunk 204 optimal weight: 9.9990 chunk 183 optimal weight: 4.9990 chunk 304 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 338 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 265 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 HIS B 572 ASN B 990 ASN ** C 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.127777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.092475 restraints weight = 64746.109| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.98 r_work: 0.3138 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.6572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 31192 Z= 0.212 Angle : 0.665 10.723 42260 Z= 0.343 Chirality : 0.043 0.231 4708 Planarity : 0.004 0.056 5280 Dihedral : 5.106 55.966 4024 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.04 % Allowed : 16.26 % 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: 0.61 (0.14), residues: 3656 helix: 1.50 (0.11), residues: 2452 sheet: -0.92 (0.38), residues: 172 loop : -2.10 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 364 TYR 0.023 0.002 TYR B 646 PHE 0.020 0.002 PHE B1082 TRP 0.026 0.002 TRP A 898 HIS 0.009 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00497 (31188) covalent geometry : angle 0.66326 (42252) SS BOND : bond 0.00703 ( 4) SS BOND : angle 3.05596 ( 8) hydrogen bonds : bond 0.04646 ( 1754) hydrogen bonds : angle 4.22532 ( 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 459 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 391 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.7868 (tp) REVERT: A 304 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8164 (m-80) REVERT: A 646 TYR cc_start: 0.7872 (t80) cc_final: 0.7612 (t80) REVERT: A 723 LEU cc_start: 0.8113 (mm) cc_final: 0.7906 (tt) REVERT: A 725 TRP cc_start: 0.7993 (t60) cc_final: 0.7667 (t60) REVERT: A 788 MET cc_start: 0.8053 (tmm) cc_final: 0.7681 (tmm) REVERT: A 789 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8196 (t0) REVERT: A 817 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8150 (mm) REVERT: A 918 ASP cc_start: 0.8179 (p0) cc_final: 0.7863 (p0) REVERT: B 197 ARG cc_start: 0.8808 (ttp-110) cc_final: 0.8569 (ttp-110) REVERT: B 201 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.7910 (tp) REVERT: B 452 ARG cc_start: 0.7012 (ptt90) cc_final: 0.6767 (ptt-90) REVERT: B 817 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8119 (mm) REVERT: B 822 LYS cc_start: 0.8594 (mmmt) cc_final: 0.8200 (mtmt) REVERT: B 860 LEU cc_start: 0.9409 (tp) cc_final: 0.9197 (tp) REVERT: B 918 ASP cc_start: 0.8091 (p0) cc_final: 0.7657 (p0) REVERT: B 978 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8395 (mpp) REVERT: B 1003 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8469 (tm-30) REVERT: B 1051 GLU cc_start: 0.8767 (tp30) cc_final: 0.8398 (tp30) REVERT: C 186 TYR cc_start: 0.7785 (m-80) cc_final: 0.7218 (m-80) REVERT: C 646 TYR cc_start: 0.7980 (t80) cc_final: 0.7683 (t80) REVERT: C 665 ASP cc_start: 0.8825 (t0) cc_final: 0.8566 (t70) REVERT: C 697 LEU cc_start: 0.8886 (tt) cc_final: 0.8648 (tt) REVERT: C 817 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8152 (mm) REVERT: C 863 MET cc_start: 0.8716 (mmt) cc_final: 0.8336 (mmt) REVERT: C 918 ASP cc_start: 0.8063 (p0) cc_final: 0.7570 (p0) REVERT: C 1003 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8475 (tm-30) REVERT: C 1051 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8390 (tp30) REVERT: D 169 ILE cc_start: 0.9554 (mt) cc_final: 0.9338 (tp) REVERT: D 201 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8090 (tp) REVERT: D 364 ARG cc_start: 0.7854 (tmm160) cc_final: 0.7496 (ttp80) REVERT: D 396 MET cc_start: 0.6628 (mpp) cc_final: 0.6023 (mmp) REVERT: D 452 ARG cc_start: 0.6613 (ptt90) cc_final: 0.6410 (ptt90) REVERT: D 740 TRP cc_start: 0.8453 (t-100) cc_final: 0.8122 (t-100) REVERT: D 817 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8128 (mm) REVERT: D 822 LYS cc_start: 0.8571 (mmmt) cc_final: 0.8192 (mtmt) REVERT: D 863 MET cc_start: 0.8674 (mmt) cc_final: 0.8308 (mmt) REVERT: D 918 ASP cc_start: 0.8156 (p0) cc_final: 0.7757 (p0) REVERT: D 1003 GLN cc_start: 0.8831 (tm130) cc_final: 0.8502 (tm-30) outliers start: 68 outliers final: 52 residues processed: 433 average time/residue: 0.1857 time to fit residues: 132.0066 Evaluate side-chains 444 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 380 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 404 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 789 ASN 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 990 ASN 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 302 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 572 ASN 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 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 1003 GLN Chi-restraints excluded: chain B residue 1067 ILE 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 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 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 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 755 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 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 167 optimal weight: 1.9990 chunk 325 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 chunk 353 optimal weight: 3.9990 chunk 364 optimal weight: 3.9990 chunk 174 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 203 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 990 ASN ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** C 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 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 = 0.3885 r_free = 0.3885 target = 0.128646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.092879 restraints weight = 65463.192| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.04 r_work: 0.3148 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.6592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 31192 Z= 0.182 Angle : 0.777 59.141 42260 Z= 0.416 Chirality : 0.041 0.237 4708 Planarity : 0.005 0.118 5280 Dihedral : 5.128 56.116 4024 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.39 % Favored : 94.58 % Rotamer: Outliers : 2.04 % Allowed : 16.35 % Favored : 81.61 % Cbeta Deviations : 0.03 % 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: 0.64 (0.14), residues: 3656 helix: 1.52 (0.11), residues: 2452 sheet: -0.89 (0.38), residues: 172 loop : -2.08 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 364 TYR 0.033 0.002 TYR D 646 PHE 0.070 0.002 PHE B1013 TRP 0.045 0.002 TRP D 798 HIS 0.009 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00387 (31188) covalent geometry : angle 0.77566 (42252) SS BOND : bond 0.00653 ( 4) SS BOND : angle 2.93350 ( 8) hydrogen bonds : bond 0.04541 ( 1754) hydrogen bonds : angle 4.20316 ( 5214) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7832.62 seconds wall clock time: 134 minutes 51.18 seconds (8091.18 seconds total)