Starting phenix.real_space_refine on Tue Aug 26 04:41:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3y_38907/08_2025/8y3y_38907.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3y_38907/08_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_38907/08_2025/8y3y_38907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3y_38907/08_2025/8y3y_38907.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3y_38907/08_2025/8y3y_38907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3y_38907/08_2025/8y3y_38907.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.031 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 7.97, per 1000 atoms: 0.24 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: 2.85 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.37 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: 6.13 Time building geometry restraints manager: 3.69 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: 0.03 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: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 29.960 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.850 ------------------------------------------------------------------------------- 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 : 6.15 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.024 0.001 ARG B 478 TYR 0.025 0.003 TYR D 574 PHE 0.027 0.003 PHE D 722 TRP 0.044 0.005 TRP C 25 HIS 0.009 0.002 HIS B 786 Details of bonding type rmsd covalent geometry : bond 0.00726 (34350) covalent geometry : angle 1.11332 (46282) hydrogen bonds : bond 0.17684 ( 1560) hydrogen bonds : angle 8.36203 ( 4584) *********************** 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 : 1.369 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 232 VAL cc_start: 0.6358 (m) cc_final: 0.5983 (p) REVERT: A 913 MET cc_start: -0.0069 (mmm) cc_final: -0.0346 (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: 0.8447 (mt) REVERT: B 883 GLU cc_start: 0.9053 (tp30) cc_final: 0.8629 (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: 0.8546 (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: 0.7519 (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: 0.3559 (mttp) REVERT: D 913 MET cc_start: 0.1886 (mmm) cc_final: 0.0951 (mmt) REVERT: E 936 MET cc_start: 0.1366 (mpt) cc_final: 0.1075 (mpt) outliers start: 25 outliers final: 2 residues processed: 486 average time/residue: 0.2321 time to fit residues: 177.2690 Evaluate side-chains 267 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 265 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 197 optimal weight: 4.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 477 ASN A 483 GLN A 614 ASN A 702 ASN A 711 GLN A 765 ASN A 881 HIS A1002 ASN B 93 ASN B 195 GLN B 351 ASN B 391 ASN B 711 GLN B 765 ASN ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS D 391 ASN D 666 ASN 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 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.129168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.112991 restraints weight = 171370.797| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 5.06 r_work (final): 0.4424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5962 moved from start: 0.2946 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= 0.155 Angle : 0.664 11.027 46282 Z= 0.358 Chirality : 0.044 0.209 4944 Planarity : 0.005 0.056 5890 Dihedral : 6.547 56.049 4426 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.45 % Favored : 93.19 % Rotamer: Outliers : 1.86 % Allowed : 8.12 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.89 (0.12), residues: 3982 helix: -1.14 (0.10), residues: 2420 sheet: -4.17 (0.34), residues: 96 loop : -3.01 (0.14), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 72 TYR 0.026 0.002 TYR B 888 PHE 0.021 0.002 PHE F 23 TRP 0.019 0.002 TRP D 231 HIS 0.006 0.001 HIS A 881 Details of bonding type rmsd covalent geometry : bond 0.00334 (34350) covalent geometry : angle 0.66355 (46282) hydrogen bonds : bond 0.04482 ( 1560) hydrogen bonds : angle 5.16170 ( 4584) *********************** 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 368 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 299 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8030 (mpp) cc_final: 0.7406 (mpp) REVERT: A 261 TYR cc_start: 0.7012 (m-10) cc_final: 0.6596 (m-80) REVERT: A 555 THR cc_start: 0.7056 (OUTLIER) cc_final: 0.6773 (m) REVERT: A 704 MET cc_start: 0.2154 (tpp) cc_final: 0.1172 (mmp) REVERT: A 705 ASN cc_start: 0.6077 (t0) cc_final: 0.5611 (p0) REVERT: B 883 GLU cc_start: 0.8892 (tp30) cc_final: 0.8598 (mm-30) REVERT: B 920 TYR cc_start: 0.8082 (t80) cc_final: 0.7817 (t80) REVERT: B 958 TRP cc_start: 0.6932 (m-10) cc_final: 0.6583 (m-10) REVERT: C 79 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.6935 (m-80) REVERT: C 93 LYS cc_start: 0.7922 (mmpt) cc_final: 0.7209 (tptp) REVERT: C 98 ILE cc_start: 0.8947 (mt) cc_final: 0.8739 (mm) REVERT: D 21 MET cc_start: 0.3115 (mtm) cc_final: 0.2795 (tpp) REVERT: D 169 LYS cc_start: 0.4765 (mttt) cc_final: 0.4263 (mttp) REVERT: D 389 GLU cc_start: 0.5831 (mt-10) cc_final: 0.5415 (mp0) REVERT: D 421 MET cc_start: 0.1158 (OUTLIER) cc_final: 0.0854 (ttm) REVERT: D 913 MET cc_start: 0.2507 (mmm) cc_final: 0.1728 (mmt) REVERT: E 704 MET cc_start: 0.5037 (ppp) cc_final: 0.4828 (ppp) REVERT: E 841 LEU cc_start: 0.8208 (tp) cc_final: 0.7915 (mp) REVERT: E 936 MET cc_start: 0.1402 (mpt) cc_final: 0.0966 (mpt) REVERT: E 1001 MET cc_start: 0.0471 (mtp) cc_final: -0.0354 (mtt) outliers start: 69 outliers final: 19 residues processed: 355 average time/residue: 0.2006 time to fit residues: 116.8587 Evaluate side-chains 244 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 222 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 HIS 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 862 ILE Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 100 LEU 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 736 ILE Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 103 ILE 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 132 optimal weight: 5.9990 chunk 169 optimal weight: 0.9980 chunk 399 optimal weight: 7.9990 chunk 374 optimal weight: 20.0000 chunk 154 optimal weight: 2.9990 chunk 275 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 135 optimal weight: 0.0070 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 359 optimal weight: 7.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- 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 ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 HIS A 351 ASN A 606 HIS A 610 GLN A 702 ASN A 789 GLN A 863 ASN A 973 ASN B 195 GLN B 211 HIS B 658 HIS ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 ASN D 202 ASN ** D 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 HIS ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 ASN E 351 ASN E 467 ASN E 609 HIS E 658 HIS ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.123038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.108673 restraints weight = 172917.113| |-----------------------------------------------------------------------------| r_work (start): 0.4370 rms_B_bonded: 3.49 r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 34350 Z= 0.180 Angle : 0.678 13.193 46282 Z= 0.365 Chirality : 0.044 0.248 4944 Planarity : 0.004 0.065 5890 Dihedral : 6.057 50.821 4426 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.06 % Favored : 91.71 % Rotamer: Outliers : 2.40 % Allowed : 9.49 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.15 (0.12), residues: 3982 helix: -0.53 (0.10), residues: 2420 sheet: -3.85 (0.36), residues: 96 loop : -2.74 (0.15), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 145 TYR 0.030 0.002 TYR B 888 PHE 0.029 0.002 PHE A 608 TRP 0.032 0.002 TRP A 919 HIS 0.018 0.001 HIS A 979 Details of bonding type rmsd covalent geometry : bond 0.00388 (34350) covalent geometry : angle 0.67803 (46282) hydrogen bonds : bond 0.04555 ( 1560) hydrogen bonds : angle 4.86847 ( 4584) *********************** 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 366 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 277 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 ASN cc_start: 0.1798 (OUTLIER) cc_final: 0.1213 (p0) REVERT: A 531 MET cc_start: 0.2438 (mmt) cc_final: 0.2160 (mmt) REVERT: A 552 TYR cc_start: 0.5185 (p90) cc_final: 0.3480 (p90) REVERT: A 704 MET cc_start: 0.3371 (tpp) cc_final: 0.2650 (mmp) REVERT: A 705 ASN cc_start: 0.6788 (t0) cc_final: 0.6523 (p0) REVERT: A 976 MET cc_start: 0.6143 (ptp) cc_final: 0.5832 (ptm) REVERT: B 195 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.7246 (pp30) REVERT: C 27 VAL cc_start: 0.7921 (OUTLIER) cc_final: 0.7680 (t) REVERT: C 79 PHE cc_start: 0.7013 (OUTLIER) cc_final: 0.6092 (m-80) REVERT: C 93 LYS cc_start: 0.7532 (mmpt) cc_final: 0.7277 (tppt) REVERT: D 167 LEU cc_start: 0.6479 (tt) cc_final: 0.5846 (mt) REVERT: D 396 MET cc_start: 0.3976 (mmt) cc_final: 0.3057 (tpt) REVERT: D 848 ASN cc_start: 0.5319 (m-40) cc_final: 0.5087 (t0) REVERT: D 913 MET cc_start: 0.2646 (mmm) cc_final: 0.2110 (mmt) REVERT: E 920 TYR cc_start: 0.7073 (t80) cc_final: 0.6821 (t80) REVERT: E 925 ILE cc_start: 0.3098 (OUTLIER) cc_final: 0.2288 (tt) REVERT: E 936 MET cc_start: 0.1218 (mpt) cc_final: 0.0699 (mpt) REVERT: F 43 TYR cc_start: 0.5181 (OUTLIER) cc_final: 0.4971 (p90) outliers start: 89 outliers final: 33 residues processed: 353 average time/residue: 0.1983 time to fit residues: 115.9803 Evaluate side-chains 261 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 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 6 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain C residue 27 VAL 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 365 GLU Chi-restraints excluded: chain D residue 423 LYS Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 538 LYS Chi-restraints excluded: chain D residue 611 TYR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 555 THR 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 30 ASP Chi-restraints excluded: chain F residue 43 TYR Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 68 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 316 optimal weight: 4.9990 chunk 392 optimal weight: 2.9990 chunk 362 optimal weight: 0.8980 chunk 116 optimal weight: 0.5980 chunk 293 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 279 optimal weight: 0.5980 chunk 188 optimal weight: 1.9990 chunk 278 optimal weight: 0.9990 chunk 342 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 483 GLN A 666 ASN A 681 GLN A 702 ASN ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 ASN ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.123123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.109053 restraints weight = 172697.596| |-----------------------------------------------------------------------------| r_work (start): 0.4374 rms_B_bonded: 3.95 r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6036 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34350 Z= 0.120 Angle : 0.587 11.577 46282 Z= 0.312 Chirality : 0.042 0.223 4944 Planarity : 0.003 0.036 5890 Dihedral : 5.644 44.194 4426 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.63 % Favored : 93.17 % Rotamer: Outliers : 1.59 % Allowed : 11.00 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.13), residues: 3982 helix: -0.06 (0.10), residues: 2414 sheet: -3.65 (0.37), residues: 96 loop : -2.65 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 669 TYR 0.021 0.001 TYR A 455 PHE 0.039 0.001 PHE D 381 TRP 0.016 0.001 TRP D 231 HIS 0.009 0.001 HIS A 979 Details of bonding type rmsd covalent geometry : bond 0.00255 (34350) covalent geometry : angle 0.58716 (46282) hydrogen bonds : bond 0.03713 ( 1560) hydrogen bonds : angle 4.47455 ( 4584) *********************** 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 301 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 242 time to evaluate : 1.243 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: 0.7941 (mpp) cc_final: 0.7025 (mtm) REVERT: A 453 ASP cc_start: 0.5641 (t0) cc_final: 0.5421 (t0) REVERT: A 467 ASN cc_start: 0.1838 (OUTLIER) cc_final: 0.1399 (p0) REVERT: A 552 TYR cc_start: 0.4989 (OUTLIER) cc_final: 0.2892 (p90) REVERT: A 704 MET cc_start: 0.3391 (tpp) cc_final: 0.2790 (mmp) REVERT: C 79 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.6465 (m-80) REVERT: D 167 LEU cc_start: 0.6387 (tt) cc_final: 0.5689 (mt) REVERT: D 396 MET cc_start: 0.3809 (mmt) cc_final: 0.3216 (tpt) REVERT: D 519 MET cc_start: -0.2441 (mtt) cc_final: -0.2737 (mtm) REVERT: D 913 MET cc_start: 0.2501 (mmm) cc_final: 0.2104 (mmt) REVERT: E 531 MET cc_start: 0.8426 (mmm) cc_final: 0.8178 (mmt) REVERT: E 920 TYR cc_start: 0.7047 (t80) cc_final: 0.6739 (t80) REVERT: E 925 ILE cc_start: 0.2531 (OUTLIER) cc_final: 0.1825 (tt) REVERT: E 930 MET cc_start: 0.2962 (mtm) cc_final: 0.2690 (mtm) REVERT: E 936 MET cc_start: 0.0997 (mpt) cc_final: 0.0504 (mpt) outliers start: 59 outliers final: 28 residues processed: 288 average time/residue: 0.2014 time to fit residues: 95.8448 Evaluate side-chains 245 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 1.264 ------------------------------------------------------------------------------- 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 385 PHE Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 552 TYR 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 862 ILE Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 794 VAL 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 241 HIS Chi-restraints excluded: chain D residue 365 GLU Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 555 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 E residue 925 ILE Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 73 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 76 optimal weight: 6.9990 chunk 324 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 337 optimal weight: 4.9990 chunk 294 optimal weight: 10.0000 chunk 317 optimal weight: 3.9990 chunk 196 optimal weight: 30.0000 chunk 161 optimal weight: 0.9990 chunk 331 optimal weight: 0.5980 chunk 285 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 ASN A 658 HIS A 702 ASN A 863 ASN B 195 GLN B 351 ASN B 609 HIS ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 654 ASN ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 927 ASN ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 939 GLN E 973 ASN E 992 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.122826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.105752 restraints weight = 163983.472| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 4.93 r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.6229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 34350 Z= 0.157 Angle : 0.628 11.456 46282 Z= 0.334 Chirality : 0.044 0.210 4944 Planarity : 0.004 0.045 5890 Dihedral : 5.551 43.205 4426 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.01 % Favored : 91.84 % Rotamer: Outliers : 2.05 % Allowed : 11.65 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.13), residues: 3982 helix: 0.00 (0.10), residues: 2426 sheet: -3.90 (0.41), residues: 68 loop : -2.61 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 613 TYR 0.031 0.002 TYR A 479 PHE 0.028 0.002 PHE D 699 TRP 0.025 0.002 TRP D 231 HIS 0.011 0.001 HIS A 979 Details of bonding type rmsd covalent geometry : bond 0.00347 (34350) covalent geometry : angle 0.62818 (46282) hydrogen bonds : bond 0.04107 ( 1560) hydrogen bonds : angle 4.57219 ( 4584) *********************** 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 324 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 248 time to evaluate : 1.015 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: 0.8144 (mpp) cc_final: 0.7916 (mpp) REVERT: A 108 PHE cc_start: 0.3249 (m-80) cc_final: 0.2546 (t80) REVERT: A 169 LYS cc_start: 0.4892 (mttt) cc_final: 0.4671 (mttt) REVERT: A 357 MET cc_start: 0.6971 (ttt) cc_final: 0.6458 (tpp) REVERT: A 385 PHE cc_start: 0.6203 (OUTLIER) cc_final: 0.5923 (t80) REVERT: A 389 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7389 (mt-10) REVERT: A 395 CYS cc_start: 0.6813 (p) cc_final: 0.6495 (p) REVERT: A 467 ASN cc_start: 0.2439 (OUTLIER) cc_final: 0.2049 (p0) REVERT: A 552 TYR cc_start: 0.5248 (OUTLIER) cc_final: 0.2947 (p90) REVERT: A 704 MET cc_start: 0.4064 (tpp) cc_final: 0.3512 (mmm) REVERT: A 913 MET cc_start: -0.0941 (mmt) cc_final: -0.1350 (tmm) REVERT: A 976 MET cc_start: 0.4996 (ptm) cc_final: 0.4400 (ptt) REVERT: B 866 MET cc_start: 0.8764 (tpp) cc_final: 0.8419 (tpp) REVERT: B 883 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8227 (mm-30) REVERT: B 933 PHE cc_start: 0.7426 (m-80) cc_final: 0.7079 (m-80) REVERT: D 21 MET cc_start: 0.2838 (mtm) cc_final: 0.2518 (ttt) REVERT: D 167 LEU cc_start: 0.6901 (tt) cc_final: 0.5974 (mt) REVERT: D 385 PHE cc_start: 0.4351 (OUTLIER) cc_final: 0.4016 (m-10) REVERT: D 711 GLN cc_start: -0.0696 (pt0) cc_final: -0.1722 (mt0) REVERT: D 815 PHE cc_start: 0.4838 (t80) cc_final: 0.4518 (t80) REVERT: D 913 MET cc_start: 0.2694 (mmm) cc_final: 0.2362 (mmt) REVERT: E 920 TYR cc_start: 0.7325 (t80) cc_final: 0.7016 (t80) REVERT: E 925 ILE cc_start: 0.3157 (OUTLIER) cc_final: 0.2298 (tt) REVERT: E 930 MET cc_start: 0.2943 (mtm) cc_final: 0.2737 (mtm) REVERT: E 936 MET cc_start: 0.0994 (mpt) cc_final: 0.0675 (mpt) REVERT: F 43 TYR cc_start: 0.5248 (OUTLIER) cc_final: 0.4937 (p90) outliers start: 76 outliers final: 27 residues processed: 309 average time/residue: 0.1887 time to fit residues: 96.9311 Evaluate side-chains 247 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 552 TYR 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 342 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 385 PHE Chi-restraints excluded: chain D residue 423 LYS Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 508 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 925 ILE Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 43 TYR 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 271 optimal weight: 6.9990 chunk 304 optimal weight: 1.9990 chunk 383 optimal weight: 8.9990 chunk 191 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 199 optimal weight: 3.9990 chunk 309 optimal weight: 0.6980 chunk 326 optimal weight: 0.0000 chunk 375 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 chunk 308 optimal weight: 3.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 ASN A 927 ASN B 195 GLN B 666 ASN ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.120939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.106418 restraints weight = 166969.272| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 3.49 r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 moved from start: 0.6651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34350 Z= 0.124 Angle : 0.592 12.023 46282 Z= 0.313 Chirality : 0.043 0.246 4944 Planarity : 0.003 0.042 5890 Dihedral : 5.325 41.735 4426 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.93 % Favored : 92.94 % Rotamer: Outliers : 1.86 % Allowed : 12.51 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.13), residues: 3982 helix: 0.20 (0.11), residues: 2424 sheet: -3.77 (0.43), residues: 68 loop : -2.51 (0.15), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 52 TYR 0.041 0.001 TYR A 479 PHE 0.023 0.001 PHE E 712 TRP 0.012 0.001 TRP D 231 HIS 0.009 0.001 HIS A 979 Details of bonding type rmsd covalent geometry : bond 0.00265 (34350) covalent geometry : angle 0.59232 (46282) hydrogen bonds : bond 0.03629 ( 1560) hydrogen bonds : angle 4.38650 ( 4584) *********************** 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 306 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 237 time to evaluate : 1.418 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: A 98 MET cc_start: 0.7775 (mpp) cc_final: 0.7046 (mtm) REVERT: A 169 LYS cc_start: 0.4337 (mttt) cc_final: 0.3908 (mttt) REVERT: A 200 ILE cc_start: -0.2348 (OUTLIER) cc_final: -0.2604 (tt) REVERT: A 357 MET cc_start: 0.6197 (ttt) cc_final: 0.5922 (tpp) REVERT: A 385 PHE cc_start: 0.5914 (OUTLIER) cc_final: 0.5605 (t80) REVERT: A 389 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7326 (mt-10) REVERT: A 396 MET cc_start: 0.7643 (tpp) cc_final: 0.7354 (tpp) REVERT: A 467 ASN cc_start: 0.1353 (OUTLIER) cc_final: 0.1115 (p0) REVERT: A 552 TYR cc_start: 0.4868 (OUTLIER) cc_final: 0.2856 (p90) REVERT: A 704 MET cc_start: 0.3771 (tpp) cc_final: 0.3391 (mmp) REVERT: A 913 MET cc_start: -0.0722 (mmt) cc_final: -0.1154 (tmm) REVERT: B 107 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.8138 (t80) REVERT: B 195 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7321 (pp30) REVERT: B 933 PHE cc_start: 0.6478 (m-80) cc_final: 0.6034 (m-80) REVERT: C 79 PHE cc_start: 0.7400 (OUTLIER) cc_final: 0.6815 (m-80) REVERT: D 167 LEU cc_start: 0.6895 (tt) cc_final: 0.5984 (mt) REVERT: D 295 GLU cc_start: 0.3950 (OUTLIER) cc_final: 0.3476 (pt0) REVERT: D 385 PHE cc_start: 0.4210 (OUTLIER) cc_final: 0.3884 (m-10) REVERT: D 457 ASN cc_start: 0.5626 (m-40) cc_final: 0.5421 (m-40) REVERT: D 514 ARG cc_start: 0.6080 (mtp-110) cc_final: 0.5392 (tmm160) REVERT: D 711 GLN cc_start: -0.0851 (pt0) cc_final: -0.1523 (mt0) REVERT: D 815 PHE cc_start: 0.4664 (t80) cc_final: 0.4436 (t80) REVERT: D 913 MET cc_start: 0.2533 (mmm) cc_final: 0.2209 (mmt) REVERT: D 1001 MET cc_start: 0.0629 (tmm) cc_final: 0.0114 (ppp) REVERT: E 829 GLN cc_start: 0.7499 (pp30) cc_final: 0.7008 (tp40) REVERT: E 920 TYR cc_start: 0.7160 (t80) cc_final: 0.6875 (t80) REVERT: E 925 ILE cc_start: 0.2841 (OUTLIER) cc_final: 0.1955 (tt) REVERT: E 936 MET cc_start: 0.0607 (mpt) cc_final: 0.0289 (mpt) REVERT: F 23 PHE cc_start: 0.7297 (m-80) cc_final: 0.7095 (m-10) REVERT: F 43 TYR cc_start: 0.5240 (p90) cc_final: 0.5031 (p90) outliers start: 69 outliers final: 33 residues processed: 290 average time/residue: 0.2047 time to fit residues: 97.7883 Evaluate side-chains 256 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 581 ASP 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 107 PHE Chi-restraints excluded: chain B residue 195 GLN 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 385 PHE Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 743 TYR Chi-restraints excluded: chain D residue 767 LEU Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 508 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 913 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 386 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 377 optimal weight: 0.6980 chunk 168 optimal weight: 0.5980 chunk 222 optimal weight: 0.9980 chunk 390 optimal weight: 7.9990 chunk 190 optimal weight: 0.2980 chunk 287 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 179 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 HIS D 606 HIS ** 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 = 0.4650 r_free = 0.4650 target = 0.121754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.104949 restraints weight = 161500.663| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 4.54 r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.7100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34350 Z= 0.134 Angle : 0.600 11.848 46282 Z= 0.316 Chirality : 0.043 0.188 4944 Planarity : 0.003 0.045 5890 Dihedral : 5.283 41.729 4426 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.91 % Favored : 91.99 % Rotamer: Outliers : 1.59 % Allowed : 13.03 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.13), residues: 3982 helix: 0.27 (0.11), residues: 2426 sheet: -3.28 (0.40), residues: 92 loop : -2.44 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 72 TYR 0.044 0.001 TYR A 479 PHE 0.042 0.001 PHE F 81 TRP 0.010 0.001 TRP D 231 HIS 0.007 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00294 (34350) covalent geometry : angle 0.59978 (46282) hydrogen bonds : bond 0.03696 ( 1560) hydrogen bonds : angle 4.39248 ( 4584) *********************** 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 292 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 233 time to evaluate : 1.083 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 108 PHE cc_start: 0.3139 (m-80) cc_final: 0.2913 (m-80) REVERT: A 357 MET cc_start: 0.7010 (ttt) cc_final: 0.6081 (tpp) REVERT: A 396 MET cc_start: 0.7765 (tpp) cc_final: 0.7353 (tpp) REVERT: A 467 ASN cc_start: 0.1738 (OUTLIER) cc_final: 0.1522 (p0) REVERT: A 552 TYR cc_start: 0.4849 (OUTLIER) cc_final: 0.2992 (p90) REVERT: A 578 MET cc_start: 0.5641 (tpp) cc_final: 0.5333 (tpp) REVERT: A 704 MET cc_start: 0.4086 (tpp) cc_final: 0.3662 (mmp) REVERT: B 107 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.8158 (t80) REVERT: C 79 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7199 (m-80) REVERT: D 21 MET cc_start: 0.2522 (mtm) cc_final: 0.2135 (ttt) REVERT: D 167 LEU cc_start: 0.7276 (tt) cc_final: 0.6229 (mt) REVERT: D 295 GLU cc_start: 0.4126 (OUTLIER) cc_final: 0.3636 (pt0) REVERT: D 385 PHE cc_start: 0.4283 (OUTLIER) cc_final: 0.3963 (m-10) REVERT: D 578 MET cc_start: 0.2940 (mmp) cc_final: 0.2512 (mmm) REVERT: D 711 GLN cc_start: -0.0636 (pt0) cc_final: -0.1307 (mt0) REVERT: D 815 PHE cc_start: 0.4875 (t80) cc_final: 0.4608 (t80) REVERT: D 913 MET cc_start: 0.2522 (mmm) cc_final: 0.2218 (mmt) REVERT: D 1001 MET cc_start: 0.0674 (tmm) cc_final: 0.0221 (ppp) REVERT: E 829 GLN cc_start: 0.7675 (pp30) cc_final: 0.7098 (tp40) REVERT: E 920 TYR cc_start: 0.7293 (t80) cc_final: 0.6526 (t80) REVERT: E 930 MET cc_start: 0.3192 (mtm) cc_final: 0.2633 (ptp) REVERT: E 936 MET cc_start: 0.0695 (mpt) cc_final: 0.0471 (mpt) REVERT: F 43 TYR cc_start: 0.5349 (p90) cc_final: 0.5089 (p90) REVERT: F 64 ILE cc_start: 0.7924 (tp) cc_final: 0.7707 (tp) outliers start: 59 outliers final: 33 residues processed: 279 average time/residue: 0.1962 time to fit residues: 89.7767 Evaluate side-chains 248 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 227 MET 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 442 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 581 ASP 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 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 241 HIS Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 580 SER 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 E residue 69 GLU Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 508 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 51 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 185 optimal weight: 5.9990 chunk 293 optimal weight: 0.9980 chunk 201 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 chunk 355 optimal weight: 0.0040 chunk 309 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 140 optimal weight: 0.7980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.122243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.105587 restraints weight = 162256.758| |-----------------------------------------------------------------------------| r_work (start): 0.4296 rms_B_bonded: 4.58 r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.7351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34350 Z= 0.109 Angle : 0.579 12.851 46282 Z= 0.302 Chirality : 0.042 0.198 4944 Planarity : 0.003 0.045 5890 Dihedral : 5.115 40.663 4426 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.01 % Favored : 92.94 % Rotamer: Outliers : 1.48 % Allowed : 13.86 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.13), residues: 3982 helix: 0.43 (0.11), residues: 2418 sheet: -3.51 (0.45), residues: 68 loop : -2.38 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 145 TYR 0.040 0.001 TYR A 479 PHE 0.021 0.001 PHE F 81 TRP 0.012 0.001 TRP D 231 HIS 0.006 0.001 HIS D 658 Details of bonding type rmsd covalent geometry : bond 0.00232 (34350) covalent geometry : angle 0.57912 (46282) hydrogen bonds : bond 0.03371 ( 1560) hydrogen bonds : angle 4.25692 ( 4584) *********************** 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 277 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 222 time to evaluate : 1.079 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 98 MET cc_start: 0.8001 (mpp) cc_final: 0.7256 (mtm) REVERT: A 108 PHE cc_start: 0.2473 (m-80) cc_final: 0.2255 (m-80) REVERT: A 169 LYS cc_start: 0.4088 (mttt) cc_final: 0.3764 (mmtt) REVERT: A 357 MET cc_start: 0.6978 (ttt) cc_final: 0.5891 (tpp) REVERT: A 385 PHE cc_start: 0.6603 (t80) cc_final: 0.5391 (t80) REVERT: A 396 MET cc_start: 0.7874 (tpp) cc_final: 0.7504 (tpp) REVERT: A 552 TYR cc_start: 0.4482 (OUTLIER) cc_final: 0.2193 (p90) REVERT: A 704 MET cc_start: 0.4144 (tpp) cc_final: 0.3784 (mmm) REVERT: B 107 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8130 (t80) REVERT: B 290 MET cc_start: 0.7965 (mmm) cc_final: 0.7656 (mmm) REVERT: B 519 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7234 (mmt) REVERT: B 883 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8002 (mm-30) REVERT: C 79 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7284 (m-80) REVERT: D 21 MET cc_start: 0.2437 (mtm) cc_final: 0.2134 (ttt) REVERT: D 295 GLU cc_start: 0.3909 (OUTLIER) cc_final: 0.3484 (pt0) REVERT: D 357 MET cc_start: 0.4665 (tpp) cc_final: 0.4221 (tpt) REVERT: D 385 PHE cc_start: 0.4205 (OUTLIER) cc_final: 0.3895 (m-10) REVERT: D 457 ASN cc_start: 0.5489 (m-40) cc_final: 0.5263 (m-40) REVERT: D 552 TYR cc_start: 0.3895 (OUTLIER) cc_final: 0.1680 (p90) REVERT: D 578 MET cc_start: 0.2706 (mmp) cc_final: 0.2271 (mmm) REVERT: D 704 MET cc_start: -0.2298 (tpt) cc_final: -0.3168 (tpp) REVERT: D 815 PHE cc_start: 0.5104 (t80) cc_final: 0.4737 (t80) REVERT: D 913 MET cc_start: 0.2623 (mmm) cc_final: 0.2353 (mmt) REVERT: D 1001 MET cc_start: 0.0442 (tmm) cc_final: -0.0033 (ppp) REVERT: E 829 GLN cc_start: 0.7681 (pp30) cc_final: 0.7109 (tp40) REVERT: E 920 TYR cc_start: 0.7351 (t80) cc_final: 0.6573 (t80) REVERT: E 930 MET cc_start: 0.3574 (mtm) cc_final: 0.3007 (ptp) REVERT: E 994 LYS cc_start: 0.6974 (mttm) cc_final: 0.6685 (mptt) outliers start: 55 outliers final: 29 residues processed: 265 average time/residue: 0.1984 time to fit residues: 87.9360 Evaluate side-chains 241 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 431 SER Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 552 TYR 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 107 PHE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 519 MET 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 295 GLU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 580 SER 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 810 HIS Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 592 LEU 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 51 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 58 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 355 optimal weight: 0.8980 chunk 391 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 275 optimal weight: 6.9990 chunk 284 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 GLN ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 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 939 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.120418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.102500 restraints weight = 161477.385| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 4.81 r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.7866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34350 Z= 0.145 Angle : 0.637 12.417 46282 Z= 0.332 Chirality : 0.043 0.270 4944 Planarity : 0.003 0.045 5890 Dihedral : 5.196 41.278 4426 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.39 % Favored : 91.56 % Rotamer: Outliers : 1.48 % Allowed : 14.13 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.13), residues: 3982 helix: 0.37 (0.11), residues: 2412 sheet: -3.65 (0.43), residues: 80 loop : -2.36 (0.15), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 145 TYR 0.031 0.002 TYR A 479 PHE 0.031 0.002 PHE B 559 TRP 0.021 0.002 TRP D 757 HIS 0.007 0.001 HIS A 979 Details of bonding type rmsd covalent geometry : bond 0.00323 (34350) covalent geometry : angle 0.63682 (46282) hydrogen bonds : bond 0.03870 ( 1560) hydrogen bonds : angle 4.41791 ( 4584) *********************** 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 273 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 218 time to evaluate : 1.653 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 169 LYS cc_start: 0.4297 (mttt) cc_final: 0.3929 (mmtt) REVERT: A 357 MET cc_start: 0.6986 (ttt) cc_final: 0.5946 (tpt) REVERT: A 385 PHE cc_start: 0.6640 (t80) cc_final: 0.6090 (t80) REVERT: A 396 MET cc_start: 0.8091 (tpp) cc_final: 0.7609 (tpp) REVERT: A 550 PHE cc_start: 0.2579 (OUTLIER) cc_final: 0.1243 (t80) REVERT: A 552 TYR cc_start: 0.4719 (OUTLIER) cc_final: 0.2306 (p90) REVERT: A 704 MET cc_start: 0.4394 (tpp) cc_final: 0.4020 (mmm) REVERT: A 769 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7451 (tptt) REVERT: B 107 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8175 (t80) REVERT: B 883 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7582 (mm-30) REVERT: B 955 ILE cc_start: 0.5376 (mt) cc_final: 0.5123 (mm) REVERT: C 79 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7019 (m-80) REVERT: D 357 MET cc_start: 0.4904 (tpp) cc_final: 0.4574 (tpt) REVERT: D 385 PHE cc_start: 0.4377 (OUTLIER) cc_final: 0.4000 (m-10) REVERT: D 434 ASP cc_start: 0.4380 (OUTLIER) cc_final: 0.4026 (m-30) REVERT: D 552 TYR cc_start: 0.4001 (OUTLIER) cc_final: 0.1730 (p90) REVERT: D 578 MET cc_start: 0.2955 (mmp) cc_final: 0.2519 (mmm) REVERT: D 704 MET cc_start: -0.2240 (tpt) cc_final: -0.3145 (tpp) REVERT: D 815 PHE cc_start: 0.5303 (t80) cc_final: 0.4810 (t80) REVERT: E 531 MET cc_start: 0.8389 (mmm) cc_final: 0.7183 (mmm) REVERT: E 829 GLN cc_start: 0.7801 (pp30) cc_final: 0.7137 (tp40) REVERT: E 920 TYR cc_start: 0.7613 (t80) cc_final: 0.6964 (t80) REVERT: E 930 MET cc_start: 0.3575 (mtm) cc_final: 0.2954 (ptp) REVERT: F 43 TYR cc_start: 0.5324 (OUTLIER) cc_final: 0.5010 (p90) outliers start: 55 outliers final: 35 residues processed: 262 average time/residue: 0.1902 time to fit residues: 83.9661 Evaluate side-chains 247 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 203 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 227 MET 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 431 SER Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 552 TYR 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 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 385 PHE Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 666 ASN Chi-restraints excluded: chain D residue 714 SER Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 743 TYR Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 810 HIS Chi-restraints excluded: chain D residue 973 ASN Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 592 LEU 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 43 TYR Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 16 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 293 optimal weight: 3.9990 chunk 362 optimal weight: 0.6980 chunk 305 optimal weight: 0.8980 chunk 131 optimal weight: 0.1980 chunk 10 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 259 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 166 optimal weight: 0.4980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 711 GLN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN B 789 GLN ** E 666 ASN ** 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 = 0.4645 r_free = 0.4645 target = 0.121180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.104371 restraints weight = 162901.361| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 4.80 r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.8034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 34350 Z= 0.114 Angle : 0.605 13.276 46282 Z= 0.312 Chirality : 0.042 0.301 4944 Planarity : 0.003 0.045 5890 Dihedral : 5.028 40.436 4426 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.23 % Favored : 92.74 % Rotamer: Outliers : 1.00 % Allowed : 14.72 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.13), residues: 3982 helix: 0.46 (0.11), residues: 2432 sheet: -3.05 (0.44), residues: 96 loop : -2.29 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 72 TYR 0.024 0.001 TYR A 479 PHE 0.027 0.001 PHE A 385 TRP 0.014 0.001 TRP F 25 HIS 0.007 0.001 HIS D 658 Details of bonding type rmsd covalent geometry : bond 0.00243 (34350) covalent geometry : angle 0.60461 (46282) hydrogen bonds : bond 0.03433 ( 1560) hydrogen bonds : angle 4.25694 ( 4584) ********************** 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 246 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 LYS cc_start: 0.3938 (mttt) cc_final: 0.3627 (mttm) REVERT: A 396 MET cc_start: 0.7985 (tpp) cc_final: 0.7603 (tpp) REVERT: A 552 TYR cc_start: 0.4594 (OUTLIER) cc_final: 0.2310 (p90) REVERT: A 647 MET cc_start: 0.8332 (mmp) cc_final: 0.7921 (mmt) REVERT: A 769 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7675 (tppt) REVERT: B 107 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.8132 (t80) REVERT: B 290 MET cc_start: 0.7734 (mmm) cc_final: 0.7443 (mmm) REVERT: B 519 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7313 (mmt) REVERT: B 883 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8036 (mm-30) REVERT: B 955 ILE cc_start: 0.5583 (mt) cc_final: 0.5289 (mm) REVERT: C 79 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7311 (m-80) REVERT: D 21 MET cc_start: 0.3561 (ttt) cc_final: 0.2647 (mtm) REVERT: D 385 PHE cc_start: 0.4194 (OUTLIER) cc_final: 0.3847 (m-10) REVERT: D 434 ASP cc_start: 0.4371 (OUTLIER) cc_final: 0.4021 (m-30) REVERT: D 552 TYR cc_start: 0.4089 (OUTLIER) cc_final: 0.2020 (p90) REVERT: D 578 MET cc_start: 0.2928 (mmp) cc_final: 0.2489 (mmm) REVERT: D 704 MET cc_start: -0.2111 (tpt) cc_final: -0.2930 (tpp) REVERT: D 1001 MET cc_start: -0.0011 (tmm) cc_final: -0.0229 (ppp) REVERT: E 616 MET cc_start: 0.7396 (mmm) cc_final: 0.6839 (mmm) REVERT: E 829 GLN cc_start: 0.7823 (pp30) cc_final: 0.7244 (tp40) REVERT: E 920 TYR cc_start: 0.7487 (t80) cc_final: 0.6858 (t80) REVERT: E 930 MET cc_start: 0.3632 (mtm) cc_final: 0.3157 (ptp) REVERT: E 994 LYS cc_start: 0.6931 (mttm) cc_final: 0.6668 (mptt) REVERT: F 100 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7898 (pp) REVERT: F 102 LEU cc_start: 0.7970 (mt) cc_final: 0.7467 (tp) outliers start: 37 outliers final: 22 residues processed: 240 average time/residue: 0.1979 time to fit residues: 79.5559 Evaluate side-chains 233 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 442 LEU Chi-restraints excluded: chain A residue 552 TYR 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 107 PHE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 519 MET 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 434 ASP Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 666 ASN Chi-restraints excluded: chain D residue 973 ASN Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 592 LEU 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 51 TYR Chi-restraints excluded: chain F residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 223 optimal weight: 1.9990 chunk 204 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 145 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 305 optimal weight: 0.4980 chunk 77 optimal weight: 9.9990 chunk 383 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 711 GLN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 GLN B 711 GLN E 230 ASN ** E 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.126124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.109951 restraints weight = 156155.887| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 3.79 r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.8243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 34350 Z= 0.115 Angle : 0.609 13.782 46282 Z= 0.313 Chirality : 0.042 0.300 4944 Planarity : 0.003 0.044 5890 Dihedral : 4.955 39.863 4426 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.84 % Favored : 92.14 % Rotamer: Outliers : 1.05 % Allowed : 14.81 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.14), residues: 3982 helix: 0.53 (0.11), residues: 2420 sheet: -2.91 (0.45), residues: 96 loop : -2.24 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 72 TYR 0.027 0.001 TYR B 888 PHE 0.030 0.001 PHE D 361 TRP 0.015 0.001 TRP D 757 HIS 0.007 0.001 HIS D 658 Details of bonding type rmsd covalent geometry : bond 0.00248 (34350) covalent geometry : angle 0.60898 (46282) hydrogen bonds : bond 0.03408 ( 1560) hydrogen bonds : angle 4.24429 ( 4584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6517.71 seconds wall clock time: 113 minutes 23.71 seconds (6803.71 seconds total)