Starting phenix.real_space_refine on Thu Jun 26 08:24:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wrc_32722/06_2025/7wrc_32722.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrc_32722/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wrc_32722/06_2025/7wrc_32722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrc_32722/06_2025/7wrc_32722.map" model { file = "/net/cci-nas-00/data/ceres_data/7wrc_32722/06_2025/7wrc_32722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrc_32722/06_2025/7wrc_32722.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, D Time building chain proxies: 21.58, per 1000 atoms: 0.71 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 C 929 " - pdb=" SG CYS C 940 " distance=2.01 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 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: 9.17 Conformation dependent library (CDL) restraints added in 3.8 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: 3.72 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: 11.95 Time building geometry restraints manager: 10.42 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: 0.23 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.330 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 74.370 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.480 ------------------------------------------------------------------------------- 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 : 5.92 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.030 0.004 TRP B 377 HIS 0.008 0.002 HIS D 185 PHE 0.030 0.003 PHE C 832 TYR 0.040 0.004 TYR D1005 ARG 0.007 0.001 ARG B 688 Details of bonding type rmsd hydrogen bonds : bond 0.15042 ( 1754) hydrogen bonds : angle 6.56168 ( 5214) SS BOND : bond 0.01733 ( 4) SS BOND : angle 4.39080 ( 8) covalent geometry : bond 0.01000 (31188) covalent geometry : angle 1.06775 (42252) *********************** 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 : 3.341 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: 0.8055 (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: 0.9039 (p) REVERT: A 723 LEU cc_start: 0.7606 (mm) cc_final: 0.7294 (tt) REVERT: A 859 MET cc_start: 0.8255 (ttp) cc_final: 0.7377 (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: 0.8955 (tp) REVERT: B 1023 MET cc_start: 0.5629 (mmm) cc_final: 0.5273 (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 723 LEU cc_start: 0.7960 (mm) cc_final: 0.7720 (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: 0.5356 (mmm) outliers start: 4 outliers final: 0 residues processed: 802 average time/residue: 0.4420 time to fit residues: 550.3099 Evaluate side-chains 463 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 463 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 1.9990 chunk 281 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 190 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 291 optimal weight: 30.0000 chunk 112 optimal weight: 8.9990 chunk 177 optimal weight: 0.9980 chunk 217 optimal weight: 2.9990 chunk 337 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 609 ASN A 671 GLN B 136 HIS B 257 HIS B 270 HIS B 483 ASN B 671 GLN B 675 GLN C 136 HIS C 257 HIS ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 HIS ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 989 ASN D 136 HIS ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 HIS D 294 ASN ** D 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 789 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.138296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.103674 restraints weight = 65110.817| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.19 r_work: 0.3336 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31192 Z= 0.143 Angle : 0.657 8.364 42260 Z= 0.345 Chirality : 0.042 0.173 4708 Planarity : 0.005 0.139 5280 Dihedral : 6.015 48.921 4024 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.77 % Allowed : 9.59 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.13), residues: 3656 helix: -0.27 (0.10), residues: 2472 sheet: -1.50 (0.35), residues: 188 loop : -2.97 (0.16), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 898 HIS 0.005 0.001 HIS C 138 PHE 0.017 0.002 PHE C 809 TYR 0.018 0.002 TYR D 981 ARG 0.007 0.001 ARG B1079 Details of bonding type rmsd hydrogen bonds : bond 0.04973 ( 1754) hydrogen bonds : angle 4.56982 ( 5214) SS BOND : bond 0.00696 ( 4) SS BOND : angle 1.63595 ( 8) covalent geometry : bond 0.00301 (31188) covalent geometry : angle 0.65629 (42252) *********************** 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: 59 poor density : 532 time to evaluate : 3.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 GLN cc_start: 0.7511 (pp30) cc_final: 0.6860 (tm-30) REVERT: A 330 GLU cc_start: 0.8790 (mp0) cc_final: 0.8364 (mp0) REVERT: A 507 ARG cc_start: 0.8409 (mmm-85) cc_final: 0.8128 (tpt90) REVERT: A 713 ARG cc_start: 0.7372 (tpm170) cc_final: 0.7053 (tpp80) REVERT: A 723 LEU cc_start: 0.7555 (mm) cc_final: 0.7307 (tt) REVERT: A 860 LEU cc_start: 0.9222 (tp) cc_final: 0.9020 (tp) REVERT: A 918 ASP cc_start: 0.8167 (p0) cc_final: 0.7953 (p0) REVERT: A 955 ILE cc_start: 0.8543 (tp) cc_final: 0.8343 (tt) REVERT: A 989 ASN cc_start: 0.7819 (t0) cc_final: 0.7601 (t0) REVERT: B 201 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8047 (tp) REVERT: B 306 GLN cc_start: 0.7710 (pp30) cc_final: 0.7505 (tm-30) REVERT: B 364 ARG cc_start: 0.7993 (mtm180) cc_final: 0.7789 (tmt170) REVERT: B 435 GLU cc_start: 0.8747 (tp30) cc_final: 0.8388 (tm-30) REVERT: B 661 VAL cc_start: 0.9455 (OUTLIER) cc_final: 0.9165 (m) REVERT: B 723 LEU cc_start: 0.7920 (mm) cc_final: 0.7681 (tt) REVERT: B 801 MET cc_start: 0.8441 (ptm) cc_final: 0.8186 (ptt) REVERT: B 860 LEU cc_start: 0.9134 (tp) cc_final: 0.8916 (tp) REVERT: B 906 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8240 (tp30) REVERT: B 918 ASP cc_start: 0.8170 (p0) cc_final: 0.7905 (p0) REVERT: B 937 LYS cc_start: 0.7644 (mtmm) cc_final: 0.7302 (mtmt) REVERT: B 989 ASN cc_start: 0.7902 (t0) cc_final: 0.7667 (t0) REVERT: C 306 GLN cc_start: 0.7783 (tm-30) cc_final: 0.7466 (tp-100) REVERT: C 325 PRO cc_start: 0.7731 (Cg_endo) cc_final: 0.7496 (Cg_exo) REVERT: C 364 ARG cc_start: 0.8127 (mtm-85) cc_final: 0.7517 (mtm180) REVERT: C 431 LYS cc_start: 0.9022 (mttm) cc_final: 0.8733 (mttp) REVERT: C 435 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8393 (tm-30) REVERT: C 445 GLU cc_start: 0.8208 (mp0) cc_final: 0.7865 (mp0) REVERT: C 451 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6660 (ptt-90) REVERT: C 661 VAL cc_start: 0.9467 (t) cc_final: 0.9228 (m) REVERT: C 859 MET cc_start: 0.8832 (ttm) cc_final: 0.8496 (mtp) REVERT: C 863 MET cc_start: 0.8400 (mmt) cc_final: 0.8152 (mmt) REVERT: D 201 ILE cc_start: 0.8396 (tp) cc_final: 0.8169 (tp) REVERT: D 252 ILE cc_start: 0.7908 (mm) cc_final: 0.7602 (tt) REVERT: D 306 GLN cc_start: 0.7451 (tm-30) cc_final: 0.6913 (tp-100) REVERT: D 325 PRO cc_start: 0.7655 (Cg_endo) cc_final: 0.7428 (Cg_exo) REVERT: D 431 LYS cc_start: 0.8979 (mttm) cc_final: 0.8705 (mttp) REVERT: D 435 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8409 (tm-30) REVERT: D 445 GLU cc_start: 0.8160 (mp0) cc_final: 0.7957 (mp0) REVERT: D 789 ASN cc_start: 0.8084 (OUTLIER) cc_final: 0.7790 (t0) REVERT: D 863 MET cc_start: 0.8481 (mmt) cc_final: 0.8249 (mmt) REVERT: D 989 ASN cc_start: 0.7847 (t0) cc_final: 0.7577 (t0) REVERT: D 1013 PHE cc_start: 0.6814 (t80) cc_final: 0.6413 (t80) REVERT: D 1059 MET cc_start: 0.8858 (mpp) cc_final: 0.8552 (mmm) outliers start: 59 outliers final: 26 residues processed: 571 average time/residue: 0.4053 time to fit residues: 370.6208 Evaluate side-chains 475 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 445 time to evaluate : 3.494 ------------------------------------------------------------------------------- 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 403 ILE Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain C residue 227 ILE 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 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain D residue 260 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 81 optimal weight: 6.9990 chunk 209 optimal weight: 0.0970 chunk 263 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 328 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 104 optimal weight: 20.0000 chunk 129 optimal weight: 4.9990 chunk 197 optimal weight: 20.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 572 ASN A 675 GLN B 572 ASN B 609 ASN C 204 ASN C 294 ASN C 483 ASN C 675 GLN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN D 483 ASN D 675 GLN D 741 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.132867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.097344 restraints weight = 65319.139| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.20 r_work: 0.3224 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 31192 Z= 0.205 Angle : 0.659 9.213 42260 Z= 0.347 Chirality : 0.043 0.182 4708 Planarity : 0.005 0.106 5280 Dihedral : 5.613 47.066 4024 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.67 % Allowed : 11.78 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.14), residues: 3656 helix: 0.56 (0.10), residues: 2468 sheet: -1.43 (0.36), residues: 184 loop : -2.74 (0.17), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 898 HIS 0.013 0.001 HIS C 185 PHE 0.019 0.002 PHE D 752 TYR 0.019 0.002 TYR A 130 ARG 0.023 0.001 ARG C1083 Details of bonding type rmsd hydrogen bonds : bond 0.04911 ( 1754) hydrogen bonds : angle 4.38032 ( 5214) SS BOND : bond 0.00707 ( 4) SS BOND : angle 1.41092 ( 8) covalent geometry : bond 0.00452 (31188) covalent geometry : angle 0.65861 (42252) *********************** 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 569 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 480 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.9041 (t80) cc_final: 0.8658 (t80) REVERT: A 201 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8296 (tp) REVERT: A 393 VAL cc_start: 0.9110 (p) cc_final: 0.8836 (t) REVERT: A 507 ARG cc_start: 0.8642 (mmm-85) cc_final: 0.8397 (tpt90) REVERT: A 723 LEU cc_start: 0.7644 (mm) cc_final: 0.7368 (tt) REVERT: A 789 ASN cc_start: 0.8704 (OUTLIER) cc_final: 0.7894 (t0) REVERT: A 801 MET cc_start: 0.8570 (ptm) cc_final: 0.8315 (ptp) REVERT: A 918 ASP cc_start: 0.8447 (p0) cc_final: 0.8200 (p0) REVERT: A 931 PHE cc_start: 0.8515 (m-80) cc_final: 0.8157 (m-80) REVERT: A 955 ILE cc_start: 0.8870 (tp) cc_final: 0.8606 (tt) REVERT: A 989 ASN cc_start: 0.8047 (t0) cc_final: 0.7743 (t0) REVERT: B 197 ARG cc_start: 0.8780 (ttp-110) cc_final: 0.8560 (ttp-110) REVERT: B 201 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8182 (tp) REVERT: B 364 ARG cc_start: 0.8011 (mtm180) cc_final: 0.7775 (tmt170) REVERT: B 689 ASP cc_start: 0.8274 (p0) cc_final: 0.8043 (p0) REVERT: B 740 TRP cc_start: 0.8294 (t-100) cc_final: 0.8031 (t-100) REVERT: B 789 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8095 (t0) REVERT: B 801 MET cc_start: 0.8657 (ptm) cc_final: 0.8392 (ptp) REVERT: B 860 LEU cc_start: 0.9313 (tp) cc_final: 0.9088 (tp) REVERT: B 874 PHE cc_start: 0.8844 (t80) cc_final: 0.8568 (t80) REVERT: B 918 ASP cc_start: 0.8403 (p0) cc_final: 0.8089 (p0) REVERT: B 935 GLU cc_start: 0.8074 (pt0) cc_final: 0.7633 (pm20) REVERT: B 937 LYS cc_start: 0.7651 (mtmm) cc_final: 0.7230 (mtmt) REVERT: B 989 ASN cc_start: 0.8054 (t0) cc_final: 0.7833 (t0) REVERT: C 189 MET cc_start: 0.7913 (mpp) cc_final: 0.7671 (mpp) REVERT: C 201 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.7232 (tp) REVERT: C 364 ARG cc_start: 0.8088 (mtm-85) cc_final: 0.7860 (tmt170) REVERT: C 445 GLU cc_start: 0.8308 (mp0) cc_final: 0.8047 (mp0) REVERT: C 740 TRP cc_start: 0.8245 (t-100) cc_final: 0.7945 (t-100) REVERT: C 789 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8079 (t0) REVERT: C 863 MET cc_start: 0.8718 (mmt) cc_final: 0.8418 (mmt) REVERT: C 989 ASN cc_start: 0.7893 (t0) cc_final: 0.7647 (t0) REVERT: C 997 GLN cc_start: 0.8880 (mp10) cc_final: 0.8671 (mp10) REVERT: D 189 MET cc_start: 0.7855 (mpp) cc_final: 0.7603 (mpp) REVERT: D 201 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8132 (tp) REVERT: D 325 PRO cc_start: 0.7856 (Cg_endo) cc_final: 0.7651 (Cg_exo) REVERT: D 396 MET cc_start: 0.6582 (mpp) cc_final: 0.5880 (mmp) REVERT: D 445 GLU cc_start: 0.8328 (mp0) cc_final: 0.8079 (mp0) REVERT: D 613 GLU cc_start: 0.7847 (tp30) cc_final: 0.7625 (tp30) REVERT: D 740 TRP cc_start: 0.8222 (t-100) cc_final: 0.7908 (t-100) REVERT: D 863 MET cc_start: 0.8710 (mmt) cc_final: 0.8440 (mmt) REVERT: D 918 ASP cc_start: 0.8108 (p0) cc_final: 0.7667 (p0) REVERT: D 989 ASN cc_start: 0.7955 (t0) cc_final: 0.7698 (t0) outliers start: 89 outliers final: 39 residues processed: 535 average time/residue: 0.4133 time to fit residues: 352.7121 Evaluate side-chains 467 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 421 time to evaluate : 3.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 789 ASN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 789 ASN Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 789 ASN Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain D residue 201 ILE 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 584 THR Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 967 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 335 optimal weight: 7.9990 chunk 151 optimal weight: 0.9990 chunk 250 optimal weight: 3.9990 chunk 334 optimal weight: 0.6980 chunk 259 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 347 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 254 optimal weight: 0.9990 chunk 253 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN B 199 ASN B 572 ASN B 741 ASN B 789 ASN C 671 GLN C 789 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 ASN D 671 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.135057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.099426 restraints weight = 65342.075| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.23 r_work: 0.3263 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31192 Z= 0.120 Angle : 0.569 9.389 42260 Z= 0.294 Chirality : 0.040 0.169 4708 Planarity : 0.004 0.125 5280 Dihedral : 5.317 46.854 4024 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.95 % Allowed : 13.67 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3656 helix: 1.06 (0.10), residues: 2460 sheet: -1.05 (0.37), residues: 180 loop : -2.56 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 898 HIS 0.004 0.001 HIS A1080 PHE 0.018 0.001 PHE C1021 TYR 0.019 0.001 TYR B 646 ARG 0.011 0.000 ARG A1081 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 1754) hydrogen bonds : angle 4.07794 ( 5214) SS BOND : bond 0.00881 ( 4) SS BOND : angle 2.40836 ( 8) covalent geometry : bond 0.00261 (31188) covalent geometry : angle 0.56777 (42252) *********************** 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 538 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 473 time to evaluate : 3.224 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 167 ARG cc_start: 0.8658 (tpp80) cc_final: 0.8379 (tpp80) REVERT: A 197 ARG cc_start: 0.8659 (ttp-110) cc_final: 0.8283 (ttp-110) REVERT: A 201 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8339 (tp) REVERT: A 304 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.8065 (m-80) REVERT: A 393 VAL cc_start: 0.9124 (p) cc_final: 0.8897 (t) REVERT: A 485 GLN cc_start: 0.8260 (pm20) cc_final: 0.7670 (mm-40) REVERT: A 507 ARG cc_start: 0.8637 (mmm-85) cc_final: 0.8437 (tpt90) REVERT: A 723 LEU cc_start: 0.7725 (mm) cc_final: 0.7462 (tt) REVERT: A 725 TRP cc_start: 0.7754 (t60) cc_final: 0.7357 (t60) REVERT: A 797 LEU cc_start: 0.6817 (pt) cc_final: 0.6519 (pp) REVERT: A 798 TRP cc_start: 0.8014 (m100) cc_final: 0.7455 (m100) REVERT: A 831 ILE cc_start: 0.8871 (mm) cc_final: 0.8543 (mt) REVERT: A 918 ASP cc_start: 0.8450 (p0) cc_final: 0.8162 (p0) REVERT: A 931 PHE cc_start: 0.8468 (m-80) cc_final: 0.8080 (m-80) REVERT: A 955 ILE cc_start: 0.8865 (tp) cc_final: 0.8609 (tt) REVERT: A 973 ASN cc_start: 0.8830 (m-40) cc_final: 0.8601 (m-40) REVERT: A 989 ASN cc_start: 0.7992 (t0) cc_final: 0.7748 (t0) REVERT: B 189 MET cc_start: 0.7481 (mpp) cc_final: 0.7272 (mpp) REVERT: B 197 ARG cc_start: 0.8782 (ttp-110) cc_final: 0.8485 (ttp-110) REVERT: B 201 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8035 (tp) REVERT: B 304 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8214 (m-80) REVERT: B 364 ARG cc_start: 0.8075 (mtm180) cc_final: 0.7872 (tmt170) REVERT: B 740 TRP cc_start: 0.8303 (t-100) cc_final: 0.8046 (t-100) REVERT: B 801 MET cc_start: 0.8685 (ptm) cc_final: 0.8387 (ptp) REVERT: B 817 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8111 (mm) REVERT: B 860 LEU cc_start: 0.9285 (tp) cc_final: 0.9046 (tp) REVERT: B 874 PHE cc_start: 0.8800 (t80) cc_final: 0.8490 (t80) REVERT: B 918 ASP cc_start: 0.8365 (p0) cc_final: 0.8001 (p0) REVERT: C 186 TYR cc_start: 0.7666 (m-80) cc_final: 0.7226 (m-80) REVERT: C 364 ARG cc_start: 0.8129 (mtm-85) cc_final: 0.7706 (mtm180) REVERT: C 445 GLU cc_start: 0.8322 (mp0) cc_final: 0.7748 (mp0) REVERT: C 521 LEU cc_start: 0.9107 (tp) cc_final: 0.8760 (tp) REVERT: C 697 LEU cc_start: 0.8600 (tt) cc_final: 0.8386 (tt) REVERT: C 740 TRP cc_start: 0.8324 (t-100) cc_final: 0.8041 (t-100) REVERT: C 789 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.8102 (t0) REVERT: C 817 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8144 (mm) REVERT: C 863 MET cc_start: 0.8611 (mmt) cc_final: 0.8299 (mmt) REVERT: C 989 ASN cc_start: 0.7793 (t0) cc_final: 0.7533 (t0) REVERT: C 997 GLN cc_start: 0.8864 (mp10) cc_final: 0.8663 (mp10) REVERT: C 1051 GLU cc_start: 0.8929 (tp30) cc_final: 0.8606 (tp30) REVERT: D 186 TYR cc_start: 0.7764 (m-80) cc_final: 0.7506 (m-80) REVERT: D 201 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8158 (tp) REVERT: D 445 GLU cc_start: 0.8315 (mp0) cc_final: 0.8029 (mp0) REVERT: D 507 ARG cc_start: 0.8726 (tpt90) cc_final: 0.8486 (tpp-160) REVERT: D 521 LEU cc_start: 0.9128 (tp) cc_final: 0.8798 (tp) REVERT: D 613 GLU cc_start: 0.7796 (tp30) cc_final: 0.7536 (tp30) REVERT: D 740 TRP cc_start: 0.8330 (t-100) cc_final: 0.8009 (t-100) REVERT: D 801 MET cc_start: 0.8649 (ptm) cc_final: 0.8325 (ptp) REVERT: D 817 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8102 (mm) REVERT: D 863 MET cc_start: 0.8721 (mmt) cc_final: 0.8487 (mmt) REVERT: D 989 ASN cc_start: 0.7854 (t0) cc_final: 0.7632 (t0) outliers start: 65 outliers final: 24 residues processed: 514 average time/residue: 0.4208 time to fit residues: 343.9287 Evaluate side-chains 448 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 415 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 304 PHE 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 572 ASN Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 791 VAL 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 521 LEU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 789 ASN 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 D residue 201 ILE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 662 GLU 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 859 MET Chi-restraints excluded: chain D residue 967 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 136 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 chunk 352 optimal weight: 6.9990 chunk 294 optimal weight: 4.9990 chunk 272 optimal weight: 20.0000 chunk 50 optimal weight: 0.8980 chunk 355 optimal weight: 20.0000 chunk 321 optimal weight: 3.9990 chunk 249 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 300 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 204 ASN A 268 HIS A 459 GLN A 572 ASN B 789 ASN D 257 HIS D 306 GLN D 572 ASN D 609 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.129760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.093773 restraints weight = 65710.307| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.21 r_work: 0.3161 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.5436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 31192 Z= 0.215 Angle : 0.647 9.000 42260 Z= 0.337 Chirality : 0.043 0.182 4708 Planarity : 0.004 0.070 5280 Dihedral : 5.405 52.934 4024 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.88 % Allowed : 13.52 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.14), residues: 3656 helix: 1.12 (0.10), residues: 2468 sheet: -1.21 (0.36), residues: 184 loop : -2.44 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 898 HIS 0.006 0.001 HIS D1080 PHE 0.022 0.002 PHE A 155 TYR 0.027 0.002 TYR C 787 ARG 0.012 0.001 ARG A 452 Details of bonding type rmsd hydrogen bonds : bond 0.04946 ( 1754) hydrogen bonds : angle 4.28732 ( 5214) SS BOND : bond 0.00792 ( 4) SS BOND : angle 2.29859 ( 8) covalent geometry : bond 0.00500 (31188) covalent geometry : angle 0.64662 (42252) *********************** 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 516 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 420 time to evaluate : 3.409 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 197 ARG cc_start: 0.8727 (ttp-110) cc_final: 0.8458 (ttp-110) REVERT: A 201 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8377 (tp) REVERT: A 304 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8107 (m-80) REVERT: A 393 VAL cc_start: 0.9187 (p) cc_final: 0.8962 (t) REVERT: A 457 ASP cc_start: 0.7957 (p0) cc_final: 0.7756 (p0) REVERT: A 723 LEU cc_start: 0.7892 (mm) cc_final: 0.7632 (tt) REVERT: A 725 TRP cc_start: 0.7881 (t60) cc_final: 0.7498 (t60) REVERT: A 789 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8089 (t0) REVERT: A 797 LEU cc_start: 0.6558 (pt) cc_final: 0.6233 (pp) REVERT: A 874 PHE cc_start: 0.9095 (t80) cc_final: 0.8888 (t80) REVERT: A 918 ASP cc_start: 0.8458 (p0) cc_final: 0.7936 (p0) REVERT: A 989 ASN cc_start: 0.8118 (t0) cc_final: 0.7840 (t0) REVERT: B 161 MET cc_start: 0.7585 (mmm) cc_final: 0.7355 (mmm) REVERT: B 201 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.7850 (tp) REVERT: B 304 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.8279 (m-80) REVERT: B 485 GLN cc_start: 0.8243 (pm20) cc_final: 0.7651 (mm-40) REVERT: B 496 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8961 (mp) REVERT: B 646 TYR cc_start: 0.7639 (t80) cc_final: 0.7369 (t80) REVERT: B 788 MET cc_start: 0.8066 (tmm) cc_final: 0.7664 (tmm) REVERT: B 817 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8150 (mm) REVERT: B 822 LYS cc_start: 0.8652 (mmmt) cc_final: 0.8256 (mtmt) REVERT: B 918 ASP cc_start: 0.8366 (p0) cc_final: 0.8032 (p0) REVERT: C 186 TYR cc_start: 0.7718 (m-80) cc_final: 0.7148 (m-80) REVERT: C 364 ARG cc_start: 0.8243 (mtm-85) cc_final: 0.7963 (tmm160) REVERT: C 445 GLU cc_start: 0.8343 (mp0) cc_final: 0.8067 (mp0) REVERT: C 801 MET cc_start: 0.8735 (ptm) cc_final: 0.8477 (ptp) REVERT: C 817 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8118 (mm) REVERT: C 863 MET cc_start: 0.8706 (mmt) cc_final: 0.8402 (mmt) REVERT: C 989 ASN cc_start: 0.7961 (t0) cc_final: 0.7713 (t0) REVERT: C 1051 GLU cc_start: 0.8973 (tp30) cc_final: 0.8456 (tp30) REVERT: D 186 TYR cc_start: 0.8006 (m-80) cc_final: 0.7776 (m-80) REVERT: D 201 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8075 (tp) REVERT: D 251 TYR cc_start: 0.7257 (m-10) cc_final: 0.6998 (m-10) REVERT: D 396 MET cc_start: 0.6540 (mpp) cc_final: 0.5820 (mmt) REVERT: D 445 GLU cc_start: 0.8347 (mp0) cc_final: 0.8058 (mp0) REVERT: D 507 ARG cc_start: 0.8896 (tpt90) cc_final: 0.8683 (tpp-160) REVERT: D 613 GLU cc_start: 0.7984 (tp30) cc_final: 0.7514 (tp30) REVERT: D 801 MET cc_start: 0.8692 (ptm) cc_final: 0.8484 (ptp) REVERT: D 817 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8145 (mm) REVERT: D 863 MET cc_start: 0.8761 (mmt) cc_final: 0.8439 (mmt) REVERT: D 918 ASP cc_start: 0.8375 (p0) cc_final: 0.7962 (p0) outliers start: 96 outliers final: 54 residues processed: 485 average time/residue: 0.4074 time to fit residues: 317.6649 Evaluate side-chains 450 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 386 time to evaluate : 3.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE 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 392 THR 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 736 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 789 ASN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 787 TYR Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 294 ASN 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 441 LEU Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 662 GLU 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 859 MET Chi-restraints excluded: chain D residue 878 MET Chi-restraints excluded: chain D residue 967 THR Chi-restraints excluded: chain D residue 1001 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 74 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 229 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 286 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 185 optimal weight: 6.9990 chunk 238 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN B 268 HIS ** B1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 ASN ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.130881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.095230 restraints weight = 65725.962| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.19 r_work: 0.3184 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 31192 Z= 0.163 Angle : 0.604 9.532 42260 Z= 0.312 Chirality : 0.041 0.217 4708 Planarity : 0.004 0.051 5280 Dihedral : 5.251 58.024 4024 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.52 % Allowed : 14.69 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.14), residues: 3656 helix: 1.32 (0.11), residues: 2472 sheet: -1.30 (0.36), residues: 184 loop : -2.41 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 898 HIS 0.003 0.001 HIS A1080 PHE 0.029 0.001 PHE A 155 TYR 0.015 0.001 TYR B 787 ARG 0.013 0.000 ARG D1083 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 1754) hydrogen bonds : angle 4.11397 ( 5214) SS BOND : bond 0.00558 ( 4) SS BOND : angle 1.44320 ( 8) covalent geometry : bond 0.00381 (31188) covalent geometry : angle 0.60397 (42252) *********************** 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 514 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 430 time to evaluate : 3.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.7889 (tpp) cc_final: 0.7590 (mmm) REVERT: A 201 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8429 (tp) REVERT: A 304 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.8141 (m-80) REVERT: A 353 MET cc_start: 0.7788 (pmm) cc_final: 0.7095 (pmm) REVERT: A 393 VAL cc_start: 0.9207 (p) cc_final: 0.8996 (t) REVERT: A 457 ASP cc_start: 0.7922 (p0) cc_final: 0.7685 (p0) REVERT: A 723 LEU cc_start: 0.7898 (mm) cc_final: 0.7644 (tt) REVERT: A 725 TRP cc_start: 0.7907 (t60) cc_final: 0.7553 (t60) REVERT: A 789 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8369 (t0) REVERT: A 817 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8082 (mm) REVERT: A 918 ASP cc_start: 0.8357 (p0) cc_final: 0.7856 (p0) REVERT: B 201 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.7892 (tp) REVERT: B 304 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8232 (m-80) REVERT: B 364 ARG cc_start: 0.7873 (tmt170) cc_final: 0.7187 (tmm160) REVERT: B 485 GLN cc_start: 0.8303 (pm20) cc_final: 0.7993 (mm-40) REVERT: B 496 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9018 (mp) REVERT: B 646 TYR cc_start: 0.7804 (t80) cc_final: 0.7563 (t80) REVERT: B 788 MET cc_start: 0.8017 (tmm) cc_final: 0.7660 (tmm) REVERT: B 817 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8030 (mm) REVERT: B 860 LEU cc_start: 0.9390 (tp) cc_final: 0.9170 (tp) REVERT: B 918 ASP cc_start: 0.8296 (p0) cc_final: 0.7954 (p0) REVERT: B 978 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8022 (mpp) REVERT: C 186 TYR cc_start: 0.7641 (m-80) cc_final: 0.7145 (m-80) REVERT: C 251 TYR cc_start: 0.7188 (m-10) cc_final: 0.6816 (m-10) REVERT: C 304 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8081 (m-80) REVERT: C 364 ARG cc_start: 0.8312 (mtm-85) cc_final: 0.8023 (tmm160) REVERT: C 445 GLU cc_start: 0.8326 (mp0) cc_final: 0.8034 (mp0) REVERT: C 697 LEU cc_start: 0.8717 (tt) cc_final: 0.8477 (tt) REVERT: C 801 MET cc_start: 0.8773 (ptm) cc_final: 0.8508 (ptp) REVERT: C 817 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8092 (mm) REVERT: C 863 MET cc_start: 0.8668 (mmt) cc_final: 0.8304 (mmt) REVERT: C 1051 GLU cc_start: 0.9001 (tp30) cc_final: 0.8489 (tp30) REVERT: D 186 TYR cc_start: 0.7675 (m-80) cc_final: 0.7408 (m-80) REVERT: D 201 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.8083 (tp) REVERT: D 251 TYR cc_start: 0.7437 (m-10) cc_final: 0.7177 (m-10) REVERT: D 364 ARG cc_start: 0.7781 (tmm160) cc_final: 0.7481 (ttp-170) REVERT: D 396 MET cc_start: 0.6717 (mpp) cc_final: 0.6083 (mmt) REVERT: D 445 GLU cc_start: 0.8308 (mp0) cc_final: 0.7996 (mp0) REVERT: D 507 ARG cc_start: 0.8883 (tpt90) cc_final: 0.8667 (tpp-160) REVERT: D 613 GLU cc_start: 0.7909 (tp30) cc_final: 0.7628 (tp30) REVERT: D 713 ARG cc_start: 0.7607 (tpm170) cc_final: 0.7204 (tpm170) REVERT: D 817 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8087 (mm) REVERT: D 822 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8204 (mtmt) REVERT: D 863 MET cc_start: 0.8716 (mmt) cc_final: 0.8311 (mmt) REVERT: D 918 ASP cc_start: 0.8270 (p0) cc_final: 0.7847 (p0) outliers start: 84 outliers final: 50 residues processed: 481 average time/residue: 0.4072 time to fit residues: 315.9763 Evaluate side-chains 453 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 390 time to evaluate : 3.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE 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 392 THR Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 441 LEU 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 789 ASN 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 941 VAL Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 978 MET Chi-restraints excluded: chain B residue 985 ILE 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 338 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 662 GLU 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 817 LEU Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 878 MET Chi-restraints excluded: chain D residue 967 THR Chi-restraints excluded: chain D residue 985 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 23 optimal weight: 8.9990 chunk 230 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 136 optimal weight: 6.9990 chunk 226 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 293 optimal weight: 6.9990 chunk 334 optimal weight: 0.5980 chunk 286 optimal weight: 9.9990 chunk 177 optimal weight: 0.9990 chunk 186 optimal weight: 20.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN A1062 ASN B 204 ASN B 268 HIS B 990 ASN B1062 ASN C 572 ASN C1062 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.127726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.092625 restraints weight = 65141.564| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.00 r_work: 0.3144 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.6070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 31192 Z= 0.231 Angle : 0.654 9.081 42260 Z= 0.341 Chirality : 0.044 0.226 4708 Planarity : 0.004 0.055 5280 Dihedral : 5.292 54.614 4024 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.31 % Allowed : 14.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3656 helix: 1.30 (0.11), residues: 2460 sheet: -1.28 (0.37), residues: 184 loop : -2.37 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 898 HIS 0.005 0.001 HIS C 235 PHE 0.031 0.002 PHE B 155 TYR 0.020 0.002 TYR A1005 ARG 0.013 0.001 ARG B 452 Details of bonding type rmsd hydrogen bonds : bond 0.04888 ( 1754) hydrogen bonds : angle 4.28902 ( 5214) SS BOND : bond 0.00659 ( 4) SS BOND : angle 1.81135 ( 8) covalent geometry : bond 0.00542 (31188) covalent geometry : angle 0.65365 (42252) *********************** 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 511 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 401 time to evaluate : 3.231 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: 0.8733 (OUTLIER) cc_final: 0.7919 (tp) REVERT: A 304 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8233 (m-80) REVERT: A 364 ARG cc_start: 0.7807 (tmt170) cc_final: 0.7334 (ttp-170) REVERT: A 393 VAL cc_start: 0.9199 (p) cc_final: 0.8997 (t) REVERT: A 723 LEU cc_start: 0.7942 (mm) cc_final: 0.7723 (tt) REVERT: A 725 TRP cc_start: 0.7945 (t60) cc_final: 0.7660 (t60) REVERT: A 789 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8097 (t0) REVERT: A 817 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8167 (mm) REVERT: A 918 ASP cc_start: 0.8253 (p0) cc_final: 0.7787 (p0) REVERT: B 201 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.7763 (tp) REVERT: B 304 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8250 (m-80) REVERT: B 364 ARG cc_start: 0.7814 (tmt170) cc_final: 0.7207 (tmm160) REVERT: B 496 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9056 (mp) REVERT: B 646 TYR cc_start: 0.7958 (t80) cc_final: 0.7607 (t80) REVERT: B 788 MET cc_start: 0.8025 (tmm) cc_final: 0.7678 (tmm) REVERT: B 817 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8132 (mm) REVERT: B 822 LYS cc_start: 0.8615 (mmmt) cc_final: 0.8254 (mtmt) REVERT: B 918 ASP cc_start: 0.8209 (p0) cc_final: 0.7763 (p0) REVERT: B 978 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8359 (mpp) REVERT: B 1003 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8454 (tm-30) REVERT: B 1051 GLU cc_start: 0.8689 (tp30) cc_final: 0.8456 (tp30) REVERT: C 186 TYR cc_start: 0.7612 (m-80) cc_final: 0.7123 (m-80) REVERT: C 441 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8733 (mp) REVERT: C 445 GLU cc_start: 0.8389 (mp0) cc_final: 0.8176 (mp0) REVERT: C 697 LEU cc_start: 0.8893 (tt) cc_final: 0.8670 (tt) REVERT: C 801 MET cc_start: 0.8781 (ptm) cc_final: 0.8559 (ptp) REVERT: C 817 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8144 (mm) REVERT: C 863 MET cc_start: 0.8697 (mmt) cc_final: 0.8306 (mmt) REVERT: C 1013 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7491 (t80) REVERT: C 1051 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8337 (tp30) REVERT: D 186 TYR cc_start: 0.7604 (m-80) cc_final: 0.7255 (m-80) REVERT: D 189 MET cc_start: 0.7986 (mpp) cc_final: 0.7696 (mpp) REVERT: D 201 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8097 (tp) REVERT: D 251 TYR cc_start: 0.7583 (m-10) cc_final: 0.7282 (m-10) REVERT: D 441 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8773 (mm) REVERT: D 445 GLU cc_start: 0.8361 (mp0) cc_final: 0.8014 (mp0) REVERT: D 613 GLU cc_start: 0.7842 (tp30) cc_final: 0.7562 (tp30) REVERT: D 817 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8077 (mm) REVERT: D 863 MET cc_start: 0.8706 (mmt) cc_final: 0.8305 (mmt) REVERT: D 918 ASP cc_start: 0.8167 (p0) cc_final: 0.7773 (p0) REVERT: D 1013 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7593 (t80) outliers start: 110 outliers final: 71 residues processed: 473 average time/residue: 0.4493 time to fit residues: 343.3252 Evaluate side-chains 455 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 367 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 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 392 THR Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 572 ASN 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 789 ASN 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 911 MET Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1067 ILE Chi-restraints excluded: chain A residue 1069 THR 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 353 MET Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 783 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 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 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 441 LEU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain C residue 1051 GLU Chi-restraints excluded: chain C residue 1067 ILE Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 294 ASN 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 441 LEU Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 787 TYR Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 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 1001 LEU Chi-restraints excluded: chain D residue 1013 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 34 optimal weight: 0.7980 chunk 1 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 223 optimal weight: 4.9990 chunk 309 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 225 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 185 optimal weight: 6.9990 chunk 286 optimal weight: 9.9990 chunk 201 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 572 ASN B 268 HIS ** B 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.131608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.096272 restraints weight = 65453.742| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.09 r_work: 0.3212 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.6218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31192 Z= 0.121 Angle : 0.593 12.133 42260 Z= 0.304 Chirality : 0.040 0.204 4708 Planarity : 0.004 0.059 5280 Dihedral : 5.059 54.118 4024 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.19 % Allowed : 15.78 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.14), residues: 3656 helix: 1.53 (0.11), residues: 2476 sheet: -0.93 (0.38), residues: 176 loop : -2.39 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 898 HIS 0.003 0.000 HIS A 185 PHE 0.019 0.001 PHE D1021 TYR 0.013 0.001 TYR B 787 ARG 0.013 0.000 ARG C 364 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 1754) hydrogen bonds : angle 4.00418 ( 5214) SS BOND : bond 0.00467 ( 4) SS BOND : angle 1.78900 ( 8) covalent geometry : bond 0.00266 (31188) covalent geometry : angle 0.59234 (42252) *********************** 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 504 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 431 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.7874 (tp) REVERT: A 304 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.8114 (m-80) REVERT: A 364 ARG cc_start: 0.7915 (tmt170) cc_final: 0.7495 (ttp-170) REVERT: A 457 ASP cc_start: 0.7797 (p0) cc_final: 0.7505 (p0) REVERT: A 665 ASP cc_start: 0.8789 (t0) cc_final: 0.8541 (t70) REVERT: A 723 LEU cc_start: 0.8032 (mm) cc_final: 0.7800 (tt) REVERT: A 725 TRP cc_start: 0.7917 (t60) cc_final: 0.7643 (t60) REVERT: A 817 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8147 (mm) REVERT: A 918 ASP cc_start: 0.8204 (p0) cc_final: 0.7728 (p0) REVERT: A 928 HIS cc_start: 0.8308 (m-70) cc_final: 0.8100 (m-70) REVERT: B 201 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8041 (tp) REVERT: B 304 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8148 (m-80) REVERT: B 496 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9084 (mp) REVERT: B 646 TYR cc_start: 0.7910 (t80) cc_final: 0.7706 (t80) REVERT: B 788 MET cc_start: 0.8022 (tmm) cc_final: 0.7680 (tmm) REVERT: B 817 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8053 (mm) REVERT: B 822 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8158 (mtmt) REVERT: B 918 ASP cc_start: 0.8143 (p0) cc_final: 0.7791 (p0) REVERT: B 978 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8192 (mpp) REVERT: B 1003 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8390 (tm-30) REVERT: B 1051 GLU cc_start: 0.8757 (tp30) cc_final: 0.8498 (tp30) REVERT: C 186 TYR cc_start: 0.7591 (m-80) cc_final: 0.7225 (m-80) REVERT: C 251 TYR cc_start: 0.7321 (m-10) cc_final: 0.7089 (m-10) REVERT: C 304 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8152 (m-80) REVERT: C 396 MET cc_start: 0.6884 (mpp) cc_final: 0.6340 (mmt) REVERT: C 441 LEU cc_start: 0.9074 (tp) cc_final: 0.8686 (mm) REVERT: C 445 GLU cc_start: 0.8340 (mp0) cc_final: 0.7942 (mp0) REVERT: C 697 LEU cc_start: 0.8808 (tt) cc_final: 0.8533 (tt) REVERT: C 740 TRP cc_start: 0.8322 (t-100) cc_final: 0.7978 (t-100) REVERT: C 788 MET cc_start: 0.8133 (ttm) cc_final: 0.7860 (tmm) REVERT: C 801 MET cc_start: 0.8744 (ptm) cc_final: 0.8516 (ptp) REVERT: C 817 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8069 (mm) REVERT: C 863 MET cc_start: 0.8578 (mmt) cc_final: 0.8207 (mmt) REVERT: C 1013 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7218 (t80) REVERT: C 1051 GLU cc_start: 0.8921 (tp30) cc_final: 0.8512 (tp30) REVERT: C 1066 LYS cc_start: 0.8797 (mtmm) cc_final: 0.8508 (mtmm) REVERT: D 189 MET cc_start: 0.7945 (mpp) cc_final: 0.7687 (mpp) REVERT: D 190 LYS cc_start: 0.8604 (ttpt) cc_final: 0.8363 (mtpp) REVERT: D 201 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8083 (tp) REVERT: D 251 TYR cc_start: 0.7416 (m-10) cc_final: 0.7080 (m-10) REVERT: D 304 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8179 (m-80) REVERT: D 364 ARG cc_start: 0.7855 (tmm160) cc_final: 0.7576 (ttp80) REVERT: D 396 MET cc_start: 0.6657 (mpp) cc_final: 0.6010 (mmp) REVERT: D 441 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8709 (mm) REVERT: D 445 GLU cc_start: 0.8342 (mp0) cc_final: 0.7910 (mp0) REVERT: D 613 GLU cc_start: 0.7782 (tp30) cc_final: 0.7489 (tp30) REVERT: D 817 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8084 (mm) REVERT: D 822 LYS cc_start: 0.8564 (mmmt) cc_final: 0.8126 (mtmt) REVERT: D 863 MET cc_start: 0.8622 (mmt) cc_final: 0.8185 (mmt) REVERT: D 918 ASP cc_start: 0.8149 (p0) cc_final: 0.7755 (p0) REVERT: D 1003 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8351 (tm-30) REVERT: D 1013 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7282 (t80) outliers start: 73 outliers final: 38 residues processed: 469 average time/residue: 0.4527 time to fit residues: 347.2394 Evaluate side-chains 450 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 396 time to evaluate : 5.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE 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 779 PHE Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 911 MET Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1067 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 521 LEU 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 846 ILE Chi-restraints excluded: chain B residue 978 MET Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain C residue 1067 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 783 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 176 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 260 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 265 optimal weight: 0.2980 chunk 137 optimal weight: 0.6980 chunk 186 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 327 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN B 268 HIS B 666 GLN ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 990 ASN D1062 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.132993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.098369 restraints weight = 64852.091| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.01 r_work: 0.3246 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.6354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31192 Z= 0.114 Angle : 0.586 11.725 42260 Z= 0.300 Chirality : 0.039 0.175 4708 Planarity : 0.004 0.066 5280 Dihedral : 4.842 59.461 4024 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.92 % Allowed : 16.35 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.14), residues: 3656 helix: 1.66 (0.11), residues: 2472 sheet: -0.75 (0.39), residues: 172 loop : -2.24 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 898 HIS 0.006 0.001 HIS D 185 PHE 0.022 0.001 PHE C1021 TYR 0.033 0.001 TYR D 646 ARG 0.013 0.000 ARG D 452 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 1754) hydrogen bonds : angle 3.88637 ( 5214) SS BOND : bond 0.00686 ( 4) SS BOND : angle 2.30143 ( 8) covalent geometry : bond 0.00254 (31188) covalent geometry : angle 0.58548 (42252) *********************** 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 485 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 421 time to evaluate : 8.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.7860 (tp) REVERT: A 304 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8139 (m-80) REVERT: A 364 ARG cc_start: 0.7914 (tmt170) cc_final: 0.7521 (ttp-170) REVERT: A 445 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8526 (mp0) REVERT: A 665 ASP cc_start: 0.8808 (t0) cc_final: 0.8559 (t70) REVERT: A 725 TRP cc_start: 0.7947 (t60) cc_final: 0.7680 (t60) REVERT: A 817 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8076 (mm) REVERT: A 918 ASP cc_start: 0.8263 (p0) cc_final: 0.7786 (p0) REVERT: A 928 HIS cc_start: 0.8214 (m-70) cc_final: 0.7988 (m-70) REVERT: A 1003 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8260 (pp30) REVERT: A 1051 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8484 (tm-30) REVERT: B 201 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.7890 (tp) REVERT: B 209 ILE cc_start: 0.8959 (tp) cc_final: 0.8705 (mm) REVERT: B 364 ARG cc_start: 0.7876 (tmt170) cc_final: 0.7467 (tmm160) REVERT: B 445 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8363 (mp0) REVERT: B 496 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9082 (mp) REVERT: B 725 TRP cc_start: 0.8238 (t60) cc_final: 0.7926 (t60) REVERT: B 788 MET cc_start: 0.8049 (tmm) cc_final: 0.7700 (tmm) REVERT: B 817 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7954 (mm) REVERT: B 918 ASP cc_start: 0.8114 (p0) cc_final: 0.7750 (p0) REVERT: B 974 LEU cc_start: 0.8700 (tp) cc_final: 0.8455 (tp) REVERT: B 978 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8362 (mpp) REVERT: B 1051 GLU cc_start: 0.8723 (tp30) cc_final: 0.8452 (tp30) REVERT: C 186 TYR cc_start: 0.7560 (m-80) cc_final: 0.7222 (m-80) REVERT: C 396 MET cc_start: 0.6832 (mpp) cc_final: 0.6364 (mmt) REVERT: C 441 LEU cc_start: 0.9046 (tp) cc_final: 0.8651 (mm) REVERT: C 445 GLU cc_start: 0.8266 (mp0) cc_final: 0.7839 (mp0) REVERT: C 740 TRP cc_start: 0.8272 (t-100) cc_final: 0.7947 (t-100) REVERT: C 788 MET cc_start: 0.8073 (ttm) cc_final: 0.7822 (tmm) REVERT: C 801 MET cc_start: 0.8726 (ptm) cc_final: 0.8526 (ptp) REVERT: C 817 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8057 (mm) REVERT: C 863 MET cc_start: 0.8577 (mmt) cc_final: 0.8257 (mmt) REVERT: C 874 PHE cc_start: 0.8900 (t80) cc_final: 0.8696 (t80) REVERT: C 1013 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7305 (t80) REVERT: C 1051 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8504 (tp30) REVERT: D 189 MET cc_start: 0.7879 (mpp) cc_final: 0.7670 (mpp) REVERT: D 190 LYS cc_start: 0.8545 (ttpt) cc_final: 0.8331 (mtpp) REVERT: D 201 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8035 (tp) REVERT: D 364 ARG cc_start: 0.7873 (tmm160) cc_final: 0.7494 (ttp80) REVERT: D 396 MET cc_start: 0.6612 (mpp) cc_final: 0.5973 (mmp) REVERT: D 441 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8709 (mm) REVERT: D 445 GLU cc_start: 0.8215 (mp0) cc_final: 0.7790 (mp0) REVERT: D 713 ARG cc_start: 0.7363 (tpm170) cc_final: 0.6806 (tpm170) REVERT: D 801 MET cc_start: 0.8789 (ptm) cc_final: 0.8567 (ptp) REVERT: D 817 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8021 (mm) REVERT: D 863 MET cc_start: 0.8591 (mmt) cc_final: 0.8207 (mmt) REVERT: D 918 ASP cc_start: 0.8071 (p0) cc_final: 0.7676 (p0) REVERT: D 1013 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7365 (t80) outliers start: 64 outliers final: 38 residues processed: 456 average time/residue: 0.6743 time to fit residues: 509.6781 Evaluate side-chains 445 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 393 time to evaluate : 4.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE 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 521 LEU Chi-restraints excluded: chain A residue 572 ASN 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 911 MET Chi-restraints excluded: chain A residue 967 THR 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 353 MET Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 846 ILE 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 1067 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 338 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 985 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1013 PHE 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 441 LEU Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 967 THR Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 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 140 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 chunk 352 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 306 optimal weight: 0.9990 chunk 371 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 194 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 156 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN B 268 HIS ** C 990 ASN ** 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 = 0.3951 r_free = 0.3951 target = 0.133176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.098123 restraints weight = 65215.028| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.10 r_work: 0.3242 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.6441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31192 Z= 0.116 Angle : 0.588 10.763 42260 Z= 0.300 Chirality : 0.039 0.166 4708 Planarity : 0.003 0.049 5280 Dihedral : 4.794 55.379 4024 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.89 % Allowed : 16.44 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.14), residues: 3656 helix: 1.69 (0.11), residues: 2468 sheet: -0.69 (0.40), residues: 172 loop : -2.24 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 453 HIS 0.002 0.000 HIS A 185 PHE 0.020 0.001 PHE D1021 TYR 0.013 0.001 TYR B 787 ARG 0.008 0.000 ARG D 452 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 1754) hydrogen bonds : angle 3.85644 ( 5214) SS BOND : bond 0.00536 ( 4) SS BOND : angle 2.70934 ( 8) covalent geometry : bond 0.00261 (31188) covalent geometry : angle 0.58652 (42252) ********************** 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 461 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 398 time to evaluate : 3.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.7905 (tp) REVERT: A 304 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.8115 (m-80) REVERT: A 353 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7018 (pmm) REVERT: A 364 ARG cc_start: 0.7913 (tmt170) cc_final: 0.7535 (ttp-170) REVERT: A 445 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8539 (mp0) REVERT: A 457 ASP cc_start: 0.7857 (p0) cc_final: 0.7568 (p0) REVERT: A 665 ASP cc_start: 0.8761 (t0) cc_final: 0.8529 (t70) REVERT: A 725 TRP cc_start: 0.7903 (t60) cc_final: 0.7661 (t60) REVERT: A 801 MET cc_start: 0.8712 (ptm) cc_final: 0.8480 (ptp) REVERT: A 817 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8084 (mm) REVERT: A 918 ASP cc_start: 0.8200 (p0) cc_final: 0.7818 (p0) REVERT: A 928 HIS cc_start: 0.8206 (m-70) cc_final: 0.7978 (m-70) REVERT: A 1003 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8379 (pp30) REVERT: A 1051 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8492 (tm-30) REVERT: B 201 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.7904 (tp) REVERT: B 209 ILE cc_start: 0.8983 (tp) cc_final: 0.8713 (mm) REVERT: B 364 ARG cc_start: 0.7965 (tmt170) cc_final: 0.7537 (tmm160) REVERT: B 496 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9079 (mp) REVERT: B 725 TRP cc_start: 0.8189 (t60) cc_final: 0.7885 (t60) REVERT: B 788 MET cc_start: 0.8106 (tmm) cc_final: 0.7756 (tmm) REVERT: B 801 MET cc_start: 0.8781 (ptm) cc_final: 0.8574 (ptp) REVERT: B 817 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7954 (mm) REVERT: B 918 ASP cc_start: 0.7994 (p0) cc_final: 0.7590 (p0) REVERT: B 974 LEU cc_start: 0.8675 (tp) cc_final: 0.8020 (tp) REVERT: B 978 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8078 (mpp) REVERT: B 1051 GLU cc_start: 0.8695 (tp30) cc_final: 0.8453 (tp30) REVERT: C 186 TYR cc_start: 0.7605 (m-80) cc_final: 0.7243 (m-80) REVERT: C 304 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8253 (m-80) REVERT: C 396 MET cc_start: 0.6910 (mpp) cc_final: 0.6422 (mmt) REVERT: C 441 LEU cc_start: 0.9040 (tp) cc_final: 0.8639 (mm) REVERT: C 445 GLU cc_start: 0.8228 (mp0) cc_final: 0.7789 (mp0) REVERT: C 740 TRP cc_start: 0.8312 (t-100) cc_final: 0.7991 (t-100) REVERT: C 788 MET cc_start: 0.8061 (ttm) cc_final: 0.7831 (tmm) REVERT: C 801 MET cc_start: 0.8735 (ptm) cc_final: 0.8495 (ptp) REVERT: C 817 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8017 (mm) REVERT: C 863 MET cc_start: 0.8594 (mmt) cc_final: 0.8247 (mmt) REVERT: C 1013 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7384 (t80) REVERT: C 1051 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8495 (tp30) REVERT: D 189 MET cc_start: 0.7899 (mpp) cc_final: 0.7689 (mpp) REVERT: D 190 LYS cc_start: 0.8562 (ttpt) cc_final: 0.8350 (mtpp) REVERT: D 201 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.8007 (tp) REVERT: D 304 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8277 (m-80) REVERT: D 364 ARG cc_start: 0.7886 (tmm160) cc_final: 0.7402 (tmm-80) REVERT: D 396 MET cc_start: 0.6602 (mpp) cc_final: 0.5978 (mmp) REVERT: D 441 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8687 (mm) REVERT: D 445 GLU cc_start: 0.8253 (mp0) cc_final: 0.7814 (mp0) REVERT: D 452 ARG cc_start: 0.6361 (ptt90) cc_final: 0.5911 (ptt90) REVERT: D 725 TRP cc_start: 0.8329 (t60) cc_final: 0.7784 (t60) REVERT: D 817 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7998 (mm) REVERT: D 863 MET cc_start: 0.8612 (mmt) cc_final: 0.8181 (mmt) REVERT: D 918 ASP cc_start: 0.8036 (p0) cc_final: 0.7588 (p0) REVERT: D 1013 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7458 (t80) outliers start: 63 outliers final: 43 residues processed: 434 average time/residue: 0.4263 time to fit residues: 305.3167 Evaluate side-chains 448 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 388 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE 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 521 LEU Chi-restraints excluded: chain A residue 572 ASN 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 878 MET Chi-restraints excluded: chain A residue 911 MET Chi-restraints excluded: chain A residue 967 THR 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 329 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 496 LEU 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 846 ILE 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 1013 PHE Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 797 LEU 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 985 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain C residue 1051 GLU Chi-restraints excluded: chain C residue 1067 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 967 THR Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 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 104 optimal weight: 20.0000 chunk 172 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 chunk 139 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 350 optimal weight: 0.7980 chunk 328 optimal weight: 0.9980 chunk 197 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN A 789 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** C 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.131866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.096989 restraints weight = 64871.940| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.01 r_work: 0.3222 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.6529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31192 Z= 0.133 Angle : 0.597 9.992 42260 Z= 0.305 Chirality : 0.040 0.166 4708 Planarity : 0.004 0.049 5280 Dihedral : 4.803 55.743 4024 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.89 % Allowed : 16.44 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3656 helix: 1.70 (0.11), residues: 2472 sheet: -0.73 (0.40), residues: 172 loop : -2.26 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 453 HIS 0.003 0.001 HIS A 185 PHE 0.021 0.001 PHE C1021 TYR 0.045 0.001 TYR C 646 ARG 0.007 0.000 ARG D 197 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 1754) hydrogen bonds : angle 3.87231 ( 5214) SS BOND : bond 0.00606 ( 4) SS BOND : angle 2.76244 ( 8) covalent geometry : bond 0.00309 (31188) covalent geometry : angle 0.59548 (42252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17028.84 seconds wall clock time: 304 minutes 15.16 seconds (18255.16 seconds total)