Starting phenix.real_space_refine on Sun Jul 5 07:05:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gd2_51244/07_2026/9gd2_51244.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gd2_51244/07_2026/9gd2_51244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gd2_51244/07_2026/9gd2_51244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gd2_51244/07_2026/9gd2_51244.map" model { file = "/net/cci-nas-00/data/ceres_data/9gd2_51244/07_2026/9gd2_51244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gd2_51244/07_2026/9gd2_51244.cif" } resolution = 4.2 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= 0.032 sd= 1.319 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: 8 Type Number sf(0) Gaussians P 476 5.49 5 Mg 1 5.21 5 S 48 5.16 5 Be 1 3.05 5 C 15283 2.51 5 N 4916 2.21 5 O 5910 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26638 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 763 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 786 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "D" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 763 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "F" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "G" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 742 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "H" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 4828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 4828 Classifications: {'DNA': 237} Link IDs: {'rna3p': 236} Chain: "J" Number of atoms: 4889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 4889 Classifications: {'DNA': 237} Link IDs: {'rna3p': 236} Chain: "K" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 592 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "L" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 626 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "M" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "N" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "O" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 795 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "P" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "Q" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "R" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 719 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "S" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 122 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "T" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 196 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "W" Number of atoms: 5274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5274 Classifications: {'peptide': 641} Link IDs: {'PTRANS': 20, 'TRANS': 620} Chain breaks: 3 Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.44, per 1000 atoms: 0.17 Number of scatterers: 26638 At special positions: 0 Unit cell: (127.602, 134.274, 219.342, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 48 16.00 P 476 15.00 Mg 1 11.99 F 3 9.00 O 5910 8.00 N 4916 7.00 C 15283 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 646.3 milliseconds 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3974 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 24 sheets defined 69.9% alpha, 5.8% beta 237 base pairs and 470 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.570A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 115 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 77 removed outlier: 3.663A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 74 removed outlier: 4.341A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.751A pdb=" N THR D 93 " --> pdb=" O ARG D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.932A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.568A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.650A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 3.887A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.624A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 79 Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 132 Processing helix chain 'L' and resid 23 through 28 removed outlier: 3.711A pdb=" N GLN L 27 " --> pdb=" O ARG L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 76 removed outlier: 3.967A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP L 68 " --> pdb=" O ASN L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 97 Processing helix chain 'M' and resid 16 through 22 Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.239A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU M 65 " --> pdb=" O GLU M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 90 Processing helix chain 'M' and resid 90 through 97 Processing helix chain 'M' and resid 112 through 116 Processing helix chain 'N' and resid 34 through 46 Processing helix chain 'N' and resid 52 through 81 Processing helix chain 'N' and resid 87 through 99 removed outlier: 3.668A pdb=" N ARG N 96 " --> pdb=" O GLN N 92 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 121 Processing helix chain 'O' and resid 44 through 57 Processing helix chain 'O' and resid 63 through 77 removed outlier: 3.709A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 115 Processing helix chain 'O' and resid 120 through 131 Processing helix chain 'P' and resid 22 through 29 removed outlier: 3.767A pdb=" N GLN P 27 " --> pdb=" O ARG P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 41 Processing helix chain 'P' and resid 49 through 76 removed outlier: 3.608A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 94 Processing helix chain 'Q' and resid 34 through 46 Processing helix chain 'Q' and resid 52 through 81 Processing helix chain 'Q' and resid 87 through 99 Processing helix chain 'Q' and resid 100 through 121 Processing helix chain 'R' and resid 16 through 22 Processing helix chain 'R' and resid 26 through 37 removed outlier: 3.627A pdb=" N ARG R 35 " --> pdb=" O HIS R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 73 removed outlier: 3.939A pdb=" N VAL R 49 " --> pdb=" O ALA R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 90 Processing helix chain 'R' and resid 90 through 97 Processing helix chain 'W' and resid 205 through 211 removed outlier: 3.846A pdb=" N TYR W 211 " --> pdb=" O CYS W 207 " (cutoff:3.500A) Processing helix chain 'W' and resid 221 through 225 Processing helix chain 'W' and resid 230 through 234 Processing helix chain 'W' and resid 238 through 258 removed outlier: 4.166A pdb=" N LEU W 242 " --> pdb=" O GLY W 238 " (cutoff:3.500A) Processing helix chain 'W' and resid 263 through 285 Processing helix chain 'W' and resid 324 through 331 removed outlier: 4.227A pdb=" N LYS W 329 " --> pdb=" O THR W 325 " (cutoff:3.500A) Processing helix chain 'W' and resid 331 through 342 Processing helix chain 'W' and resid 347 through 351 Processing helix chain 'W' and resid 353 through 357 removed outlier: 4.210A pdb=" N SER W 356 " --> pdb=" O ASN W 353 " (cutoff:3.500A) Processing helix chain 'W' and resid 377 through 394 Processing helix chain 'W' and resid 406 through 421 Processing helix chain 'W' and resid 433 through 435 No H-bonds generated for 'chain 'W' and resid 433 through 435' Processing helix chain 'W' and resid 436 through 448 Processing helix chain 'W' and resid 459 through 470 Processing helix chain 'W' and resid 491 through 497 Processing helix chain 'W' and resid 498 through 504 Processing helix chain 'W' and resid 514 through 518 Processing helix chain 'W' and resid 523 through 532 Processing helix chain 'W' and resid 548 through 560 removed outlier: 3.576A pdb=" N LEU W 552 " --> pdb=" O ASN W 548 " (cutoff:3.500A) Processing helix chain 'W' and resid 576 through 591 Processing helix chain 'W' and resid 598 through 603 Processing helix chain 'W' and resid 619 through 631 Processing helix chain 'W' and resid 633 through 639 Processing helix chain 'W' and resid 650 through 661 Processing helix chain 'W' and resid 662 through 664 No H-bonds generated for 'chain 'W' and resid 662 through 664' Processing helix chain 'W' and resid 665 through 677 removed outlier: 4.088A pdb=" N GLU W 669 " --> pdb=" O PHE W 665 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU W 670 " --> pdb=" O ASP W 666 " (cutoff:3.500A) Processing helix chain 'W' and resid 678 through 681 Processing helix chain 'W' and resid 682 through 692 Processing helix chain 'W' and resid 694 through 711 Processing helix chain 'W' and resid 720 through 734 Processing helix chain 'W' and resid 746 through 759 Processing helix chain 'W' and resid 794 through 806 removed outlier: 3.969A pdb=" N ASP W 798 " --> pdb=" O ASN W 794 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA W 805 " --> pdb=" O ALA W 801 " (cutoff:3.500A) Processing helix chain 'W' and resid 825 through 844 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.800A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.132A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.748A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.702A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 83 through 84 removed outlier: 6.665A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'K' and resid 118 through 119 Processing sheet with id=AB4, first strand: chain 'M' and resid 42 through 43 removed outlier: 6.866A pdb=" N ARG M 42 " --> pdb=" O ILE N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'M' and resid 77 through 78 Processing sheet with id=AB6, first strand: chain 'M' and resid 100 through 101 Processing sheet with id=AB7, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AB8, first strand: chain 'Q' and resid 50 through 51 removed outlier: 6.618A pdb=" N GLY Q 50 " --> pdb=" O ILE R 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'Q' and resid 85 through 86 Processing sheet with id=AC1, first strand: chain 'W' and resid 179 through 180 Processing sheet with id=AC2, first strand: chain 'W' and resid 179 through 180 removed outlier: 3.534A pdb=" N THR W 226 " --> pdb=" O ILE W 215 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'W' and resid 287 through 297 removed outlier: 6.621A pdb=" N LEU W 308 " --> pdb=" O ILE W 291 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER W 293 " --> pdb=" O GLN W 306 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN W 306 " --> pdb=" O SER W 293 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ARG W 295 " --> pdb=" O GLN W 304 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLN W 304 " --> pdb=" O ARG W 295 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'W' and resid 453 through 456 removed outlier: 6.599A pdb=" N ILE W 454 " --> pdb=" O LEU W 489 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N MET W 510 " --> pdb=" O MET W 538 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE W 540 " --> pdb=" O MET W 510 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL W 512 " --> pdb=" O ILE W 540 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY W 397 " --> pdb=" O LEU W 539 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE W 398 " --> pdb=" O LEU W 595 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'W' and resid 472 through 473 removed outlier: 4.003A pdb=" N THR W 482 " --> pdb=" O THR W 473 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'W' and resid 609 through 616 removed outlier: 6.634A pdb=" N VAL W 786 " --> pdb=" O TYR W 817 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LEU W 819 " --> pdb=" O VAL W 786 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE W 788 " --> pdb=" O LEU W 819 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER W 821 " --> pdb=" O ILE W 788 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU W 715 " --> pdb=" O VAL W 787 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLN W 739 " --> pdb=" O LEU W 768 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N SER W 770 " --> pdb=" O GLN W 739 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU W 741 " --> pdb=" O SER W 770 " (cutoff:3.500A) 1085 hydrogen bonds defined for protein. 3198 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 608 hydrogen bonds 1216 hydrogen bond angles 0 basepair planarities 237 basepair parallelities 470 stacking parallelities Total time for adding SS restraints: 7.18 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6981 1.34 - 1.45: 7343 1.45 - 1.57: 12711 1.57 - 1.69: 949 1.69 - 1.81: 88 Bond restraints: 28072 Sorted by residual: bond pdb=" N LYS L 91 " pdb=" CA LYS L 91 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.45e+00 bond pdb=" N GLY W 178 " pdb=" CA GLY W 178 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.34e+00 bond pdb=" N ARG P 78 " pdb=" CA ARG P 78 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.27e-02 6.20e+03 6.32e+00 bond pdb=" N ARG L 92 " pdb=" CA ARG L 92 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.19e-02 7.06e+03 6.13e+00 bond pdb=" N THR L 96 " pdb=" CA THR L 96 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.12e+00 ... (remaining 28067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 39615 2.86 - 5.71: 318 5.71 - 8.57: 6 8.57 - 11.42: 4 11.42 - 14.28: 3 Bond angle restraints: 39946 Sorted by residual: angle pdb=" F1 BEF W1502 " pdb="BE BEF W1502 " pdb=" F2 BEF W1502 " ideal model delta sigma weight residual 119.91 105.63 14.28 3.00e+00 1.11e-01 2.26e+01 angle pdb=" F2 BEF W1502 " pdb="BE BEF W1502 " pdb=" F3 BEF W1502 " ideal model delta sigma weight residual 119.96 105.79 14.17 3.00e+00 1.11e-01 2.23e+01 angle pdb=" F1 BEF W1502 " pdb="BE BEF W1502 " pdb=" F3 BEF W1502 " ideal model delta sigma weight residual 120.12 106.25 13.87 3.00e+00 1.11e-01 2.14e+01 angle pdb=" O3' DG I 25 " pdb=" C3' DG I 25 " pdb=" C2' DG I 25 " ideal model delta sigma weight residual 109.40 120.25 -10.85 2.50e+00 1.60e-01 1.88e+01 angle pdb=" O5' DA J 39 " pdb=" C5' DA J 39 " pdb=" C4' DA J 39 " ideal model delta sigma weight residual 109.40 112.77 -3.37 8.00e-01 1.56e+00 1.77e+01 ... (remaining 39941 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 13143 35.91 - 71.82: 2539 71.82 - 107.73: 21 107.73 - 143.64: 3 143.64 - 179.55: 2 Dihedral angle restraints: 15708 sinusoidal: 9570 harmonic: 6138 Sorted by residual: dihedral pdb=" O1B ADP W1501 " pdb=" O3A ADP W1501 " pdb=" PB ADP W1501 " pdb=" PA ADP W1501 " ideal model delta sinusoidal sigma weight residual 300.00 120.44 179.55 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP W1501 " pdb=" O5' ADP W1501 " pdb=" PA ADP W1501 " pdb=" O2A ADP W1501 " ideal model delta sinusoidal sigma weight residual -60.00 101.33 -161.33 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" CA ASP W 180 " pdb=" C ASP W 180 " pdb=" N ILE W 181 " pdb=" CA ILE W 181 " ideal model delta harmonic sigma weight residual -180.00 -150.77 -29.23 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 15705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4211 0.096 - 0.192: 315 0.192 - 0.287: 3 0.287 - 0.383: 1 0.383 - 0.479: 2 Chirality restraints: 4532 Sorted by residual: chirality pdb=" C3' DG I -78 " pdb=" C4' DG I -78 " pdb=" O3' DG I -78 " pdb=" C2' DG I -78 " both_signs ideal model delta sigma weight residual False -2.73 -2.25 -0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" C3' DG I 25 " pdb=" C4' DG I 25 " pdb=" O3' DG I 25 " pdb=" C2' DG I 25 " both_signs ideal model delta sigma weight residual False -2.73 -2.26 -0.47 2.00e-01 2.50e+01 5.55e+00 chirality pdb=" C3' DG I -41 " pdb=" C4' DG I -41 " pdb=" O3' DG I -41 " pdb=" C2' DG I -41 " both_signs ideal model delta sigma weight residual False -2.73 -2.42 -0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 4529 not shown) Planarity restraints: 3427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR W 245 " 0.003 2.00e-02 2.50e+03 2.60e-02 1.35e+01 pdb=" CG TYR W 245 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR W 245 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR W 245 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR W 245 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR W 245 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR W 245 " 0.031 2.00e-02 2.50e+03 pdb=" OH TYR W 245 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR L 51 " -0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C TYR L 51 " 0.060 2.00e-02 2.50e+03 pdb=" O TYR L 51 " -0.022 2.00e-02 2.50e+03 pdb=" N GLU L 52 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA L 69 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C ALA L 69 " 0.059 2.00e-02 2.50e+03 pdb=" O ALA L 69 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL L 70 " -0.020 2.00e-02 2.50e+03 ... (remaining 3424 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1049 2.70 - 3.25: 26077 3.25 - 3.80: 51378 3.80 - 4.35: 63561 4.35 - 4.90: 93870 Nonbonded interactions: 235935 Sorted by model distance: nonbonded pdb=" OD1 ASP W 513 " pdb="MG MG W1503 " model vdw 2.148 2.170 nonbonded pdb=" OD2 ASP W 513 " pdb="MG MG W1503 " model vdw 2.156 2.170 nonbonded pdb=" OD1 ASN W 486 " pdb=" N VAL W 487 " model vdw 2.238 3.120 nonbonded pdb=" O LYS K 79 " pdb=" OG1 THR K 80 " model vdw 2.251 3.040 nonbonded pdb=" OE2 GLU O 50 " pdb=" NE ARG P 39 " model vdw 2.297 3.120 ... (remaining 235930 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = (chain 'O' and resid 41 through 133) } ncs_group { reference = (chain 'B' and resid 25 through 97) selection = (chain 'F' and resid 25 through 97) selection = (chain 'L' and resid 25 through 97) selection = (chain 'P' and resid 25 through 97) } ncs_group { reference = (chain 'C' and resid 16 through 107) selection = (chain 'G' and resid 16 through 107) selection = (chain 'M' and resid 16 through 107) selection = (chain 'R' and resid 16 through 107) } ncs_group { reference = (chain 'D' and resid 32 through 120) selection = (chain 'H' and resid 32 through 120) selection = (chain 'N' and resid 32 through 120) selection = (chain 'Q' and resid 32 through 120) } 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 group one per residue 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: 5.920 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.710 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 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 : 0.006 0.423 28073 Z= 0.378 Angle : 0.760 14.276 39946 Z= 0.514 Chirality : 0.051 0.479 4532 Planarity : 0.011 0.104 3427 Dihedral : 25.641 179.554 11734 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.94 % Allowed : 7.53 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.16), residues: 2060 helix: -0.05 (0.12), residues: 1347 sheet: -0.30 (0.53), residues: 98 loop : -0.88 (0.22), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.003 ARG W 807 TYR 0.042 0.005 TYR W 245 PHE 0.016 0.003 PHE M 25 TRP 0.028 0.005 TRP W 311 HIS 0.015 0.004 HIS W 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.28 (28072) covalent geometry : angle 0.75956 / 0.51 (39946) hydrogen bonds : bond 0.13584 / 9.27 ( 1691) hydrogen bonds : angle 5.92584 / 4.33 ( 4414) Misc. bond : bond 0.42299 / 22.26 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 243 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9548 (mm-30) cc_final: 0.9338 (mm-30) REVERT: B 63 GLU cc_start: 0.9303 (mt-10) cc_final: 0.9029 (mt-10) REVERT: B 84 MET cc_start: 0.9108 (tpp) cc_final: 0.8839 (tpp) REVERT: C 56 GLU cc_start: 0.9243 (pt0) cc_final: 0.8252 (pp20) REVERT: D 65 ASP cc_start: 0.9430 (t70) cc_final: 0.8678 (t70) REVERT: E 90 MET cc_start: 0.9496 (mmp) cc_final: 0.9080 (mmm) REVERT: E 94 GLU cc_start: 0.9445 (mm-30) cc_final: 0.9159 (mm-30) REVERT: E 97 GLU cc_start: 0.9470 (mt-10) cc_final: 0.9057 (mt-10) REVERT: E 120 MET cc_start: 0.9196 (mmm) cc_final: 0.8726 (mmm) REVERT: H 65 ASP cc_start: 0.9404 (t70) cc_final: 0.9099 (t0) REVERT: H 73 GLU cc_start: 0.9695 (mm-30) cc_final: 0.9354 (mm-30) REVERT: H 97 LEU cc_start: 0.9793 (mt) cc_final: 0.9557 (mt) REVERT: K 90 MET cc_start: 0.9164 (tmm) cc_final: 0.8962 (tmm) REVERT: L 44 LYS cc_start: 0.9679 (mmpt) cc_final: 0.9284 (mtmt) REVERT: M 112 GLN cc_start: 0.9600 (mm110) cc_final: 0.9388 (tm-30) REVERT: N 59 MET cc_start: 0.9820 (mmt) cc_final: 0.9521 (mmm) REVERT: N 68 GLU cc_start: 0.9669 (mt-10) cc_final: 0.9410 (mm-30) REVERT: O 97 GLU cc_start: 0.9544 (mm-30) cc_final: 0.9106 (mt-10) REVERT: O 130 ILE cc_start: 0.9635 (mm) cc_final: 0.9376 (tp) REVERT: P 53 GLU cc_start: 0.9637 (tp30) cc_final: 0.9436 (tt0) REVERT: Q 59 MET cc_start: 0.9888 (mmp) cc_final: 0.9646 (mmm) REVERT: Q 118 TYR cc_start: 0.9413 (t80) cc_final: 0.9209 (t80) REVERT: R 56 GLU cc_start: 0.9568 (tt0) cc_final: 0.9123 (tt0) REVERT: R 95 LYS cc_start: 0.9877 (pptt) cc_final: 0.9588 (pttp) REVERT: S 127 PHE cc_start: 0.8820 (t80) cc_final: 0.8423 (p90) REVERT: S 131 GLN cc_start: 0.9152 (mp-120) cc_final: 0.8853 (mm-40) REVERT: T 132 ASN cc_start: 0.9183 (t0) cc_final: 0.8780 (m-40) REVERT: W 237 ARG cc_start: 0.8845 (ttm170) cc_final: 0.8569 (tpt170) REVERT: W 403 MET cc_start: 0.9220 (mpp) cc_final: 0.8476 (mpp) REVERT: W 493 GLU cc_start: 0.9499 (OUTLIER) cc_final: 0.9083 (pp20) REVERT: W 510 MET cc_start: 0.9423 (mtt) cc_final: 0.9120 (mtt) REVERT: W 697 MET cc_start: 0.7734 (mtm) cc_final: 0.7416 (mtm) outliers start: 17 outliers final: 6 residues processed: 260 average time/residue: 0.1782 time to fit residues: 70.8163 Evaluate side-chains 138 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 216 optimal weight: 0.0000 chunk 98 optimal weight: 30.0000 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 50.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 31 HIS D 81 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 GLN W 224 HIS W 337 HIS ** W 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 424 GLN W 459 ASN W 574 ASN ** W 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 737 ASN W 810 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.041038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.025908 restraints weight = 297269.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.026156 restraints weight = 179908.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.026281 restraints weight = 132171.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.026281 restraints weight = 117786.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.026281 restraints weight = 117782.570| |-----------------------------------------------------------------------------| r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 28073 Z= 0.266 Angle : 0.843 13.083 39946 Z= 0.471 Chirality : 0.051 0.318 4532 Planarity : 0.007 0.206 3427 Dihedral : 30.002 168.264 7522 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.11 % Allowed : 3.49 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.17), residues: 2060 helix: 0.85 (0.13), residues: 1393 sheet: -0.62 (0.53), residues: 94 loop : -0.64 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 29 TYR 0.023 0.002 TYR R 50 PHE 0.018 0.002 PHE K 104 TRP 0.012 0.002 TRP W 417 HIS 0.015 0.002 HIS W 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.27 (28072) covalent geometry : angle 0.84266 / 0.47 (39946) hydrogen bonds : bond 0.07805 / 5.29 ( 1691) hydrogen bonds : angle 4.63888 / 3.39 ( 4414) Misc. bond : bond 0.01543 / 0.81 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 194 time to evaluate : 0.798 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 90 MET cc_start: 0.9475 (mmp) cc_final: 0.9254 (mmp) REVERT: A 119 ILE cc_start: 0.9652 (pt) cc_final: 0.9226 (pt) REVERT: A 120 MET cc_start: 0.9229 (mmm) cc_final: 0.8741 (mmm) REVERT: B 67 ARG cc_start: 0.9447 (ttp-110) cc_final: 0.9209 (ttp-110) REVERT: B 84 MET cc_start: 0.9062 (tpp) cc_final: 0.8826 (tpp) REVERT: C 56 GLU cc_start: 0.9185 (pt0) cc_final: 0.8277 (pp20) REVERT: C 90 ASP cc_start: 0.8892 (t0) cc_final: 0.8541 (t70) REVERT: D 65 ASP cc_start: 0.9210 (t70) cc_final: 0.8569 (t0) REVERT: D 110 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8887 (tm-30) REVERT: E 90 MET cc_start: 0.9390 (mmp) cc_final: 0.9081 (mmp) REVERT: E 97 GLU cc_start: 0.9346 (mt-10) cc_final: 0.8907 (mt-10) REVERT: F 63 GLU cc_start: 0.9326 (pt0) cc_final: 0.9086 (pp20) REVERT: H 56 MET cc_start: 0.9488 (mmm) cc_final: 0.9249 (tpp) REVERT: H 65 ASP cc_start: 0.9343 (t70) cc_final: 0.9129 (t0) REVERT: K 106 ASP cc_start: 0.9386 (m-30) cc_final: 0.9096 (m-30) REVERT: L 44 LYS cc_start: 0.9659 (mmpt) cc_final: 0.9411 (pttt) REVERT: L 84 MET cc_start: 0.9222 (tpp) cc_final: 0.8823 (tpp) REVERT: N 59 MET cc_start: 0.9758 (mmt) cc_final: 0.9446 (mmm) REVERT: N 69 ARG cc_start: 0.9537 (mtp180) cc_final: 0.9271 (mtp180) REVERT: N 73 GLU cc_start: 0.9662 (mm-30) cc_final: 0.9449 (mm-30) REVERT: O 97 GLU cc_start: 0.9298 (mm-30) cc_final: 0.9021 (mt-10) REVERT: O 106 ASP cc_start: 0.9459 (m-30) cc_final: 0.9059 (m-30) REVERT: O 130 ILE cc_start: 0.9740 (mm) cc_final: 0.9466 (tp) REVERT: P 68 ASP cc_start: 0.9597 (m-30) cc_final: 0.9333 (m-30) REVERT: R 56 GLU cc_start: 0.9629 (tt0) cc_final: 0.9222 (tt0) REVERT: S 127 PHE cc_start: 0.8825 (t80) cc_final: 0.8410 (p90) REVERT: T 132 ASN cc_start: 0.9226 (t0) cc_final: 0.8633 (m-40) REVERT: W 237 ARG cc_start: 0.8909 (ttm170) cc_final: 0.8614 (tpt170) REVERT: W 387 MET cc_start: 0.9362 (mtm) cc_final: 0.9142 (mtt) REVERT: W 403 MET cc_start: 0.9178 (mpp) cc_final: 0.8802 (mtm) REVERT: W 483 MET cc_start: 0.9332 (mmp) cc_final: 0.9072 (mmp) REVERT: W 720 MET cc_start: 0.9112 (tpt) cc_final: 0.8897 (tpp) outliers start: 2 outliers final: 0 residues processed: 194 average time/residue: 0.1717 time to fit residues: 52.8671 Evaluate side-chains 125 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 33 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 chunk 192 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 233 optimal weight: 30.0000 chunk 160 optimal weight: 7.9990 chunk 220 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 214 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 ASN ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 385 ASN W 520 ASN W 530 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.041620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.026390 restraints weight = 291555.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.026528 restraints weight = 174518.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.026669 restraints weight = 129619.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.026669 restraints weight = 114980.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.026669 restraints weight = 114980.090| |-----------------------------------------------------------------------------| r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28073 Z= 0.172 Angle : 0.674 10.034 39946 Z= 0.395 Chirality : 0.048 0.253 4532 Planarity : 0.005 0.072 3427 Dihedral : 30.042 156.747 7522 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.17 % Allowed : 3.10 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.18), residues: 2060 helix: 1.29 (0.14), residues: 1390 sheet: -0.63 (0.52), residues: 94 loop : -0.58 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG W 341 TYR 0.036 0.002 TYR H 80 PHE 0.028 0.002 PHE M 25 TRP 0.010 0.001 TRP W 507 HIS 0.010 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.17 (28072) covalent geometry : angle 0.67421 / 0.40 (39946) hydrogen bonds : bond 0.05559 / 3.71 ( 1691) hydrogen bonds : angle 4.20974 / 3.09 ( 4414) Misc. bond : bond 0.00112 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 191 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8777 (pm20) cc_final: 0.8518 (pm20) REVERT: A 120 MET cc_start: 0.9184 (mmm) cc_final: 0.8725 (mmm) REVERT: B 67 ARG cc_start: 0.9438 (ttp-110) cc_final: 0.9089 (ttp-110) REVERT: C 56 GLU cc_start: 0.9116 (pt0) cc_final: 0.8119 (pp20) REVERT: C 73 ASN cc_start: 0.9045 (t0) cc_final: 0.8680 (t0) REVERT: C 90 ASP cc_start: 0.8832 (t0) cc_final: 0.8485 (t70) REVERT: D 65 ASP cc_start: 0.9158 (t70) cc_final: 0.8493 (t0) REVERT: E 90 MET cc_start: 0.9307 (mmp) cc_final: 0.8974 (mmp) REVERT: E 94 GLU cc_start: 0.9303 (mm-30) cc_final: 0.8892 (mm-30) REVERT: E 97 GLU cc_start: 0.9314 (mt-10) cc_final: 0.8869 (mt-10) REVERT: E 120 MET cc_start: 0.9121 (mmp) cc_final: 0.8444 (mmm) REVERT: F 58 LEU cc_start: 0.9744 (tp) cc_final: 0.9493 (tt) REVERT: F 84 MET cc_start: 0.8932 (tpp) cc_final: 0.8688 (tpp) REVERT: H 73 GLU cc_start: 0.9468 (mm-30) cc_final: 0.9179 (mm-30) REVERT: K 106 ASP cc_start: 0.9273 (m-30) cc_final: 0.9049 (m-30) REVERT: L 84 MET cc_start: 0.9141 (tpp) cc_final: 0.8722 (tpp) REVERT: M 61 GLU cc_start: 0.9452 (tm-30) cc_final: 0.9037 (tm-30) REVERT: N 34 TYR cc_start: 0.9696 (m-80) cc_final: 0.8994 (m-80) REVERT: N 59 MET cc_start: 0.9734 (mmt) cc_final: 0.9464 (mmm) REVERT: N 67 PHE cc_start: 0.9689 (t80) cc_final: 0.9364 (t80) REVERT: O 97 GLU cc_start: 0.9259 (mm-30) cc_final: 0.8998 (mt-10) REVERT: O 130 ILE cc_start: 0.9748 (mm) cc_final: 0.9410 (tp) REVERT: P 25 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.8309 (m110) REVERT: Q 59 MET cc_start: 0.9881 (mmp) cc_final: 0.9651 (mmm) REVERT: Q 73 GLU cc_start: 0.9697 (mm-30) cc_final: 0.9469 (mm-30) REVERT: Q 97 LEU cc_start: 0.9788 (tt) cc_final: 0.9447 (tt) REVERT: R 56 GLU cc_start: 0.9583 (tt0) cc_final: 0.9202 (tt0) REVERT: S 127 PHE cc_start: 0.8777 (t80) cc_final: 0.8422 (p90) REVERT: T 132 ASN cc_start: 0.9193 (t0) cc_final: 0.8593 (m-40) REVERT: W 237 ARG cc_start: 0.8933 (ttm170) cc_final: 0.8636 (tpt170) REVERT: W 387 MET cc_start: 0.9364 (mtm) cc_final: 0.9143 (mtt) REVERT: W 403 MET cc_start: 0.9110 (mpp) cc_final: 0.8586 (mtm) REVERT: W 483 MET cc_start: 0.9283 (mmp) cc_final: 0.9028 (mmp) REVERT: W 720 MET cc_start: 0.9109 (tpt) cc_final: 0.8896 (tpp) outliers start: 3 outliers final: 1 residues processed: 192 average time/residue: 0.1787 time to fit residues: 54.5041 Evaluate side-chains 127 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 163 optimal weight: 1.9990 chunk 227 optimal weight: 10.0000 chunk 104 optimal weight: 50.0000 chunk 120 optimal weight: 10.0000 chunk 196 optimal weight: 30.0000 chunk 246 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS K 113 HIS O 68 GLN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.041813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.026553 restraints weight = 290098.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.026718 restraints weight = 169180.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.026873 restraints weight = 126236.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.027171 restraints weight = 111762.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.027354 restraints weight = 101901.321| |-----------------------------------------------------------------------------| r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 28073 Z= 0.157 Angle : 0.647 9.176 39946 Z= 0.377 Chirality : 0.045 0.300 4532 Planarity : 0.004 0.066 3427 Dihedral : 29.881 150.188 7522 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.18), residues: 2060 helix: 1.35 (0.13), residues: 1396 sheet: -0.31 (0.54), residues: 88 loop : -0.69 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 23 TYR 0.027 0.002 TYR R 39 PHE 0.018 0.001 PHE W 789 TRP 0.009 0.001 TRP W 311 HIS 0.008 0.001 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.16 (28072) covalent geometry : angle 0.64687 / 0.38 (39946) hydrogen bonds : bond 0.04908 / 3.28 ( 1691) hydrogen bonds : angle 4.03062 / 2.95 ( 4414) Misc. bond : bond 0.00246 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.780 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 59 GLU cc_start: 0.8780 (pm20) cc_final: 0.8424 (pm20) REVERT: A 119 ILE cc_start: 0.9651 (pt) cc_final: 0.9276 (pt) REVERT: A 120 MET cc_start: 0.9213 (mmm) cc_final: 0.8736 (mmm) REVERT: B 67 ARG cc_start: 0.9423 (ttp-110) cc_final: 0.9210 (ttp-110) REVERT: C 56 GLU cc_start: 0.8971 (pt0) cc_final: 0.8167 (pp20) REVERT: C 73 ASN cc_start: 0.9105 (t0) cc_final: 0.8726 (t0) REVERT: C 90 ASP cc_start: 0.8766 (t0) cc_final: 0.8409 (t70) REVERT: D 65 ASP cc_start: 0.9167 (t70) cc_final: 0.8505 (t0) REVERT: E 90 MET cc_start: 0.9273 (mmp) cc_final: 0.8897 (mmp) REVERT: E 94 GLU cc_start: 0.9291 (mm-30) cc_final: 0.8871 (mm-30) REVERT: E 97 GLU cc_start: 0.9296 (mt-10) cc_final: 0.8853 (mt-10) REVERT: E 120 MET cc_start: 0.9267 (mmp) cc_final: 0.8515 (mmm) REVERT: F 58 LEU cc_start: 0.9741 (tp) cc_final: 0.9515 (tt) REVERT: F 84 MET cc_start: 0.8942 (tpp) cc_final: 0.8659 (tpp) REVERT: H 65 ASP cc_start: 0.9466 (t70) cc_final: 0.9137 (t0) REVERT: H 73 GLU cc_start: 0.9443 (mm-30) cc_final: 0.9176 (mm-30) REVERT: L 84 MET cc_start: 0.9126 (tpp) cc_final: 0.8674 (tpp) REVERT: M 61 GLU cc_start: 0.9428 (tm-30) cc_final: 0.9146 (tp30) REVERT: N 34 TYR cc_start: 0.9706 (m-80) cc_final: 0.9009 (m-80) REVERT: N 59 MET cc_start: 0.9768 (mmt) cc_final: 0.9472 (mmm) REVERT: N 67 PHE cc_start: 0.9682 (t80) cc_final: 0.9362 (t80) REVERT: O 97 GLU cc_start: 0.9296 (mm-30) cc_final: 0.8984 (mt-10) REVERT: O 106 ASP cc_start: 0.9379 (m-30) cc_final: 0.9106 (m-30) REVERT: P 68 ASP cc_start: 0.9506 (m-30) cc_final: 0.9239 (m-30) REVERT: P 92 ARG cc_start: 0.9402 (tmt-80) cc_final: 0.9103 (ttp80) REVERT: R 56 GLU cc_start: 0.9545 (tt0) cc_final: 0.9167 (tt0) REVERT: S 127 PHE cc_start: 0.8770 (t80) cc_final: 0.8424 (p90) REVERT: T 132 ASN cc_start: 0.9155 (t0) cc_final: 0.8537 (m110) REVERT: W 237 ARG cc_start: 0.8951 (ttm170) cc_final: 0.8644 (tpt170) REVERT: W 387 MET cc_start: 0.9354 (mtm) cc_final: 0.9131 (mtt) REVERT: W 403 MET cc_start: 0.9179 (mpp) cc_final: 0.8618 (mpp) REVERT: W 483 MET cc_start: 0.9255 (mmp) cc_final: 0.9042 (mmp) REVERT: W 697 MET cc_start: 0.9446 (mpp) cc_final: 0.9232 (mpp) REVERT: W 781 MET cc_start: 0.9196 (mmp) cc_final: 0.8964 (mmp) REVERT: W 802 MET cc_start: 0.9646 (ptp) cc_final: 0.9323 (ppp) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1674 time to fit residues: 47.2682 Evaluate side-chains 126 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 195 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 11 optimal weight: 0.3980 chunk 180 optimal weight: 6.9990 chunk 232 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 187 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 70 optimal weight: 50.0000 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** W 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 653 ASN ** W 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.041425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.025757 restraints weight = 293384.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.026357 restraints weight = 175621.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.026491 restraints weight = 132873.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.026491 restraints weight = 117598.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.026491 restraints weight = 117598.349| |-----------------------------------------------------------------------------| r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28073 Z= 0.181 Angle : 0.638 8.795 39946 Z= 0.372 Chirality : 0.044 0.244 4532 Planarity : 0.004 0.069 3427 Dihedral : 29.822 140.190 7522 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.06 % Allowed : 2.05 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.18), residues: 2060 helix: 1.44 (0.13), residues: 1397 sheet: -0.48 (0.54), residues: 93 loop : -0.73 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 69 TYR 0.018 0.001 TYR R 39 PHE 0.014 0.001 PHE O 104 TRP 0.010 0.001 TRP W 311 HIS 0.008 0.001 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.18 (28072) covalent geometry : angle 0.63789 / 0.37 (39946) hydrogen bonds : bond 0.05302 / 3.59 ( 1691) hydrogen bonds : angle 4.01402 / 2.94 ( 4414) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ILE cc_start: 0.9647 (pt) cc_final: 0.9232 (pt) REVERT: A 120 MET cc_start: 0.9189 (mmm) cc_final: 0.8728 (mmm) REVERT: B 67 ARG cc_start: 0.9428 (ttp-110) cc_final: 0.9226 (ttp-110) REVERT: B 84 MET cc_start: 0.9027 (tpp) cc_final: 0.8804 (tpp) REVERT: C 56 GLU cc_start: 0.9002 (pt0) cc_final: 0.8203 (pp20) REVERT: C 73 ASN cc_start: 0.9182 (t0) cc_final: 0.8781 (t0) REVERT: C 90 ASP cc_start: 0.8820 (t0) cc_final: 0.8465 (t70) REVERT: D 65 ASP cc_start: 0.9162 (t70) cc_final: 0.8561 (t0) REVERT: E 90 MET cc_start: 0.9269 (mmp) cc_final: 0.8908 (mmp) REVERT: E 94 GLU cc_start: 0.9282 (mm-30) cc_final: 0.8905 (mm-30) REVERT: E 97 GLU cc_start: 0.9313 (mt-10) cc_final: 0.8848 (mt-10) REVERT: E 120 MET cc_start: 0.9303 (mmp) cc_final: 0.8484 (mmm) REVERT: F 58 LEU cc_start: 0.9732 (tp) cc_final: 0.9508 (tt) REVERT: F 84 MET cc_start: 0.8969 (tpp) cc_final: 0.8630 (tpp) REVERT: H 56 MET cc_start: 0.9430 (tpt) cc_final: 0.9083 (tpp) REVERT: H 65 ASP cc_start: 0.9453 (t70) cc_final: 0.9124 (t0) REVERT: K 97 GLU cc_start: 0.9471 (mt-10) cc_final: 0.9023 (mm-30) REVERT: L 84 MET cc_start: 0.9100 (tpp) cc_final: 0.8640 (tpp) REVERT: M 61 GLU cc_start: 0.9415 (tm-30) cc_final: 0.9149 (tp30) REVERT: N 34 TYR cc_start: 0.9706 (m-80) cc_final: 0.8965 (m-10) REVERT: N 59 MET cc_start: 0.9753 (mmt) cc_final: 0.9451 (mmm) REVERT: N 65 ASP cc_start: 0.9578 (t70) cc_final: 0.9193 (t0) REVERT: N 69 ARG cc_start: 0.9433 (mtp180) cc_final: 0.8785 (ttm110) REVERT: N 73 GLU cc_start: 0.9023 (mp0) cc_final: 0.8657 (mp0) REVERT: O 106 ASP cc_start: 0.9387 (m-30) cc_final: 0.9089 (m-30) REVERT: Q 59 MET cc_start: 0.9878 (mmp) cc_final: 0.9649 (mmm) REVERT: Q 73 GLU cc_start: 0.9754 (mm-30) cc_final: 0.9251 (tp30) REVERT: Q 97 LEU cc_start: 0.9790 (tt) cc_final: 0.9580 (tt) REVERT: R 56 GLU cc_start: 0.9552 (tt0) cc_final: 0.9160 (tt0) REVERT: S 127 PHE cc_start: 0.8845 (t80) cc_final: 0.8428 (p90) REVERT: T 132 ASN cc_start: 0.9157 (t0) cc_final: 0.8533 (m-40) REVERT: T 140 ASP cc_start: 0.8917 (t0) cc_final: 0.8423 (p0) REVERT: W 237 ARG cc_start: 0.8949 (ttm170) cc_final: 0.8687 (tpt170) REVERT: W 387 MET cc_start: 0.9414 (mtm) cc_final: 0.9182 (mtt) REVERT: W 403 MET cc_start: 0.9163 (mpp) cc_final: 0.8308 (mpp) REVERT: W 483 MET cc_start: 0.9269 (mmp) cc_final: 0.9068 (mmp) REVERT: W 781 MET cc_start: 0.9218 (mmp) cc_final: 0.8790 (mmp) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.1651 time to fit residues: 45.4224 Evaluate side-chains 125 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 33 optimal weight: 0.6980 chunk 86 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 239 optimal weight: 6.9990 chunk 106 optimal weight: 30.0000 chunk 5 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 247 optimal weight: 0.0870 chunk 230 optimal weight: 20.0000 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 GLN W 210 ASN ** W 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.042253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.026713 restraints weight = 285800.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.026984 restraints weight = 173751.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.027123 restraints weight = 127087.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.027411 restraints weight = 114283.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.027675 restraints weight = 103377.946| |-----------------------------------------------------------------------------| r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 28073 Z= 0.134 Angle : 0.603 7.262 39946 Z= 0.353 Chirality : 0.043 0.227 4532 Planarity : 0.004 0.065 3427 Dihedral : 29.650 137.539 7522 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.06 % Allowed : 1.55 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.18), residues: 2060 helix: 1.54 (0.14), residues: 1397 sheet: -0.43 (0.55), residues: 93 loop : -0.69 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 804 TYR 0.033 0.001 TYR W 230 PHE 0.019 0.001 PHE W 379 TRP 0.010 0.001 TRP W 311 HIS 0.006 0.001 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.13 (28072) covalent geometry : angle 0.60278 / 0.35 (39946) hydrogen bonds : bond 0.04007 / 2.69 ( 1691) hydrogen bonds : angle 3.84349 / 2.81 ( 4414) Misc. bond : bond 0.00060 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.560 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 59 GLU cc_start: 0.8304 (pm20) cc_final: 0.8092 (pm20) REVERT: A 119 ILE cc_start: 0.9632 (pt) cc_final: 0.9253 (pt) REVERT: A 120 MET cc_start: 0.9209 (mmm) cc_final: 0.8704 (mmm) REVERT: C 56 GLU cc_start: 0.8930 (pt0) cc_final: 0.8094 (pp20) REVERT: C 73 ASN cc_start: 0.9157 (t0) cc_final: 0.8742 (t0) REVERT: C 90 ASP cc_start: 0.8711 (t0) cc_final: 0.8361 (t70) REVERT: D 65 ASP cc_start: 0.9153 (t70) cc_final: 0.8514 (t0) REVERT: E 90 MET cc_start: 0.9257 (mmp) cc_final: 0.8894 (mmp) REVERT: E 94 GLU cc_start: 0.9291 (mm-30) cc_final: 0.8864 (mm-30) REVERT: E 97 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8809 (mt-10) REVERT: E 120 MET cc_start: 0.9296 (mmp) cc_final: 0.8499 (mmm) REVERT: F 84 MET cc_start: 0.8950 (tpp) cc_final: 0.8608 (tpp) REVERT: H 65 ASP cc_start: 0.9443 (t70) cc_final: 0.9116 (t0) REVERT: H 73 GLU cc_start: 0.9424 (mm-30) cc_final: 0.9180 (mm-30) REVERT: K 97 GLU cc_start: 0.9448 (mt-10) cc_final: 0.9000 (mm-30) REVERT: K 106 ASP cc_start: 0.9468 (m-30) cc_final: 0.9267 (m-30) REVERT: L 84 MET cc_start: 0.9049 (tpp) cc_final: 0.8723 (tpp) REVERT: M 61 GLU cc_start: 0.9425 (tm-30) cc_final: 0.9155 (tp30) REVERT: M 84 GLN cc_start: 0.9486 (tp-100) cc_final: 0.9211 (tp40) REVERT: N 34 TYR cc_start: 0.9710 (m-80) cc_final: 0.9342 (m-10) REVERT: N 59 MET cc_start: 0.9758 (mmt) cc_final: 0.9453 (mmm) REVERT: N 65 ASP cc_start: 0.9555 (t70) cc_final: 0.9145 (t0) REVERT: N 69 ARG cc_start: 0.9442 (mtp180) cc_final: 0.8978 (ttm110) REVERT: O 94 GLU cc_start: 0.9510 (mm-30) cc_final: 0.8878 (tp30) REVERT: O 106 ASP cc_start: 0.9342 (m-30) cc_final: 0.8623 (m-30) REVERT: Q 77 LEU cc_start: 0.9919 (tt) cc_final: 0.9709 (pp) REVERT: R 56 GLU cc_start: 0.9513 (tt0) cc_final: 0.9117 (tt0) REVERT: S 127 PHE cc_start: 0.8820 (t80) cc_final: 0.8433 (p90) REVERT: T 132 ASN cc_start: 0.9171 (t0) cc_final: 0.8569 (m110) REVERT: T 140 ASP cc_start: 0.8926 (t0) cc_final: 0.8453 (p0) REVERT: W 387 MET cc_start: 0.9385 (mtm) cc_final: 0.9122 (mtt) REVERT: W 403 MET cc_start: 0.8966 (mpp) cc_final: 0.8402 (mpp) REVERT: W 483 MET cc_start: 0.9210 (mmp) cc_final: 0.8991 (mmp) REVERT: W 697 MET cc_start: 0.9349 (mpp) cc_final: 0.9121 (mpp) REVERT: W 781 MET cc_start: 0.9224 (mmp) cc_final: 0.8871 (mmp) REVERT: W 802 MET cc_start: 0.9734 (ptp) cc_final: 0.9369 (ppp) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.1507 time to fit residues: 46.1951 Evaluate side-chains 139 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 120 optimal weight: 8.9990 chunk 190 optimal weight: 20.0000 chunk 80 optimal weight: 50.0000 chunk 212 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 72 optimal weight: 30.0000 chunk 166 optimal weight: 20.0000 chunk 192 optimal weight: 30.0000 chunk 221 optimal weight: 6.9990 chunk 189 optimal weight: 30.0000 chunk 63 optimal weight: 0.9980 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** W 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.041236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.026005 restraints weight = 293195.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.026224 restraints weight = 181272.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.026376 restraints weight = 134153.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.026701 restraints weight = 119419.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.026908 restraints weight = 108770.984| |-----------------------------------------------------------------------------| r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 28073 Z= 0.203 Angle : 0.644 8.407 39946 Z= 0.374 Chirality : 0.042 0.240 4532 Planarity : 0.004 0.063 3427 Dihedral : 29.611 129.744 7522 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.18), residues: 2060 helix: 1.55 (0.14), residues: 1397 sheet: -0.43 (0.54), residues: 93 loop : -0.70 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG W 241 TYR 0.020 0.001 TYR P 88 PHE 0.019 0.001 PHE P 61 TRP 0.008 0.001 TRP W 217 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.20 (28072) covalent geometry : angle 0.64393 / 0.37 (39946) hydrogen bonds : bond 0.05363 / 3.63 ( 1691) hydrogen bonds : angle 4.00758 / 2.94 ( 4414) Misc. bond : bond 0.00077 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.053 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 119 ILE cc_start: 0.9621 (pt) cc_final: 0.9236 (pt) REVERT: A 120 MET cc_start: 0.9229 (mmm) cc_final: 0.8761 (mmm) REVERT: C 56 GLU cc_start: 0.9014 (pt0) cc_final: 0.8240 (pp20) REVERT: C 73 ASN cc_start: 0.9250 (t0) cc_final: 0.8857 (t0) REVERT: C 90 ASP cc_start: 0.8573 (t0) cc_final: 0.8248 (t70) REVERT: D 65 ASP cc_start: 0.9171 (t70) cc_final: 0.8578 (t0) REVERT: D 68 GLU cc_start: 0.9244 (pp20) cc_final: 0.9038 (pp20) REVERT: E 90 MET cc_start: 0.9279 (mmp) cc_final: 0.8928 (mmp) REVERT: E 94 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8890 (mm-30) REVERT: E 97 GLU cc_start: 0.9295 (mt-10) cc_final: 0.8857 (mt-10) REVERT: E 120 MET cc_start: 0.9349 (mmp) cc_final: 0.8655 (mmm) REVERT: F 84 MET cc_start: 0.8849 (tpp) cc_final: 0.8587 (tpp) REVERT: H 56 MET cc_start: 0.9480 (tpt) cc_final: 0.9159 (tpp) REVERT: H 65 ASP cc_start: 0.9453 (t70) cc_final: 0.9137 (t0) REVERT: K 97 GLU cc_start: 0.9472 (mt-10) cc_final: 0.9024 (mm-30) REVERT: K 106 ASP cc_start: 0.9483 (m-30) cc_final: 0.9276 (m-30) REVERT: L 84 MET cc_start: 0.9100 (tpp) cc_final: 0.8639 (tpp) REVERT: M 61 GLU cc_start: 0.9420 (tm-30) cc_final: 0.9172 (tp30) REVERT: M 84 GLN cc_start: 0.9494 (tp-100) cc_final: 0.9160 (tp-100) REVERT: N 34 TYR cc_start: 0.9720 (m-80) cc_final: 0.8966 (m-10) REVERT: N 69 ARG cc_start: 0.9443 (mtp180) cc_final: 0.8985 (ttm110) REVERT: N 73 GLU cc_start: 0.9119 (mp0) cc_final: 0.8761 (mp0) REVERT: O 94 GLU cc_start: 0.9460 (mm-30) cc_final: 0.8988 (tp30) REVERT: O 106 ASP cc_start: 0.9106 (m-30) cc_final: 0.8663 (m-30) REVERT: O 120 MET cc_start: 0.9107 (mmm) cc_final: 0.8672 (mmm) REVERT: Q 59 MET cc_start: 0.9875 (mmp) cc_final: 0.9653 (mmm) REVERT: Q 73 GLU cc_start: 0.9676 (mm-30) cc_final: 0.9446 (tp30) REVERT: R 56 GLU cc_start: 0.9527 (tt0) cc_final: 0.9221 (tt0) REVERT: S 127 PHE cc_start: 0.8798 (t80) cc_final: 0.8389 (p90) REVERT: T 132 ASN cc_start: 0.9128 (t0) cc_final: 0.8553 (m110) REVERT: T 140 ASP cc_start: 0.8859 (t0) cc_final: 0.8391 (p0) REVERT: W 387 MET cc_start: 0.9414 (mtm) cc_final: 0.9183 (mtt) REVERT: W 403 MET cc_start: 0.9021 (mpp) cc_final: 0.8462 (mpp) REVERT: W 483 MET cc_start: 0.9265 (mmp) cc_final: 0.9048 (mmp) REVERT: W 697 MET cc_start: 0.9350 (mpp) cc_final: 0.9124 (mpp) REVERT: W 781 MET cc_start: 0.9205 (mmp) cc_final: 0.8839 (mmp) REVERT: W 802 MET cc_start: 0.9759 (ptp) cc_final: 0.9424 (ppp) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1562 time to fit residues: 43.0537 Evaluate side-chains 123 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 39 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 70 optimal weight: 50.0000 chunk 112 optimal weight: 30.0000 chunk 64 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 236 optimal weight: 0.0770 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 92 GLN ** W 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 813 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.041931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.026632 restraints weight = 283987.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.027105 restraints weight = 166459.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.027259 restraints weight = 124958.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.027262 restraints weight = 110771.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.027262 restraints weight = 110748.017| |-----------------------------------------------------------------------------| r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 28073 Z= 0.136 Angle : 0.606 8.775 39946 Z= 0.355 Chirality : 0.042 0.233 4532 Planarity : 0.004 0.062 3427 Dihedral : 29.514 128.062 7522 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.18), residues: 2060 helix: 1.59 (0.14), residues: 1398 sheet: -0.34 (0.55), residues: 93 loop : -0.71 (0.23), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG W 241 TYR 0.015 0.001 TYR W 230 PHE 0.020 0.001 PHE W 379 TRP 0.010 0.001 TRP W 311 HIS 0.006 0.001 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.14 (28072) covalent geometry : angle 0.60575 / 0.35 (39946) hydrogen bonds : bond 0.03863 / 2.60 ( 1691) hydrogen bonds : angle 3.87712 / 2.84 ( 4414) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.812 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 59 GLU cc_start: 0.8510 (pm20) cc_final: 0.8303 (pm20) REVERT: A 119 ILE cc_start: 0.9603 (pt) cc_final: 0.9279 (pt) REVERT: A 120 MET cc_start: 0.9204 (mmm) cc_final: 0.8769 (mmm) REVERT: C 56 GLU cc_start: 0.8926 (pt0) cc_final: 0.8120 (pp20) REVERT: C 73 ASN cc_start: 0.9195 (t0) cc_final: 0.8789 (t0) REVERT: C 90 ASP cc_start: 0.8577 (t0) cc_final: 0.8261 (t70) REVERT: D 65 ASP cc_start: 0.9158 (t70) cc_final: 0.8555 (t0) REVERT: E 90 MET cc_start: 0.9274 (mmp) cc_final: 0.8901 (mmp) REVERT: E 94 GLU cc_start: 0.9284 (mm-30) cc_final: 0.8855 (mm-30) REVERT: E 97 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8808 (mt-10) REVERT: E 120 MET cc_start: 0.9314 (mmp) cc_final: 0.8608 (mmm) REVERT: H 42 LEU cc_start: 0.9815 (tt) cc_final: 0.9508 (pp) REVERT: H 56 MET cc_start: 0.9417 (tpt) cc_final: 0.9078 (tpp) REVERT: H 65 ASP cc_start: 0.9441 (t70) cc_final: 0.9120 (t0) REVERT: H 73 GLU cc_start: 0.9371 (mm-30) cc_final: 0.9162 (mm-30) REVERT: K 97 GLU cc_start: 0.9447 (mt-10) cc_final: 0.8998 (mm-30) REVERT: L 84 MET cc_start: 0.9045 (tpp) cc_final: 0.8693 (tpp) REVERT: M 61 GLU cc_start: 0.9432 (tm-30) cc_final: 0.9193 (tp30) REVERT: M 84 GLN cc_start: 0.9494 (tp-100) cc_final: 0.9212 (tp40) REVERT: N 34 TYR cc_start: 0.9710 (m-80) cc_final: 0.9004 (m-10) REVERT: N 59 MET cc_start: 0.9724 (mmp) cc_final: 0.9463 (mmm) REVERT: N 69 ARG cc_start: 0.9463 (mtp180) cc_final: 0.8880 (ttm110) REVERT: N 73 GLU cc_start: 0.9039 (mp0) cc_final: 0.8643 (mp0) REVERT: O 94 GLU cc_start: 0.9473 (mm-30) cc_final: 0.8926 (tp30) REVERT: O 97 GLU cc_start: 0.9478 (pp20) cc_final: 0.9179 (pp20) REVERT: O 106 ASP cc_start: 0.9361 (m-30) cc_final: 0.9047 (m-30) REVERT: O 120 MET cc_start: 0.9019 (mmm) cc_final: 0.8585 (mmm) REVERT: Q 77 LEU cc_start: 0.9909 (tt) cc_final: 0.9703 (pp) REVERT: R 56 GLU cc_start: 0.9556 (tt0) cc_final: 0.9188 (tt0) REVERT: S 127 PHE cc_start: 0.8905 (t80) cc_final: 0.8460 (p90) REVERT: T 132 ASN cc_start: 0.9142 (t0) cc_final: 0.8577 (m110) REVERT: T 140 ASP cc_start: 0.8887 (t0) cc_final: 0.8455 (p0) REVERT: W 387 MET cc_start: 0.9421 (mtm) cc_final: 0.9180 (mtt) REVERT: W 403 MET cc_start: 0.8963 (mpp) cc_final: 0.8402 (mpp) REVERT: W 483 MET cc_start: 0.9266 (mmp) cc_final: 0.9054 (mmp) REVERT: W 781 MET cc_start: 0.9245 (mmp) cc_final: 0.8677 (mmp) REVERT: W 802 MET cc_start: 0.9758 (ptp) cc_final: 0.9352 (ppp) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1660 time to fit residues: 47.8071 Evaluate side-chains 135 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 198 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 114 optimal weight: 50.0000 chunk 17 optimal weight: 1.9990 chunk 98 optimal weight: 30.0000 chunk 116 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** W 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.041893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.026390 restraints weight = 286342.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.027012 restraints weight = 170228.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.027159 restraints weight = 127003.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.027551 restraints weight = 112678.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.027706 restraints weight = 101539.305| |-----------------------------------------------------------------------------| r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28073 Z= 0.140 Angle : 0.607 9.050 39946 Z= 0.353 Chirality : 0.041 0.232 4532 Planarity : 0.004 0.062 3427 Dihedral : 29.334 127.592 7522 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.18), residues: 2060 helix: 1.60 (0.14), residues: 1400 sheet: -0.30 (0.55), residues: 93 loop : -0.63 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG W 241 TYR 0.016 0.001 TYR W 230 PHE 0.017 0.001 PHE W 379 TRP 0.011 0.001 TRP W 311 HIS 0.007 0.001 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.14 (28072) covalent geometry : angle 0.60745 / 0.35 (39946) hydrogen bonds : bond 0.03975 / 2.68 ( 1691) hydrogen bonds : angle 3.85028 / 2.83 ( 4414) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.840 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 119 ILE cc_start: 0.9597 (pt) cc_final: 0.9265 (pt) REVERT: A 120 MET cc_start: 0.9260 (mmm) cc_final: 0.8785 (mmm) REVERT: B 46 ILE cc_start: 0.9788 (mp) cc_final: 0.9301 (tp) REVERT: C 56 GLU cc_start: 0.8956 (pt0) cc_final: 0.8189 (pp20) REVERT: C 73 ASN cc_start: 0.9237 (t0) cc_final: 0.8831 (t0) REVERT: C 90 ASP cc_start: 0.8575 (t0) cc_final: 0.8266 (t70) REVERT: D 65 ASP cc_start: 0.9110 (t70) cc_final: 0.8500 (t0) REVERT: E 50 GLU cc_start: 0.9330 (mp0) cc_final: 0.8868 (mp0) REVERT: E 90 MET cc_start: 0.9236 (mmp) cc_final: 0.8866 (mmp) REVERT: E 94 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8830 (mm-30) REVERT: E 97 GLU cc_start: 0.9272 (mt-10) cc_final: 0.8813 (mt-10) REVERT: E 120 MET cc_start: 0.9298 (mmp) cc_final: 0.8724 (mmm) REVERT: H 42 LEU cc_start: 0.9809 (tt) cc_final: 0.9497 (pp) REVERT: H 65 ASP cc_start: 0.9418 (t70) cc_final: 0.9099 (t0) REVERT: H 73 GLU cc_start: 0.9364 (mm-30) cc_final: 0.9162 (mm-30) REVERT: K 97 GLU cc_start: 0.9456 (mt-10) cc_final: 0.8975 (mm-30) REVERT: L 84 MET cc_start: 0.9030 (tpp) cc_final: 0.8575 (tpp) REVERT: M 61 GLU cc_start: 0.9417 (tm-30) cc_final: 0.9164 (tp30) REVERT: M 84 GLN cc_start: 0.9496 (tp-100) cc_final: 0.9151 (tp-100) REVERT: N 34 TYR cc_start: 0.9725 (m-80) cc_final: 0.9031 (m-10) REVERT: N 59 MET cc_start: 0.9730 (mmp) cc_final: 0.9497 (mmm) REVERT: N 65 ASP cc_start: 0.9442 (t70) cc_final: 0.9131 (t0) REVERT: N 69 ARG cc_start: 0.9477 (mtp180) cc_final: 0.8945 (ttm110) REVERT: N 73 GLU cc_start: 0.9063 (mp0) cc_final: 0.8691 (mp0) REVERT: O 94 GLU cc_start: 0.9476 (mm-30) cc_final: 0.8937 (tp30) REVERT: O 97 GLU cc_start: 0.9495 (pp20) cc_final: 0.9200 (pp20) REVERT: O 106 ASP cc_start: 0.9354 (m-30) cc_final: 0.9048 (m-30) REVERT: O 120 MET cc_start: 0.8995 (mmm) cc_final: 0.8569 (mmm) REVERT: Q 77 LEU cc_start: 0.9906 (tt) cc_final: 0.9688 (pp) REVERT: R 56 GLU cc_start: 0.9547 (tt0) cc_final: 0.9185 (tt0) REVERT: S 127 PHE cc_start: 0.8846 (t80) cc_final: 0.8417 (p90) REVERT: S 132 ASN cc_start: 0.6740 (p0) cc_final: 0.6232 (m-40) REVERT: T 132 ASN cc_start: 0.9173 (t0) cc_final: 0.8631 (m110) REVERT: T 140 ASP cc_start: 0.8828 (t0) cc_final: 0.8415 (p0) REVERT: W 387 MET cc_start: 0.9402 (mtm) cc_final: 0.9142 (mtt) REVERT: W 403 MET cc_start: 0.8935 (mpp) cc_final: 0.8386 (mpp) REVERT: W 483 MET cc_start: 0.9222 (mmp) cc_final: 0.9011 (mmp) REVERT: W 781 MET cc_start: 0.9244 (mmp) cc_final: 0.8804 (mmp) REVERT: W 802 MET cc_start: 0.9749 (ptp) cc_final: 0.9352 (ppp) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1722 time to fit residues: 48.8126 Evaluate side-chains 140 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 230 optimal weight: 20.0000 chunk 147 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 chunk 27 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 107 optimal weight: 30.0000 chunk 69 optimal weight: 50.0000 chunk 121 optimal weight: 0.9990 chunk 145 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.041099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.025729 restraints weight = 292706.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.026226 restraints weight = 175741.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.026377 restraints weight = 133374.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.026668 restraints weight = 118707.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.026822 restraints weight = 109075.749| |-----------------------------------------------------------------------------| r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 28073 Z= 0.198 Angle : 0.646 9.140 39946 Z= 0.373 Chirality : 0.041 0.238 4532 Planarity : 0.004 0.060 3427 Dihedral : 29.421 127.221 7522 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.18), residues: 2060 helix: 1.63 (0.14), residues: 1386 sheet: -0.32 (0.55), residues: 93 loop : -0.56 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG W 241 TYR 0.013 0.001 TYR W 245 PHE 0.022 0.001 PHE O 104 TRP 0.008 0.001 TRP W 217 HIS 0.007 0.001 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.20 (28072) covalent geometry : angle 0.64612 / 0.37 (39946) hydrogen bonds : bond 0.05523 / 3.75 ( 1691) hydrogen bonds : angle 4.00412 / 2.94 ( 4414) Misc. bond : bond 0.00071 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.824 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 120 MET cc_start: 0.9285 (mmm) cc_final: 0.8788 (mmm) REVERT: C 56 GLU cc_start: 0.9041 (pt0) cc_final: 0.8299 (pp20) REVERT: C 73 ASN cc_start: 0.9302 (t0) cc_final: 0.8906 (t0) REVERT: C 90 ASP cc_start: 0.8616 (t0) cc_final: 0.8319 (t70) REVERT: D 65 ASP cc_start: 0.9153 (t70) cc_final: 0.8540 (t0) REVERT: D 68 GLU cc_start: 0.9238 (pp20) cc_final: 0.9033 (pp20) REVERT: E 90 MET cc_start: 0.9286 (mmp) cc_final: 0.8937 (mmp) REVERT: E 94 GLU cc_start: 0.9285 (mm-30) cc_final: 0.9050 (mm-30) REVERT: E 120 MET cc_start: 0.9387 (mmp) cc_final: 0.8785 (mmm) REVERT: H 56 MET cc_start: 0.9517 (tpt) cc_final: 0.9189 (tpp) REVERT: H 65 ASP cc_start: 0.9430 (t70) cc_final: 0.9104 (t0) REVERT: L 84 MET cc_start: 0.9071 (tpp) cc_final: 0.8620 (tpp) REVERT: M 61 GLU cc_start: 0.9420 (tm-30) cc_final: 0.9175 (tp30) REVERT: M 84 GLN cc_start: 0.9490 (tp-100) cc_final: 0.9139 (tp-100) REVERT: N 34 TYR cc_start: 0.9701 (m-80) cc_final: 0.9028 (m-80) REVERT: N 59 MET cc_start: 0.9760 (mmp) cc_final: 0.9510 (mmm) REVERT: O 94 GLU cc_start: 0.9465 (mm-30) cc_final: 0.9166 (tp30) REVERT: O 106 ASP cc_start: 0.9377 (m-30) cc_final: 0.9073 (m-30) REVERT: O 120 MET cc_start: 0.9025 (mmm) cc_final: 0.8605 (mmm) REVERT: Q 59 MET cc_start: 0.9865 (mmp) cc_final: 0.9633 (mmm) REVERT: R 56 GLU cc_start: 0.9551 (tt0) cc_final: 0.9193 (tt0) REVERT: S 127 PHE cc_start: 0.8825 (t80) cc_final: 0.8313 (p90) REVERT: S 132 ASN cc_start: 0.6766 (p0) cc_final: 0.6272 (m-40) REVERT: T 132 ASN cc_start: 0.9183 (t0) cc_final: 0.8631 (m110) REVERT: T 140 ASP cc_start: 0.8829 (t0) cc_final: 0.8427 (p0) REVERT: W 387 MET cc_start: 0.9438 (mtm) cc_final: 0.9218 (mtt) REVERT: W 403 MET cc_start: 0.8951 (mpp) cc_final: 0.8396 (mpp) REVERT: W 483 MET cc_start: 0.9230 (mmp) cc_final: 0.9027 (mmp) REVERT: W 781 MET cc_start: 0.9162 (mmp) cc_final: 0.8656 (mmp) REVERT: W 802 MET cc_start: 0.9766 (ptp) cc_final: 0.9442 (ppp) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1659 time to fit residues: 44.4215 Evaluate side-chains 122 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 68 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 80 optimal weight: 50.0000 chunk 123 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 76 optimal weight: 30.0000 chunk 168 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** W 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.041586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.026157 restraints weight = 286687.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.026749 restraints weight = 169823.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.026893 restraints weight = 127765.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.027185 restraints weight = 112819.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.027395 restraints weight = 104525.669| |-----------------------------------------------------------------------------| r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28073 Z= 0.143 Angle : 0.606 9.082 39946 Z= 0.354 Chirality : 0.041 0.233 4532 Planarity : 0.004 0.061 3427 Dihedral : 29.400 125.536 7522 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.18), residues: 2060 helix: 1.71 (0.14), residues: 1389 sheet: -0.20 (0.54), residues: 92 loop : -0.60 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG W 241 TYR 0.012 0.001 TYR W 245 PHE 0.018 0.001 PHE O 104 TRP 0.010 0.001 TRP W 311 HIS 0.007 0.001 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (28072) covalent geometry : angle 0.60624 / 0.35 (39946) hydrogen bonds : bond 0.04074 / 2.75 ( 1691) hydrogen bonds : angle 3.87998 / 2.85 ( 4414) Misc. bond : bond 0.00026 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4891.96 seconds wall clock time: 85 minutes 25.65 seconds (5125.65 seconds total)