Starting phenix.real_space_refine on Sat Jun 28 20:11:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3y_38907/06_2025/8y3y_38907.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3y_38907/06_2025/8y3y_38907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y3y_38907/06_2025/8y3y_38907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3y_38907/06_2025/8y3y_38907.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3y_38907/06_2025/8y3y_38907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3y_38907/06_2025/8y3y_38907.cif" } resolution = 3.33 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= 0.031 sd= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 130 5.16 5 C 21754 2.51 5 N 5410 2.21 5 O 6292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33586 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 957, 7968 Classifications: {'peptide': 957} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 937} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 7996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7996 Classifications: {'peptide': 958} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 938} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 829 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 7968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 957, 7968 Classifications: {'peptide': 957} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 937} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 7996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7996 Classifications: {'peptide': 958} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 938} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 829 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 19.43, per 1000 atoms: 0.58 Number of scatterers: 33586 At special positions: 0 Unit cell: (103.421, 128.199, 274.711, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 130 16.00 O 6292 8.00 N 5410 7.00 C 21754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.04 Conformation dependent library (CDL) restraints added in 4.4 seconds 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7712 Finding SS restraints... Secondary structure from input PDB file: 212 helices and 12 sheets defined 61.9% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 23 through 39 removed outlier: 3.573A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 removed outlier: 4.003A pdb=" N SER A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 71 removed outlier: 3.863A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 95 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 95 through 109 removed outlier: 4.699A pdb=" N ALA A 99 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 removed outlier: 3.807A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 removed outlier: 3.634A pdb=" N THR A 140 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 160 removed outlier: 3.662A pdb=" N VAL A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 160' Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.520A pdb=" N ASN A 192 " --> pdb=" O ASP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 199 through 210 Processing helix chain 'A' and resid 222 through 235 Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 282 through 298 Processing helix chain 'A' and resid 304 through 317 Processing helix chain 'A' and resid 318 through 321 removed outlier: 3.830A pdb=" N ALA A 321 " --> pdb=" O PRO A 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 318 through 321' Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 366 through 373 removed outlier: 3.918A pdb=" N ARG A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 371 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 373' Processing helix chain 'A' and resid 374 through 391 Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.641A pdb=" N HIS A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 411 through 416' Processing helix chain 'A' and resid 417 through 426 Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 447 through 462 removed outlier: 3.641A pdb=" N ILE A 459 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 489 removed outlier: 4.795A pdb=" N SER A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 527 through 531 Processing helix chain 'A' and resid 532 through 539 removed outlier: 3.632A pdb=" N LYS A 537 " --> pdb=" O PHE A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 563 removed outlier: 3.679A pdb=" N GLU A 560 " --> pdb=" O VAL A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 598 removed outlier: 4.369A pdb=" N VAL A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG A 593 " --> pdb=" O TYR A 589 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.712A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 628 removed outlier: 3.667A pdb=" N HIS A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 659 removed outlier: 3.566A pdb=" N PHE A 659 " --> pdb=" O ILE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 670 Processing helix chain 'A' and resid 680 through 699 Processing helix chain 'A' and resid 705 through 722 Processing helix chain 'A' and resid 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.521A pdb=" N LEU A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 764 removed outlier: 4.454A pdb=" N CYS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 784 Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.806A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 824 Processing helix chain 'A' and resid 831 through 841 Processing helix chain 'A' and resid 846 through 854 Processing helix chain 'A' and resid 878 through 895 removed outlier: 3.772A pdb=" N GLU A 882 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 922 removed outlier: 4.164A pdb=" N PHE A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 933 Processing helix chain 'A' and resid 937 through 945 removed outlier: 3.623A pdb=" N ASP A 945 " --> pdb=" O ASP A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 954 Processing helix chain 'A' and resid 973 through 991 removed outlier: 4.014A pdb=" N HIS A 979 " --> pdb=" O HIS A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1003 removed outlier: 3.725A pdb=" N TYR A1003 " --> pdb=" O ILE A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.798A pdb=" N LEU B 15 " --> pdb=" O TYR B 11 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 39 removed outlier: 3.574A pdb=" N VAL B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 removed outlier: 4.003A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 53 " --> pdb=" O GLY B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 71 removed outlier: 3.864A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 95 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 95 through 109 removed outlier: 4.700A pdb=" N ALA B 99 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.807A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 145 removed outlier: 3.633A pdb=" N THR B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 160 removed outlier: 3.662A pdb=" N VAL B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 154 through 160' Processing helix chain 'B' and resid 186 through 192 removed outlier: 3.520A pdb=" N ASN B 192 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 199 through 210 Processing helix chain 'B' and resid 222 through 235 Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 282 through 298 Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 318 through 321 removed outlier: 3.830A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 318 through 321' Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 366 through 373 removed outlier: 3.918A pdb=" N ARG B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 371 " --> pdb=" O CYS B 367 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 373' Processing helix chain 'B' and resid 374 through 391 Processing helix chain 'B' and resid 411 through 416 removed outlier: 3.642A pdb=" N HIS B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 411 through 416' Processing helix chain 'B' and resid 417 through 426 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 462 removed outlier: 3.641A pdb=" N ILE B 459 " --> pdb=" O TYR B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 493 removed outlier: 4.795A pdb=" N SER B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR B 490 " --> pdb=" O THR B 486 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLN B 491 " --> pdb=" O GLN B 487 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE B 492 " --> pdb=" O ALA B 488 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN B 493 " --> pdb=" O VAL B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 527 through 531 Processing helix chain 'B' and resid 532 through 539 removed outlier: 3.630A pdb=" N LYS B 537 " --> pdb=" O PHE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 563 removed outlier: 3.679A pdb=" N GLU B 560 " --> pdb=" O VAL B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 598 removed outlier: 4.369A pdb=" N VAL B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG B 593 " --> pdb=" O TYR B 589 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 598 " --> pdb=" O PHE B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.712A pdb=" N VAL B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 628 removed outlier: 3.666A pdb=" N HIS B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 659 removed outlier: 3.565A pdb=" N PHE B 659 " --> pdb=" O ILE B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 670 Processing helix chain 'B' and resid 680 through 699 Processing helix chain 'B' and resid 705 through 722 Processing helix chain 'B' and resid 723 through 725 No H-bonds generated for 'chain 'B' and resid 723 through 725' Processing helix chain 'B' and resid 729 through 742 removed outlier: 3.521A pdb=" N LEU B 733 " --> pdb=" O SER B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 764 removed outlier: 4.454A pdb=" N CYS B 764 " --> pdb=" O ARG B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 784 Processing helix chain 'B' and resid 800 through 812 removed outlier: 3.806A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 824 Processing helix chain 'B' and resid 831 through 841 Processing helix chain 'B' and resid 846 through 854 Processing helix chain 'B' and resid 878 through 895 removed outlier: 3.772A pdb=" N GLU B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 922 Processing helix chain 'B' and resid 929 through 933 Processing helix chain 'B' and resid 937 through 945 removed outlier: 3.623A pdb=" N ASP B 945 " --> pdb=" O ASP B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 954 Processing helix chain 'B' and resid 973 through 991 removed outlier: 4.015A pdb=" N HIS B 979 " --> pdb=" O HIS B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1003 removed outlier: 3.725A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 14 removed outlier: 3.570A pdb=" N ASP C 13 " --> pdb=" O ALA C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 106 removed outlier: 3.583A pdb=" N ILE C 106 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 23 through 39 removed outlier: 3.573A pdb=" N VAL D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 53 removed outlier: 4.003A pdb=" N SER D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU D 53 " --> pdb=" O GLY D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.865A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 95 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 95 through 109 removed outlier: 4.700A pdb=" N ALA D 99 " --> pdb=" O LYS D 95 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 122 removed outlier: 3.807A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 145 removed outlier: 3.634A pdb=" N THR D 140 " --> pdb=" O ASN D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 160 removed outlier: 3.663A pdb=" N VAL D 158 " --> pdb=" O ALA D 154 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN D 160 " --> pdb=" O GLU D 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 154 through 160' Processing helix chain 'D' and resid 186 through 192 removed outlier: 3.520A pdb=" N ASN D 192 " --> pdb=" O ASP D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 199 through 210 Processing helix chain 'D' and resid 222 through 235 Processing helix chain 'D' and resid 254 through 265 Processing helix chain 'D' and resid 282 through 298 Processing helix chain 'D' and resid 304 through 317 Processing helix chain 'D' and resid 318 through 321 removed outlier: 3.830A pdb=" N ALA D 321 " --> pdb=" O PRO D 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 318 through 321' Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 355 through 366 Processing helix chain 'D' and resid 366 through 373 removed outlier: 3.919A pdb=" N ARG D 370 " --> pdb=" O SER D 366 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER D 371 " --> pdb=" O CYS D 367 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS D 372 " --> pdb=" O ASP D 368 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 366 through 373' Processing helix chain 'D' and resid 374 through 391 Processing helix chain 'D' and resid 411 through 416 removed outlier: 3.641A pdb=" N HIS D 415 " --> pdb=" O SER D 411 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 411 through 416' Processing helix chain 'D' and resid 417 through 426 Processing helix chain 'D' and resid 431 through 445 Processing helix chain 'D' and resid 447 through 462 removed outlier: 3.641A pdb=" N ILE D 459 " --> pdb=" O TYR D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 489 removed outlier: 4.795A pdb=" N SER D 474 " --> pdb=" O VAL D 470 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN D 475 " --> pdb=" O TYR D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 519 Processing helix chain 'D' and resid 527 through 531 Processing helix chain 'D' and resid 532 through 539 removed outlier: 3.630A pdb=" N LYS D 537 " --> pdb=" O PHE D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 563 removed outlier: 3.678A pdb=" N GLU D 560 " --> pdb=" O VAL D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 598 removed outlier: 4.370A pdb=" N VAL D 583 " --> pdb=" O SER D 579 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG D 593 " --> pdb=" O TYR D 589 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN D 598 " --> pdb=" O PHE D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 604 removed outlier: 3.711A pdb=" N VAL D 603 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 628 removed outlier: 3.667A pdb=" N HIS D 609 " --> pdb=" O PHE D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 659 removed outlier: 3.566A pdb=" N PHE D 659 " --> pdb=" O ILE D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 660 through 670 Processing helix chain 'D' and resid 680 through 699 Processing helix chain 'D' and resid 705 through 722 Processing helix chain 'D' and resid 723 through 725 No H-bonds generated for 'chain 'D' and resid 723 through 725' Processing helix chain 'D' and resid 729 through 742 removed outlier: 3.521A pdb=" N LEU D 733 " --> pdb=" O SER D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 764 removed outlier: 4.454A pdb=" N CYS D 764 " --> pdb=" O ARG D 760 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 784 Processing helix chain 'D' and resid 800 through 812 removed outlier: 3.805A pdb=" N TYR D 804 " --> pdb=" O TYR D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 824 Processing helix chain 'D' and resid 831 through 841 Processing helix chain 'D' and resid 846 through 854 Processing helix chain 'D' and resid 878 through 895 removed outlier: 3.772A pdb=" N GLU D 882 " --> pdb=" O THR D 878 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 922 removed outlier: 4.165A pdb=" N PHE D 916 " --> pdb=" O TYR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 929 through 933 Processing helix chain 'D' and resid 937 through 945 removed outlier: 3.622A pdb=" N ASP D 945 " --> pdb=" O ASP D 941 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 954 Processing helix chain 'D' and resid 973 through 991 removed outlier: 4.014A pdb=" N HIS D 979 " --> pdb=" O HIS D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1003 removed outlier: 3.725A pdb=" N TYR D1003 " --> pdb=" O ILE D 999 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 22 removed outlier: 4.106A pdb=" N LYS E 16 " --> pdb=" O GLY E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 39 removed outlier: 3.572A pdb=" N VAL E 27 " --> pdb=" O ASP E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 53 removed outlier: 4.004A pdb=" N SER E 51 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU E 53 " --> pdb=" O GLY E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 71 removed outlier: 3.864A pdb=" N LEU E 62 " --> pdb=" O GLN E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 95 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 95 through 109 removed outlier: 4.699A pdb=" N ALA E 99 " --> pdb=" O LYS E 95 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 122 removed outlier: 3.808A pdb=" N ASP E 119 " --> pdb=" O ASN E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 145 removed outlier: 3.634A pdb=" N THR E 140 " --> pdb=" O ASN E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 160 removed outlier: 3.663A pdb=" N VAL E 158 " --> pdb=" O ALA E 154 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN E 160 " --> pdb=" O GLU E 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 154 through 160' Processing helix chain 'E' and resid 186 through 192 removed outlier: 3.519A pdb=" N ASN E 192 " --> pdb=" O ASP E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 197 Processing helix chain 'E' and resid 199 through 210 Processing helix chain 'E' and resid 222 through 235 Processing helix chain 'E' and resid 254 through 265 Processing helix chain 'E' and resid 282 through 298 Processing helix chain 'E' and resid 304 through 317 Processing helix chain 'E' and resid 318 through 321 removed outlier: 3.829A pdb=" N ALA E 321 " --> pdb=" O PRO E 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 318 through 321' Processing helix chain 'E' and resid 326 through 331 Processing helix chain 'E' and resid 355 through 366 Processing helix chain 'E' and resid 366 through 373 removed outlier: 3.919A pdb=" N ARG E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER E 371 " --> pdb=" O CYS E 367 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS E 372 " --> pdb=" O ASP E 368 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU E 373 " --> pdb=" O GLU E 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 366 through 373' Processing helix chain 'E' and resid 374 through 391 Processing helix chain 'E' and resid 411 through 416 removed outlier: 3.642A pdb=" N HIS E 415 " --> pdb=" O SER E 411 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY E 416 " --> pdb=" O LEU E 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 411 through 416' Processing helix chain 'E' and resid 417 through 426 Processing helix chain 'E' and resid 431 through 445 Processing helix chain 'E' and resid 447 through 462 removed outlier: 3.641A pdb=" N ILE E 459 " --> pdb=" O TYR E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 492 removed outlier: 4.795A pdb=" N SER E 474 " --> pdb=" O VAL E 470 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN E 475 " --> pdb=" O TYR E 471 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR E 490 " --> pdb=" O THR E 486 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN E 491 " --> pdb=" O GLN E 487 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE E 492 " --> pdb=" O ALA E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 519 Processing helix chain 'E' and resid 527 through 531 Processing helix chain 'E' and resid 532 through 539 removed outlier: 3.631A pdb=" N LYS E 537 " --> pdb=" O PHE E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 563 removed outlier: 3.679A pdb=" N GLU E 560 " --> pdb=" O VAL E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 598 removed outlier: 4.370A pdb=" N VAL E 583 " --> pdb=" O SER E 579 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG E 593 " --> pdb=" O TYR E 589 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN E 598 " --> pdb=" O PHE E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 604 removed outlier: 3.711A pdb=" N VAL E 603 " --> pdb=" O LEU E 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 628 removed outlier: 3.667A pdb=" N HIS E 609 " --> pdb=" O PHE E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 648 through 659 removed outlier: 3.566A pdb=" N PHE E 659 " --> pdb=" O ILE E 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 660 through 670 Processing helix chain 'E' and resid 680 through 699 Processing helix chain 'E' and resid 705 through 722 Processing helix chain 'E' and resid 723 through 725 No H-bonds generated for 'chain 'E' and resid 723 through 725' Processing helix chain 'E' and resid 729 through 742 removed outlier: 3.521A pdb=" N LEU E 733 " --> pdb=" O SER E 729 " (cutoff:3.500A) Processing helix chain 'E' and resid 752 through 764 removed outlier: 4.454A pdb=" N CYS E 764 " --> pdb=" O ARG E 760 " (cutoff:3.500A) Processing helix chain 'E' and resid 769 through 784 Processing helix chain 'E' and resid 800 through 812 removed outlier: 3.806A pdb=" N TYR E 804 " --> pdb=" O TYR E 800 " (cutoff:3.500A) Processing helix chain 'E' and resid 817 through 824 Processing helix chain 'E' and resid 831 through 841 Processing helix chain 'E' and resid 846 through 854 Processing helix chain 'E' and resid 878 through 895 removed outlier: 3.771A pdb=" N GLU E 882 " --> pdb=" O THR E 878 " (cutoff:3.500A) Processing helix chain 'E' and resid 913 through 922 Processing helix chain 'E' and resid 929 through 933 Processing helix chain 'E' and resid 937 through 945 removed outlier: 3.623A pdb=" N ASP E 945 " --> pdb=" O ASP E 941 " (cutoff:3.500A) Processing helix chain 'E' and resid 950 through 954 Processing helix chain 'E' and resid 973 through 991 removed outlier: 4.014A pdb=" N HIS E 979 " --> pdb=" O HIS E 975 " (cutoff:3.500A) Processing helix chain 'E' and resid 994 through 1003 removed outlier: 3.724A pdb=" N TYR E1003 " --> pdb=" O ILE E 999 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 14 removed outlier: 3.570A pdb=" N ASP F 13 " --> pdb=" O ALA F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 106 removed outlier: 3.582A pdb=" N ILE F 106 " --> pdb=" O LEU F 102 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 7.089A pdb=" N VAL A 129 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE A 130 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE A 44 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA3, first strand: chain 'B' and resid 150 through 152 removed outlier: 7.089A pdb=" N VAL B 129 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE B 130 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N PHE B 44 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE B 213 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE B 246 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE B 215 " --> pdb=" O ILE B 246 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA5, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 46 Processing sheet with id=AA7, first strand: chain 'D' and resid 150 through 152 removed outlier: 7.089A pdb=" N VAL D 129 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE D 130 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE D 44 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE D 213 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE D 246 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE D 215 " --> pdb=" O ILE D 246 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 338 through 340 Processing sheet with id=AA9, first strand: chain 'E' and resid 150 through 152 removed outlier: 7.088A pdb=" N VAL E 129 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE E 130 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE E 44 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE E 213 " --> pdb=" O PHE E 244 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE E 246 " --> pdb=" O ILE E 213 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE E 215 " --> pdb=" O ILE E 246 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 338 through 340 Processing sheet with id=AB2, first strand: chain 'F' and resid 27 through 30 Processing sheet with id=AB3, first strand: chain 'F' and resid 45 through 46 1560 hydrogen bonds defined for protein. 4584 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: 12.27 Time building geometry restraints manager: 9.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5628 1.31 - 1.43: 9586 1.43 - 1.56: 18919 1.56 - 1.69: 1 1.69 - 1.81: 216 Bond restraints: 34350 Sorted by residual: bond pdb=" C LEU A 842 " pdb=" N PRO A 843 " ideal model delta sigma weight residual 1.337 1.380 -0.043 9.80e-03 1.04e+04 1.93e+01 bond pdb=" C LEU E 842 " pdb=" N PRO E 843 " ideal model delta sigma weight residual 1.337 1.379 -0.043 9.80e-03 1.04e+04 1.89e+01 bond pdb=" C LEU B 842 " pdb=" N PRO B 843 " ideal model delta sigma weight residual 1.337 1.379 -0.043 9.80e-03 1.04e+04 1.89e+01 bond pdb=" C LEU D 842 " pdb=" N PRO D 843 " ideal model delta sigma weight residual 1.337 1.379 -0.042 9.80e-03 1.04e+04 1.86e+01 bond pdb=" C VAL A 565 " pdb=" N ARG A 566 " ideal model delta sigma weight residual 1.333 1.378 -0.045 1.36e-02 5.41e+03 1.09e+01 ... (remaining 34345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 45063 2.96 - 5.92: 1096 5.92 - 8.87: 106 8.87 - 11.83: 12 11.83 - 14.79: 5 Bond angle restraints: 46282 Sorted by residual: angle pdb=" CA GLN D 377 " pdb=" CB GLN D 377 " pdb=" CG GLN D 377 " ideal model delta sigma weight residual 114.10 101.81 12.29 2.00e+00 2.50e-01 3.78e+01 angle pdb=" N GLY C 70 " pdb=" CA GLY C 70 " pdb=" C GLY C 70 " ideal model delta sigma weight residual 112.08 105.99 6.09 1.01e+00 9.80e-01 3.63e+01 angle pdb=" N GLY F 70 " pdb=" CA GLY F 70 " pdb=" C GLY F 70 " ideal model delta sigma weight residual 112.08 106.04 6.04 1.01e+00 9.80e-01 3.58e+01 angle pdb=" N VAL C 32 " pdb=" CA VAL C 32 " pdb=" C VAL C 32 " ideal model delta sigma weight residual 113.20 107.46 5.74 9.60e-01 1.09e+00 3.58e+01 angle pdb=" N VAL F 32 " pdb=" CA VAL F 32 " pdb=" C VAL F 32 " ideal model delta sigma weight residual 113.20 107.47 5.73 9.60e-01 1.09e+00 3.57e+01 ... (remaining 46277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.99: 18857 14.99 - 29.99: 1218 29.99 - 44.98: 351 44.98 - 59.97: 39 59.97 - 74.96: 9 Dihedral angle restraints: 20474 sinusoidal: 8496 harmonic: 11978 Sorted by residual: dihedral pdb=" CA SER B 957 " pdb=" C SER B 957 " pdb=" N TRP B 958 " pdb=" CA TRP B 958 " ideal model delta harmonic sigma weight residual 180.00 117.73 62.27 0 5.00e+00 4.00e-02 1.55e+02 dihedral pdb=" CA SER E 957 " pdb=" C SER E 957 " pdb=" N TRP E 958 " pdb=" CA TRP E 958 " ideal model delta harmonic sigma weight residual 180.00 117.74 62.26 0 5.00e+00 4.00e-02 1.55e+02 dihedral pdb=" CA SER D 957 " pdb=" C SER D 957 " pdb=" N TRP D 958 " pdb=" CA TRP D 958 " ideal model delta harmonic sigma weight residual 180.00 117.74 62.26 0 5.00e+00 4.00e-02 1.55e+02 ... (remaining 20471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4099 0.073 - 0.146: 735 0.146 - 0.219: 85 0.219 - 0.292: 17 0.292 - 0.364: 8 Chirality restraints: 4944 Sorted by residual: chirality pdb=" CG LEU D 330 " pdb=" CB LEU D 330 " pdb=" CD1 LEU D 330 " pdb=" CD2 LEU D 330 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CG LEU B 330 " pdb=" CB LEU B 330 " pdb=" CD1 LEU B 330 " pdb=" CD2 LEU B 330 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CG LEU E 330 " pdb=" CB LEU E 330 " pdb=" CD1 LEU E 330 " pdb=" CD2 LEU E 330 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 4941 not shown) Planarity restraints: 5890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 631 " -0.024 2.00e-02 2.50e+03 4.79e-02 2.30e+01 pdb=" C ILE E 631 " 0.083 2.00e-02 2.50e+03 pdb=" O ILE E 631 " -0.031 2.00e-02 2.50e+03 pdb=" N ASP E 632 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR F 16 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C TYR F 16 " -0.063 2.00e-02 2.50e+03 pdb=" O TYR F 16 " 0.024 2.00e-02 2.50e+03 pdb=" N HIS F 17 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 16 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C TYR C 16 " 0.062 2.00e-02 2.50e+03 pdb=" O TYR C 16 " -0.024 2.00e-02 2.50e+03 pdb=" N HIS C 17 " -0.021 2.00e-02 2.50e+03 ... (remaining 5887 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1840 2.71 - 3.26: 33504 3.26 - 3.81: 54417 3.81 - 4.35: 69343 4.35 - 4.90: 113098 Nonbonded interactions: 272202 Sorted by model distance: nonbonded pdb=" O ASN A 563 " pdb=" N ARG A 566 " model vdw 2.168 3.120 nonbonded pdb=" OE1 GLN D 236 " pdb=" OG SER D 239 " model vdw 2.214 3.040 nonbonded pdb=" OE1 GLN B 236 " pdb=" OG SER B 239 " model vdw 2.214 3.040 nonbonded pdb=" OE1 GLN A 236 " pdb=" OG SER A 239 " model vdw 2.214 3.040 nonbonded pdb=" OE1 GLN E 236 " pdb=" OG SER E 239 " model vdw 2.215 3.040 ... (remaining 272197 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: 0.08 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 376 or (resid 377 and (name N or name CA or nam \ e C or name O or name CB )) or resid 378 through 565 or resid 577 through 898 or \ resid 912 through 1005)) selection = (chain 'B' and (resid 12 through 491 or resid 506 through 628 or (resid 629 and \ (name N or name CA or name C or name O or name CB )) or resid 630 through 631 or \ resid 644 through 986 or (resid 987 and (name N or name CA or name C or name O \ or name CB )) or resid 988 through 1005)) selection = (chain 'D' and (resid 12 through 376 or (resid 377 and (name N or name CA or nam \ e C or name O or name CB )) or resid 378 through 565 or resid 577 through 898 or \ resid 912 through 1005)) selection = (chain 'E' and (resid 12 through 491 or resid 506 through 628 or (resid 629 and \ (name N or name CA or name C or name O or name CB )) or resid 630 through 631 or \ resid 644 through 986 or (resid 987 and (name N or name CA or name C or name O \ or name CB )) or resid 988 through 1005)) } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 1.300 Check model and map are aligned: 0.250 Set scattering table: 0.280 Process input model: 73.170 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.160 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:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4786 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 : 0.007 0.094 34350 Z= 0.334 Angle : 1.113 14.791 46282 Z= 0.667 Chirality : 0.059 0.364 4944 Planarity : 0.007 0.057 5890 Dihedral : 11.181 74.965 12762 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.44 % Favored : 91.19 % Rotamer: Outliers : 0.67 % Allowed : 4.05 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -4.50 (0.10), residues: 3982 helix: -2.62 (0.08), residues: 2380 sheet: -4.65 (0.31), residues: 68 loop : -3.32 (0.13), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.005 TRP C 25 HIS 0.009 0.002 HIS B 786 PHE 0.027 0.003 PHE D 722 TYR 0.025 0.003 TYR D 574 ARG 0.024 0.001 ARG B 478 Details of bonding type rmsd hydrogen bonds : bond 0.17684 ( 1560) hydrogen bonds : angle 8.36203 ( 4584) covalent geometry : bond 0.00726 (34350) covalent geometry : angle 1.11332 (46282) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 463 time to evaluate : 3.561 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: symmetry clash REVERT: A 232 VAL cc_start: 0.6358 (m) cc_final: 0.5983 (p) REVERT: A 913 MET cc_start: -0.0069 (mmm) cc_final: -0.0347 (ttt) REVERT: B 124 MET cc_start: 0.8626 (mmm) cc_final: 0.8377 (mmm) REVERT: B 781 LEU cc_start: 0.8681 (tp) cc_final: 0.8448 (mt) REVERT: B 789 GLN cc_start: 0.8331 (mm-40) cc_final: 0.7989 (mm110) REVERT: B 883 GLU cc_start: 0.9053 (tp30) cc_final: 0.8630 (mm-30) REVERT: B 920 TYR cc_start: 0.8108 (t80) cc_final: 0.7744 (t80) REVERT: B 922 LEU cc_start: 0.8919 (mm) cc_final: 0.8545 (mm) REVERT: B 930 MET cc_start: 0.8142 (mpt) cc_final: 0.7517 (mmm) REVERT: B 943 PHE cc_start: 0.8007 (m-80) cc_final: 0.7620 (m-80) REVERT: C 93 LYS cc_start: 0.8137 (mmpt) cc_final: 0.7520 (tptp) REVERT: C 98 ILE cc_start: 0.8933 (mt) cc_final: 0.8708 (mm) REVERT: C 102 LEU cc_start: 0.8214 (mt) cc_final: 0.7855 (mt) REVERT: D 21 MET cc_start: 0.3803 (mtm) cc_final: 0.2319 (tpp) REVERT: D 169 LYS cc_start: 0.4530 (mttt) cc_final: 0.3561 (mttp) REVERT: D 913 MET cc_start: 0.1886 (mmm) cc_final: 0.0952 (mmt) REVERT: E 699 PHE cc_start: 0.5787 (m-80) cc_final: 0.5513 (t80) REVERT: E 936 MET cc_start: 0.1366 (mpt) cc_final: 0.1072 (mpt) outliers start: 25 outliers final: 2 residues processed: 486 average time/residue: 0.5147 time to fit residues: 390.5999 Evaluate side-chains 269 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 267 time to evaluate : 3.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain E residue 859 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 337 optimal weight: 1.9990 chunk 303 optimal weight: 0.0040 chunk 168 optimal weight: 0.4980 chunk 103 optimal weight: 0.4980 chunk 204 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 313 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 190 optimal weight: 0.5980 chunk 233 optimal weight: 7.9990 chunk 363 optimal weight: 0.8980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 410 ASN A 483 GLN A 614 ASN A 702 ASN A 711 GLN A 765 ASN ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 881 HIS B 93 ASN B 195 GLN B 351 ASN B 391 ASN B 711 GLN B 765 ASN B 829 GLN B 863 ASN B 975 HIS B 992 ASN ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN C 88 HIS D 93 ASN D 666 ASN D 711 GLN D 765 ASN ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN E 391 ASN E 711 GLN E 765 ASN ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.130835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.114005 restraints weight = 173559.894| |-----------------------------------------------------------------------------| r_work (start): 0.4476 rms_B_bonded: 5.37 r_work (final): 0.4476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5864 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34350 Z= 0.131 Angle : 0.637 11.020 46282 Z= 0.345 Chirality : 0.043 0.208 4944 Planarity : 0.004 0.055 5890 Dihedral : 6.525 55.666 4426 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.15 % Favored : 93.52 % Rotamer: Outliers : 1.62 % Allowed : 8.31 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.12), residues: 3982 helix: -1.13 (0.10), residues: 2432 sheet: -4.20 (0.33), residues: 96 loop : -3.07 (0.14), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 231 HIS 0.005 0.001 HIS A 881 PHE 0.025 0.001 PHE E 699 TYR 0.037 0.002 TYR E 709 ARG 0.013 0.001 ARG A 370 Details of bonding type rmsd hydrogen bonds : bond 0.04337 ( 1560) hydrogen bonds : angle 5.13448 ( 4584) covalent geometry : bond 0.00272 (34350) covalent geometry : angle 0.63726 (46282) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 303 time to evaluate : 3.770 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: A 98 MET cc_start: 0.8198 (mpp) cc_final: 0.7105 (tpp) REVERT: A 261 TYR cc_start: 0.7041 (m-10) cc_final: 0.6627 (m-80) REVERT: A 555 THR cc_start: 0.6807 (OUTLIER) cc_final: 0.6553 (m) REVERT: A 704 MET cc_start: 0.2205 (tpp) cc_final: 0.1100 (mmm) REVERT: A 705 ASN cc_start: 0.5743 (t0) cc_final: 0.5095 (t0) REVERT: B 930 MET cc_start: 0.7380 (mpt) cc_final: 0.7043 (mmm) REVERT: B 958 TRP cc_start: 0.6779 (m-10) cc_final: 0.6475 (m-10) REVERT: C 79 PHE cc_start: 0.7036 (OUTLIER) cc_final: 0.6600 (m-80) REVERT: C 93 LYS cc_start: 0.7537 (mmpt) cc_final: 0.7047 (tptp) REVERT: D 169 LYS cc_start: 0.4824 (mttt) cc_final: 0.4533 (mttp) REVERT: D 389 GLU cc_start: 0.5807 (mt-10) cc_final: 0.5420 (mp0) REVERT: D 421 MET cc_start: 0.1140 (OUTLIER) cc_final: 0.0888 (ttm) REVERT: D 555 THR cc_start: 0.5887 (OUTLIER) cc_final: 0.5624 (p) REVERT: D 913 MET cc_start: 0.2497 (mmm) cc_final: 0.2029 (mmt) REVERT: E 522 PHE cc_start: 0.6605 (t80) cc_final: 0.6352 (t80) REVERT: E 704 MET cc_start: 0.4697 (ppp) cc_final: 0.4455 (ppp) REVERT: E 841 LEU cc_start: 0.8181 (tp) cc_final: 0.7853 (mm) REVERT: E 930 MET cc_start: 0.1416 (mtt) cc_final: 0.1098 (mtm) REVERT: E 936 MET cc_start: 0.1676 (mpt) cc_final: 0.1376 (mpt) REVERT: E 1001 MET cc_start: 0.0659 (mtp) cc_final: -0.0132 (mtt) REVERT: F 81 PHE cc_start: 0.5247 (t80) cc_final: 0.5005 (t80) outliers start: 60 outliers final: 17 residues processed: 352 average time/residue: 0.4732 time to fit residues: 271.8482 Evaluate side-chains 245 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 3.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 555 THR Chi-restraints excluded: chain D residue 736 ILE Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 555 THR Chi-restraints excluded: chain E residue 859 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 68 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 168 optimal weight: 3.9990 chunk 276 optimal weight: 9.9990 chunk 44 optimal weight: 0.3980 chunk 240 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 258 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 246 optimal weight: 3.9990 chunk 228 optimal weight: 4.9990 chunk 329 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN A 332 HIS A 351 ASN A 477 ASN A 614 ASN A 666 ASN A 702 ASN ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 ASN B 195 GLN B 211 HIS B 658 HIS ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN D 93 ASN ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 ASN ** D 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 GLN ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 ASN E 299 ASN E 351 ASN E 609 HIS E 658 HIS ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 992 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.122299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.107643 restraints weight = 169936.894| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 3.49 r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 34350 Z= 0.217 Angle : 0.738 15.463 46282 Z= 0.394 Chirality : 0.047 0.257 4944 Planarity : 0.005 0.080 5890 Dihedral : 6.247 51.485 4426 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.71 % Favored : 91.06 % Rotamer: Outliers : 2.24 % Allowed : 9.98 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.12), residues: 3982 helix: -0.68 (0.10), residues: 2426 sheet: -4.10 (0.33), residues: 106 loop : -2.79 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 919 HIS 0.009 0.002 HIS A 118 PHE 0.035 0.003 PHE A 608 TYR 0.032 0.003 TYR B 888 ARG 0.010 0.001 ARG D 478 Details of bonding type rmsd hydrogen bonds : bond 0.05008 ( 1560) hydrogen bonds : angle 5.02515 ( 4584) covalent geometry : bond 0.00487 (34350) covalent geometry : angle 0.73827 (46282) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 281 time to evaluate : 3.629 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 467 ASN cc_start: 0.1512 (OUTLIER) cc_final: 0.1055 (p0) REVERT: A 552 TYR cc_start: 0.5236 (p90) cc_final: 0.3554 (p90) REVERT: A 704 MET cc_start: 0.3226 (tpp) cc_final: 0.2590 (mmp) REVERT: A 705 ASN cc_start: 0.7031 (t0) cc_final: 0.6576 (p0) REVERT: B 647 MET cc_start: 0.7524 (mmm) cc_final: 0.7267 (tpp) REVERT: B 789 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7391 (mm110) REVERT: B 930 MET cc_start: 0.7757 (mpt) cc_final: 0.7543 (mmm) REVERT: C 79 PHE cc_start: 0.6942 (OUTLIER) cc_final: 0.5917 (m-80) REVERT: C 93 LYS cc_start: 0.7565 (mmpt) cc_final: 0.7338 (tptp) REVERT: D 167 LEU cc_start: 0.6586 (tt) cc_final: 0.5899 (mt) REVERT: D 169 LYS cc_start: 0.5525 (mttt) cc_final: 0.5277 (mttt) REVERT: D 555 THR cc_start: 0.6465 (OUTLIER) cc_final: 0.6208 (m) REVERT: D 848 ASN cc_start: 0.5348 (m-40) cc_final: 0.5130 (t0) REVERT: D 913 MET cc_start: 0.2581 (mmm) cc_final: 0.1975 (mmt) REVERT: E 519 MET cc_start: 0.6791 (mmp) cc_final: 0.6486 (mmt) REVERT: E 704 MET cc_start: 0.4812 (ppp) cc_final: 0.4382 (ppp) REVERT: E 920 TYR cc_start: 0.7146 (t80) cc_final: 0.6903 (t80) REVERT: E 925 ILE cc_start: 0.3589 (OUTLIER) cc_final: 0.2780 (tt) REVERT: E 930 MET cc_start: 0.2381 (mtt) cc_final: 0.2175 (mtt) REVERT: E 936 MET cc_start: 0.1154 (mpt) cc_final: 0.0547 (mpt) REVERT: F 43 TYR cc_start: 0.5347 (p90) cc_final: 0.5136 (p90) outliers start: 83 outliers final: 29 residues processed: 354 average time/residue: 0.4395 time to fit residues: 256.8631 Evaluate side-chains 257 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 224 time to evaluate : 3.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 423 LYS Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 555 THR Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 555 THR Chi-restraints excluded: chain E residue 781 LEU Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain E residue 859 VAL Chi-restraints excluded: chain E residue 871 ILE Chi-restraints excluded: chain E residue 925 ILE Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 51 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 281 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 305 optimal weight: 1.9990 chunk 10 optimal weight: 0.0370 chunk 249 optimal weight: 0.0010 chunk 71 optimal weight: 0.9990 chunk 240 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 363 optimal weight: 0.9980 overall best weight: 0.8068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN A 477 ASN A 483 GLN A 614 ASN A 702 ASN ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 ASN E 467 ASN ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.122849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.108456 restraints weight = 171886.843| |-----------------------------------------------------------------------------| r_work (start): 0.4371 rms_B_bonded: 3.50 r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34350 Z= 0.121 Angle : 0.592 11.849 46282 Z= 0.315 Chirality : 0.043 0.225 4944 Planarity : 0.003 0.037 5890 Dihedral : 5.698 44.360 4426 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.53 % Favored : 93.24 % Rotamer: Outliers : 1.70 % Allowed : 11.33 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -1.75 (0.13), residues: 3982 helix: -0.18 (0.10), residues: 2458 sheet: -4.00 (0.39), residues: 66 loop : -2.71 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 59 HIS 0.007 0.001 HIS D 658 PHE 0.030 0.001 PHE D 381 TYR 0.019 0.001 TYR B 940 ARG 0.007 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 1560) hydrogen bonds : angle 4.51353 ( 4584) covalent geometry : bond 0.00256 (34350) covalent geometry : angle 0.59184 (46282) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 248 time to evaluate : 3.809 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 357 MET cc_start: 0.6410 (OUTLIER) cc_final: 0.5790 (mmp) REVERT: A 453 ASP cc_start: 0.5405 (t0) cc_final: 0.5173 (t0) REVERT: A 467 ASN cc_start: 0.1419 (OUTLIER) cc_final: 0.1085 (p0) REVERT: A 552 TYR cc_start: 0.4886 (OUTLIER) cc_final: 0.2776 (p90) REVERT: A 704 MET cc_start: 0.3397 (tpp) cc_final: 0.2862 (mmp) REVERT: A 705 ASN cc_start: 0.6751 (t0) cc_final: 0.6393 (t0) REVERT: B 789 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7468 (mm110) REVERT: B 933 PHE cc_start: 0.6524 (m-80) cc_final: 0.6209 (m-80) REVERT: C 79 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.6520 (m-80) REVERT: C 91 THR cc_start: 0.6915 (p) cc_final: 0.6707 (t) REVERT: C 93 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7208 (tptp) REVERT: D 167 LEU cc_start: 0.6496 (tt) cc_final: 0.5791 (mt) REVERT: D 169 LYS cc_start: 0.5313 (mttt) cc_final: 0.5042 (mttt) REVERT: D 913 MET cc_start: 0.2557 (mmm) cc_final: 0.2161 (mmt) REVERT: E 519 MET cc_start: 0.6739 (mmp) cc_final: 0.6303 (mmt) REVERT: E 930 MET cc_start: 0.2413 (mtt) cc_final: 0.2202 (mtm) REVERT: E 936 MET cc_start: 0.0983 (mpt) cc_final: 0.0472 (mpt) REVERT: E 976 MET cc_start: 0.4604 (mtt) cc_final: 0.4311 (mtt) outliers start: 63 outliers final: 28 residues processed: 299 average time/residue: 0.4520 time to fit residues: 221.1376 Evaluate side-chains 257 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 224 time to evaluate : 3.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 669 ARG Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 951 TYR Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 666 ASN Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain E residue 839 PHE Chi-restraints excluded: chain E residue 859 VAL Chi-restraints excluded: chain E residue 871 ILE Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 23 PHE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 51 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 346 optimal weight: 3.9990 chunk 202 optimal weight: 0.6980 chunk 373 optimal weight: 0.9980 chunk 246 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 196 optimal weight: 9.9990 chunk 352 optimal weight: 5.9990 chunk 221 optimal weight: 6.9990 chunk 24 optimal weight: 50.0000 chunk 333 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 391 ASN A 606 HIS A 610 GLN A 614 ASN ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN B 171 HIS B 195 GLN B 351 ASN B 609 HIS ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 HIS ** D 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 927 ASN D 992 ASN ** E 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN E 351 ASN E 810 HIS ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 939 GLN E 973 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.118841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.103520 restraints weight = 161573.381| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 3.99 r_work (final): 0.4265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 0.6920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 34350 Z= 0.214 Angle : 0.726 11.962 46282 Z= 0.385 Chirality : 0.047 0.202 4944 Planarity : 0.005 0.066 5890 Dihedral : 5.913 48.689 4426 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.09 % Favored : 90.73 % Rotamer: Outliers : 2.32 % Allowed : 12.03 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.79 (0.13), residues: 3982 helix: -0.21 (0.10), residues: 2386 sheet: -4.45 (0.37), residues: 80 loop : -2.58 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 958 HIS 0.011 0.002 HIS A 118 PHE 0.039 0.002 PHE D 699 TYR 0.033 0.002 TYR A 611 ARG 0.014 0.001 ARG D 613 Details of bonding type rmsd hydrogen bonds : bond 0.04848 ( 1560) hydrogen bonds : angle 4.92493 ( 4584) covalent geometry : bond 0.00482 (34350) covalent geometry : angle 0.72607 (46282) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 275 time to evaluate : 3.597 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 382 ASN cc_start: 0.7462 (m-40) cc_final: 0.6957 (t0) REVERT: A 385 PHE cc_start: 0.6301 (OUTLIER) cc_final: 0.5770 (t80) REVERT: A 389 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7513 (mt-10) REVERT: A 434 ASP cc_start: 0.6734 (OUTLIER) cc_final: 0.6525 (t70) REVERT: A 453 ASP cc_start: 0.5854 (t0) cc_final: 0.5639 (t0) REVERT: A 467 ASN cc_start: 0.1439 (OUTLIER) cc_final: 0.1232 (p0) REVERT: A 531 MET cc_start: 0.1488 (mmt) cc_final: 0.1249 (mmt) REVERT: A 550 PHE cc_start: 0.3031 (OUTLIER) cc_final: 0.1705 (t80) REVERT: A 552 TYR cc_start: 0.5474 (OUTLIER) cc_final: 0.2605 (p90) REVERT: A 704 MET cc_start: 0.4341 (tpp) cc_final: 0.4113 (mmm) REVERT: A 913 MET cc_start: -0.0650 (mmt) cc_final: -0.0867 (tmm) REVERT: B 107 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.8177 (t80) REVERT: B 647 MET cc_start: 0.7805 (tpp) cc_final: 0.7570 (tpp) REVERT: B 789 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7465 (mm110) REVERT: B 883 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8066 (mm-30) REVERT: B 933 PHE cc_start: 0.7133 (m-80) cc_final: 0.6660 (m-80) REVERT: D 167 LEU cc_start: 0.7458 (tt) cc_final: 0.6413 (mt) REVERT: D 385 PHE cc_start: 0.4889 (OUTLIER) cc_final: 0.4414 (m-10) REVERT: D 396 MET cc_start: 0.5943 (mmt) cc_final: 0.5362 (tpp) REVERT: D 457 ASN cc_start: 0.5783 (m-40) cc_final: 0.5518 (m-40) REVERT: D 519 MET cc_start: -0.3010 (mtm) cc_final: -0.3710 (mtm) REVERT: D 711 GLN cc_start: -0.0539 (pt0) cc_final: -0.1140 (mt0) REVERT: D 812 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6463 (pm20) REVERT: D 815 PHE cc_start: 0.4676 (t80) cc_final: 0.4346 (t80) REVERT: D 835 ILE cc_start: 0.2041 (mt) cc_final: 0.1283 (mt) REVERT: D 913 MET cc_start: 0.2577 (mmm) cc_final: 0.2236 (mmt) REVERT: E 357 MET cc_start: 0.7395 (tpt) cc_final: 0.7182 (mmm) REVERT: E 862 ILE cc_start: -0.0229 (OUTLIER) cc_final: -0.0607 (tp) REVERT: E 936 MET cc_start: 0.0822 (mpt) cc_final: 0.0440 (mpt) REVERT: E 976 MET cc_start: 0.4525 (mtt) cc_final: 0.3991 (mpp) outliers start: 86 outliers final: 38 residues processed: 338 average time/residue: 0.4623 time to fit residues: 256.2383 Evaluate side-chains 273 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 227 time to evaluate : 3.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 669 ARG Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 423 LYS Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 767 LEU Chi-restraints excluded: chain D residue 810 HIS Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 555 THR Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain E residue 859 VAL Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 51 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 34 optimal weight: 6.9990 chunk 315 optimal weight: 0.5980 chunk 385 optimal weight: 0.0970 chunk 172 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 345 optimal weight: 7.9990 chunk 368 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 ASN ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN D 351 ASN ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 467 ASN ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 927 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.119805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.105260 restraints weight = 166411.647| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 3.47 r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 moved from start: 0.7127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34350 Z= 0.119 Angle : 0.594 12.446 46282 Z= 0.314 Chirality : 0.043 0.242 4944 Planarity : 0.003 0.048 5890 Dihedral : 5.444 44.859 4426 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.43 % Favored : 93.45 % Rotamer: Outliers : 1.86 % Allowed : 13.08 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.37 (0.13), residues: 3982 helix: 0.13 (0.11), residues: 2410 sheet: -3.69 (0.40), residues: 96 loop : -2.46 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 601 HIS 0.008 0.001 HIS A 979 PHE 0.033 0.001 PHE C 81 TYR 0.024 0.001 TYR A 611 ARG 0.009 0.000 ARG D 145 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 1560) hydrogen bonds : angle 4.46785 ( 4584) covalent geometry : bond 0.00251 (34350) covalent geometry : angle 0.59362 (46282) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 234 time to evaluate : 3.897 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 357 MET cc_start: 0.6167 (OUTLIER) cc_final: 0.5548 (mmp) REVERT: A 382 ASN cc_start: 0.7441 (m-40) cc_final: 0.6887 (t0) REVERT: A 453 ASP cc_start: 0.5520 (t0) cc_final: 0.5282 (t0) REVERT: A 552 TYR cc_start: 0.4820 (OUTLIER) cc_final: 0.2246 (p90) REVERT: A 647 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.6928 (mmt) REVERT: A 669 ARG cc_start: 0.4391 (OUTLIER) cc_final: 0.4181 (mmm160) REVERT: B 107 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.8107 (t80) REVERT: B 290 MET cc_start: 0.7861 (mmm) cc_final: 0.7636 (mmm) REVERT: B 647 MET cc_start: 0.7715 (tpp) cc_final: 0.7463 (tpp) REVERT: B 789 GLN cc_start: 0.7693 (mm-40) cc_final: 0.7308 (mm110) REVERT: B 933 PHE cc_start: 0.6411 (m-80) cc_final: 0.5955 (m-80) REVERT: C 79 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.6850 (m-80) REVERT: D 167 LEU cc_start: 0.7356 (tt) cc_final: 0.6317 (mt) REVERT: D 295 GLU cc_start: 0.3888 (OUTLIER) cc_final: 0.3573 (pt0) REVERT: D 385 PHE cc_start: 0.4540 (OUTLIER) cc_final: 0.4150 (m-10) REVERT: D 396 MET cc_start: 0.5751 (mmt) cc_final: 0.5133 (tpp) REVERT: D 457 ASN cc_start: 0.5655 (m-40) cc_final: 0.5380 (m-40) REVERT: D 552 TYR cc_start: 0.4101 (OUTLIER) cc_final: 0.1860 (p90) REVERT: D 913 MET cc_start: 0.2528 (mmm) cc_final: 0.2204 (mmt) REVERT: E 930 MET cc_start: 0.2972 (mtt) cc_final: 0.2625 (mtm) REVERT: E 936 MET cc_start: 0.0563 (mpt) cc_final: 0.0240 (mpt) outliers start: 69 outliers final: 32 residues processed: 282 average time/residue: 0.4494 time to fit residues: 211.2070 Evaluate side-chains 248 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 3.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 669 ARG Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 951 TYR Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 743 TYR Chi-restraints excluded: chain D residue 810 HIS Chi-restraints excluded: chain D residue 936 MET Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 859 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 51 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 297 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 chunk 282 optimal weight: 20.0000 chunk 161 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 195 optimal weight: 0.2980 chunk 133 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 ASN ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 HIS ** D 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 863 ASN ** 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 = 0.4617 r_free = 0.4617 target = 0.119787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.102456 restraints weight = 161094.218| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 4.54 r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.7758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34350 Z= 0.164 Angle : 0.641 11.195 46282 Z= 0.339 Chirality : 0.044 0.199 4944 Planarity : 0.004 0.048 5890 Dihedral : 5.454 45.002 4426 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.64 % Favored : 91.26 % Rotamer: Outliers : 2.00 % Allowed : 13.32 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.33 (0.13), residues: 3982 helix: 0.14 (0.11), residues: 2394 sheet: -3.76 (0.39), residues: 96 loop : -2.37 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 601 HIS 0.015 0.001 HIS A 979 PHE 0.034 0.002 PHE F 81 TYR 0.023 0.002 TYR A 455 ARG 0.008 0.001 ARG D 145 Details of bonding type rmsd hydrogen bonds : bond 0.04130 ( 1560) hydrogen bonds : angle 4.62046 ( 4584) covalent geometry : bond 0.00366 (34350) covalent geometry : angle 0.64122 (46282) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 237 time to evaluate : 4.185 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 169 LYS cc_start: 0.4828 (mttt) cc_final: 0.4603 (mttt) REVERT: A 357 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6424 (ttt) REVERT: A 382 ASN cc_start: 0.7344 (m-40) cc_final: 0.7083 (m110) REVERT: A 385 PHE cc_start: 0.6570 (t80) cc_final: 0.5806 (t80) REVERT: A 389 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7522 (mm-30) REVERT: A 396 MET cc_start: 0.7855 (tpp) cc_final: 0.7650 (tpp) REVERT: A 552 TYR cc_start: 0.5026 (OUTLIER) cc_final: 0.2400 (p90) REVERT: A 647 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7033 (mpp) REVERT: A 713 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8282 (tp) REVERT: B 107 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.8114 (t80) REVERT: B 647 MET cc_start: 0.7674 (tpp) cc_final: 0.7469 (tpp) REVERT: B 789 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7720 (mm-40) REVERT: B 883 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8139 (mm-30) REVERT: B 914 SER cc_start: 0.8236 (p) cc_final: 0.7914 (t) REVERT: D 85 LEU cc_start: 0.4884 (OUTLIER) cc_final: 0.3446 (pp) REVERT: D 295 GLU cc_start: 0.4073 (OUTLIER) cc_final: 0.3615 (pt0) REVERT: D 357 MET cc_start: 0.5301 (tpp) cc_final: 0.4834 (tpt) REVERT: D 385 PHE cc_start: 0.4435 (OUTLIER) cc_final: 0.4016 (m-10) REVERT: D 396 MET cc_start: 0.6227 (mmt) cc_final: 0.5522 (tpp) REVERT: D 552 TYR cc_start: 0.4230 (OUTLIER) cc_final: 0.2014 (p90) REVERT: D 569 MET cc_start: 0.8034 (ppp) cc_final: 0.7292 (ppp) REVERT: D 647 MET cc_start: 0.7160 (ttm) cc_final: 0.5967 (mtp) REVERT: D 913 MET cc_start: 0.2767 (mmm) cc_final: 0.2521 (mmt) REVERT: D 1001 MET cc_start: 0.0657 (tmm) cc_final: 0.0181 (ppp) REVERT: E 134 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.6390 (m-80) REVERT: E 704 MET cc_start: 0.5601 (ppp) cc_final: 0.5380 (ppp) REVERT: E 936 MET cc_start: 0.0595 (mpt) cc_final: 0.0348 (mpt) outliers start: 74 outliers final: 36 residues processed: 292 average time/residue: 0.4476 time to fit residues: 220.9246 Evaluate side-chains 259 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 213 time to evaluate : 4.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 810 HIS Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain E residue 859 VAL Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 102 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 72 optimal weight: 4.9990 chunk 398 optimal weight: 8.9990 chunk 358 optimal weight: 1.9990 chunk 195 optimal weight: 0.2980 chunk 348 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 2 optimal weight: 0.1980 chunk 24 optimal weight: 30.0000 chunk 235 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN B 711 GLN ** B 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 927 ASN ** 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 = 0.4632 r_free = 0.4632 target = 0.120451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.103444 restraints weight = 159415.490| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 4.59 r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.7919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34350 Z= 0.114 Angle : 0.599 13.719 46282 Z= 0.312 Chirality : 0.042 0.196 4944 Planarity : 0.003 0.046 5890 Dihedral : 5.245 42.619 4426 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.96 % Favored : 92.97 % Rotamer: Outliers : 1.38 % Allowed : 14.21 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.14 (0.13), residues: 3982 helix: 0.29 (0.11), residues: 2420 sheet: -3.61 (0.40), residues: 96 loop : -2.35 (0.15), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 601 HIS 0.007 0.001 HIS A 658 PHE 0.031 0.001 PHE C 81 TYR 0.041 0.001 TYR A 455 ARG 0.006 0.000 ARG D 145 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 1560) hydrogen bonds : angle 4.40548 ( 4584) covalent geometry : bond 0.00242 (34350) covalent geometry : angle 0.59935 (46282) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 219 time to evaluate : 3.813 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: A 98 MET cc_start: 0.8170 (mpp) cc_final: 0.7359 (ttm) REVERT: A 382 ASN cc_start: 0.7388 (m-40) cc_final: 0.7132 (m110) REVERT: A 385 PHE cc_start: 0.6659 (t80) cc_final: 0.5831 (t80) REVERT: A 389 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7526 (mm-30) REVERT: A 396 MET cc_start: 0.7881 (tpp) cc_final: 0.7531 (tpp) REVERT: A 552 TYR cc_start: 0.4630 (OUTLIER) cc_final: 0.2297 (p90) REVERT: A 647 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7019 (mpp) REVERT: A 769 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7497 (tptt) REVERT: A 882 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7540 (tp30) REVERT: B 107 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.8140 (t80) REVERT: B 647 MET cc_start: 0.7673 (tpp) cc_final: 0.7460 (tpp) REVERT: B 883 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8227 (mm-30) REVERT: B 889 LEU cc_start: 0.9271 (tp) cc_final: 0.9055 (tp) REVERT: B 955 ILE cc_start: 0.6120 (mt) cc_final: 0.5750 (mm) REVERT: C 79 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7256 (m-80) REVERT: D 295 GLU cc_start: 0.4040 (OUTLIER) cc_final: 0.3586 (pt0) REVERT: D 385 PHE cc_start: 0.4311 (OUTLIER) cc_final: 0.3913 (m-10) REVERT: D 396 MET cc_start: 0.5902 (mmt) cc_final: 0.5350 (tpp) REVERT: D 552 TYR cc_start: 0.4264 (OUTLIER) cc_final: 0.2170 (p90) REVERT: D 578 MET cc_start: 0.3090 (mmp) cc_final: 0.2615 (mmm) REVERT: D 647 MET cc_start: 0.7078 (ttm) cc_final: 0.6034 (mtp) REVERT: D 913 MET cc_start: 0.2816 (mmm) cc_final: 0.2568 (mmt) REVERT: D 1001 MET cc_start: 0.0748 (tmm) cc_final: 0.0204 (ppp) REVERT: E 616 MET cc_start: 0.7414 (mmm) cc_final: 0.6811 (mmm) REVERT: E 704 MET cc_start: 0.5790 (ppp) cc_final: 0.5536 (ppp) REVERT: E 829 GLN cc_start: 0.7831 (pp30) cc_final: 0.7202 (tp40) outliers start: 51 outliers final: 33 residues processed: 256 average time/residue: 0.4738 time to fit residues: 200.8280 Evaluate side-chains 246 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 4.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 743 TYR Chi-restraints excluded: chain D residue 810 HIS Chi-restraints excluded: chain D residue 936 MET Chi-restraints excluded: chain D residue 973 ASN Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain E residue 859 VAL Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 51 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 48 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 349 optimal weight: 0.9990 chunk 296 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 307 optimal weight: 3.9990 chunk 396 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 214 optimal weight: 0.0030 chunk 161 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN ** D 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 927 ASN ** 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 = 0.4614 r_free = 0.4614 target = 0.119562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.102907 restraints weight = 161587.902| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 4.41 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.8274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34350 Z= 0.138 Angle : 0.626 12.436 46282 Z= 0.324 Chirality : 0.043 0.193 4944 Planarity : 0.003 0.044 5890 Dihedral : 5.207 42.592 4426 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.21 % Favored : 91.71 % Rotamer: Outliers : 1.16 % Allowed : 14.83 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.11 (0.13), residues: 3982 helix: 0.34 (0.11), residues: 2402 sheet: -3.60 (0.40), residues: 96 loop : -2.35 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 601 HIS 0.006 0.001 HIS A 658 PHE 0.030 0.002 PHE C 81 TYR 0.039 0.002 TYR A 455 ARG 0.011 0.001 ARG A 478 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 1560) hydrogen bonds : angle 4.46522 ( 4584) covalent geometry : bond 0.00306 (34350) covalent geometry : angle 0.62627 (46282) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 220 time to evaluate : 3.933 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 98 MET cc_start: 0.8100 (mpp) cc_final: 0.7350 (ttm) REVERT: A 382 ASN cc_start: 0.7477 (m-40) cc_final: 0.7219 (m110) REVERT: A 385 PHE cc_start: 0.6884 (t80) cc_final: 0.6162 (t80) REVERT: A 396 MET cc_start: 0.7974 (tpp) cc_final: 0.7395 (tpp) REVERT: A 550 PHE cc_start: 0.2759 (OUTLIER) cc_final: 0.1197 (t80) REVERT: A 552 TYR cc_start: 0.4796 (OUTLIER) cc_final: 0.2408 (p90) REVERT: A 647 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7266 (mpp) REVERT: A 769 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7745 (tptt) REVERT: B 107 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.8060 (t80) REVERT: B 290 MET cc_start: 0.7763 (mmm) cc_final: 0.7540 (mmm) REVERT: B 914 SER cc_start: 0.8155 (p) cc_final: 0.7755 (t) REVERT: B 955 ILE cc_start: 0.5867 (mt) cc_final: 0.5548 (mm) REVERT: C 79 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7215 (m-80) REVERT: D 85 LEU cc_start: 0.4047 (tp) cc_final: 0.3767 (pp) REVERT: D 357 MET cc_start: 0.4530 (tpp) cc_final: 0.4116 (tpt) REVERT: D 385 PHE cc_start: 0.4748 (OUTLIER) cc_final: 0.4309 (m-10) REVERT: D 396 MET cc_start: 0.6250 (mmt) cc_final: 0.5973 (tpp) REVERT: D 552 TYR cc_start: 0.4231 (OUTLIER) cc_final: 0.2049 (p90) REVERT: D 578 MET cc_start: 0.3177 (mmp) cc_final: 0.2698 (mmm) REVERT: D 647 MET cc_start: 0.7161 (ttm) cc_final: 0.6223 (mtm) REVERT: D 913 MET cc_start: 0.2875 (mmm) cc_final: 0.2649 (mmt) REVERT: D 1001 MET cc_start: 0.0736 (tmm) cc_final: 0.0134 (ppp) REVERT: E 829 GLN cc_start: 0.7879 (pp30) cc_final: 0.7242 (tp40) REVERT: E 920 TYR cc_start: 0.6963 (t80) cc_final: 0.6464 (t80) REVERT: E 930 MET cc_start: 0.3066 (mtt) cc_final: 0.2462 (ptp) REVERT: F 23 PHE cc_start: 0.7106 (m-10) cc_final: 0.6905 (m-10) outliers start: 43 outliers final: 29 residues processed: 253 average time/residue: 0.5175 time to fit residues: 214.9848 Evaluate side-chains 241 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 204 time to evaluate : 3.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 743 TYR Chi-restraints excluded: chain D residue 936 MET Chi-restraints excluded: chain D residue 973 ASN Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain E residue 859 VAL Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 51 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 276 optimal weight: 0.9990 chunk 259 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 346 optimal weight: 0.3980 chunk 203 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 397 optimal weight: 6.9990 chunk 270 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 208 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 475 GLN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 HIS ** D 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 ASN ** E 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 927 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.119006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.102424 restraints weight = 160544.863| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 4.53 r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.8628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34350 Z= 0.135 Angle : 0.630 13.524 46282 Z= 0.324 Chirality : 0.043 0.189 4944 Planarity : 0.003 0.043 5890 Dihedral : 5.182 40.714 4426 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.68 % Favored : 92.29 % Rotamer: Outliers : 1.21 % Allowed : 14.78 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.08 (0.13), residues: 3982 helix: 0.37 (0.11), residues: 2408 sheet: -3.55 (0.40), residues: 96 loop : -2.36 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 601 HIS 0.013 0.001 HIS D 658 PHE 0.029 0.002 PHE C 81 TYR 0.037 0.002 TYR A 455 ARG 0.009 0.000 ARG D 657 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 1560) hydrogen bonds : angle 4.43564 ( 4584) covalent geometry : bond 0.00299 (34350) covalent geometry : angle 0.62967 (46282) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 217 time to evaluate : 5.334 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: A 98 MET cc_start: 0.8063 (mpp) cc_final: 0.7425 (ttm) REVERT: A 169 LYS cc_start: 0.4413 (mttt) cc_final: 0.4179 (mttt) REVERT: A 204 MET cc_start: 0.0452 (ttt) cc_final: 0.0238 (tpp) REVERT: A 290 MET cc_start: -0.0884 (OUTLIER) cc_final: -0.1169 (tpt) REVERT: A 396 MET cc_start: 0.7814 (tpp) cc_final: 0.7563 (tpp) REVERT: A 531 MET cc_start: 0.1339 (mtt) cc_final: 0.0963 (mtm) REVERT: A 550 PHE cc_start: 0.2921 (OUTLIER) cc_final: 0.1163 (t80) REVERT: A 552 TYR cc_start: 0.4610 (OUTLIER) cc_final: 0.2365 (p90) REVERT: A 647 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7443 (mpp) REVERT: A 769 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7874 (tppt) REVERT: B 107 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8088 (t80) REVERT: B 883 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8088 (mm-30) REVERT: B 955 ILE cc_start: 0.5768 (mt) cc_final: 0.5504 (mm) REVERT: C 79 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7143 (m-80) REVERT: D 357 MET cc_start: 0.4872 (tpp) cc_final: 0.4483 (tpt) REVERT: D 385 PHE cc_start: 0.4726 (OUTLIER) cc_final: 0.4311 (m-10) REVERT: D 396 MET cc_start: 0.6470 (mmt) cc_final: 0.5922 (mmm) REVERT: D 552 TYR cc_start: 0.4090 (OUTLIER) cc_final: 0.2041 (p90) REVERT: D 578 MET cc_start: 0.3266 (mmp) cc_final: 0.2792 (mmm) REVERT: D 647 MET cc_start: 0.7244 (ttm) cc_final: 0.6261 (mtp) REVERT: D 704 MET cc_start: -0.2000 (tpt) cc_final: -0.3046 (mmt) REVERT: D 1001 MET cc_start: 0.1148 (tmm) cc_final: 0.0549 (ppp) REVERT: E 134 TYR cc_start: 0.6824 (OUTLIER) cc_final: 0.6239 (m-80) REVERT: E 829 GLN cc_start: 0.7794 (pp30) cc_final: 0.7216 (tp40) REVERT: E 866 MET cc_start: 0.2002 (mmt) cc_final: 0.1796 (mmt) REVERT: E 920 TYR cc_start: 0.7012 (t80) cc_final: 0.6502 (t80) REVERT: E 930 MET cc_start: 0.2832 (mtt) cc_final: 0.2301 (ptp) REVERT: F 23 PHE cc_start: 0.6993 (m-10) cc_final: 0.6785 (m-10) REVERT: F 43 TYR cc_start: 0.5104 (p90) cc_final: 0.4621 (p90) outliers start: 45 outliers final: 30 residues processed: 252 average time/residue: 0.5324 time to fit residues: 224.7628 Evaluate side-chains 239 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 199 time to evaluate : 4.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 666 ASN Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 743 TYR Chi-restraints excluded: chain D residue 936 MET Chi-restraints excluded: chain D residue 973 ASN Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain E residue 859 VAL Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 51 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 361 optimal weight: 6.9990 chunk 358 optimal weight: 0.0770 chunk 346 optimal weight: 0.2980 chunk 142 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 195 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 chunk 362 optimal weight: 0.9980 chunk 178 optimal weight: 0.0270 chunk 347 optimal weight: 0.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN ** B 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN ** E 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 939 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.119592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.102638 restraints weight = 161196.476| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 4.42 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.8694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 34350 Z= 0.109 Angle : 0.604 12.832 46282 Z= 0.311 Chirality : 0.042 0.193 4944 Planarity : 0.003 0.040 5890 Dihedral : 5.060 41.633 4426 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.33 % Favored : 92.64 % Rotamer: Outliers : 1.13 % Allowed : 15.16 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.00 (0.13), residues: 3982 helix: 0.40 (0.11), residues: 2452 sheet: -3.48 (0.37), residues: 116 loop : -2.29 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 60 HIS 0.006 0.001 HIS A 658 PHE 0.031 0.001 PHE C 81 TYR 0.037 0.001 TYR A 455 ARG 0.007 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03468 ( 1560) hydrogen bonds : angle 4.29065 ( 4584) covalent geometry : bond 0.00229 (34350) covalent geometry : angle 0.60394 (46282) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14616.51 seconds wall clock time: 257 minutes 14.25 seconds (15434.25 seconds total)