Starting phenix.real_space_refine on Sun Jun 22 19:33:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gd2_51244/06_2025/9gd2_51244.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gd2_51244/06_2025/9gd2_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_51244/06_2025/9gd2_51244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gd2_51244/06_2025/9gd2_51244.map" model { file = "/net/cci-nas-00/data/ceres_data/9gd2_51244/06_2025/9gd2_51244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gd2_51244/06_2025/9gd2_51244.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.032 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.75, per 1000 atoms: 0.55 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: 6.16 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 12.03 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: 19.07 Time building geometry restraints manager: 7.38 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: 39389 2.86 - 5.71: 543 5.71 - 8.57: 9 8.57 - 11.42: 2 11.42 - 14.28: 3 Bond angle restraints: 39946 Sorted by residual: angle pdb=" O3' DG J 130 " pdb=" C3' DG J 130 " pdb=" C2' DG J 130 " ideal model delta sigma weight residual 111.50 102.37 9.13 1.50e+00 4.44e-01 3.70e+01 angle pdb=" O3' DG I 25 " pdb=" C3' DG I 25 " pdb=" C2' DG I 25 " ideal model delta sigma weight residual 111.50 120.25 -8.75 1.50e+00 4.44e-01 3.40e+01 angle pdb=" O3' DG I -41 " pdb=" C3' DG I -41 " pdb=" C2' DG I -41 " ideal model delta sigma weight residual 111.50 119.53 -8.03 1.50e+00 4.44e-01 2.87e+01 angle pdb=" O3' DG I -78 " pdb=" C3' DG I -78 " pdb=" C2' DG I -78 " ideal model delta sigma weight residual 111.50 119.43 -7.93 1.50e+00 4.44e-01 2.79e+01 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 ... (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 - 0.082: 3768 0.082 - 0.163: 736 0.163 - 0.245: 26 0.245 - 0.327: 0 0.327 - 0.409: 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 -2.66 -2.25 -0.41 2.00e-01 2.50e+01 4.18e+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 -2.66 -2.26 -0.40 2.00e-01 2.50e+01 4.01e+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 -2.66 -2.42 -0.24 2.00e-01 2.50e+01 1.47e+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: 5.780 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: 0.030 Extract box with map and model: 0.990 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 72.660 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.110 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 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= 0.369 Angle : 0.864 14.276 39946 Z= 0.542 Chirality : 0.058 0.409 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (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 TRP 0.028 0.005 TRP W 311 HIS 0.015 0.004 HIS W 428 PHE 0.016 0.003 PHE M 25 TYR 0.042 0.005 TYR W 245 ARG 0.025 0.003 ARG W 807 Details of bonding type rmsd hydrogen bonds : bond 0.13584 ( 1691) hydrogen bonds : angle 5.92584 ( 4414) covalent geometry : bond 0.00558 (28072) covalent geometry : angle 0.86350 (39946) Misc. bond : bond 0.42299 ( 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 : 2.104 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: 0.4312 time to fit residues: 169.9472 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 : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 211 optimal weight: 8.9990 chunk 189 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 227 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN D 81 ASN H 44 GLN ** N 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 GLN W 210 ASN W 224 HIS W 337 HIS ** W 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3067 r_free = 0.3067 target = 0.041429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.025937 restraints weight = 293454.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.026551 restraints weight = 174012.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.026677 restraints weight = 130811.673| |-----------------------------------------------------------------------------| r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 28073 Z= 0.243 Angle : 0.701 11.199 39946 Z= 0.413 Chirality : 0.038 0.161 4532 Planarity : 0.005 0.120 3427 Dihedral : 29.400 162.962 7522 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.11 % Allowed : 3.38 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.18), residues: 2060 helix: 1.14 (0.13), residues: 1393 sheet: -0.60 (0.53), residues: 94 loop : -0.53 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP W 417 HIS 0.017 0.002 HIS W 337 PHE 0.020 0.002 PHE K 104 TYR 0.020 0.002 TYR R 50 ARG 0.023 0.001 ARG Q 76 Details of bonding type rmsd hydrogen bonds : bond 0.06151 ( 1691) hydrogen bonds : angle 4.34245 ( 4414) covalent geometry : bond 0.00530 (28072) covalent geometry : angle 0.70124 (39946) Misc. bond : bond 0.00067 ( 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 211 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 209 time to evaluate : 3.640 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 90 MET cc_start: 0.9446 (mmp) cc_final: 0.9244 (mmp) REVERT: A 119 ILE cc_start: 0.9648 (pt) cc_final: 0.9196 (pt) REVERT: A 120 MET cc_start: 0.9240 (mmm) cc_final: 0.8807 (mmm) REVERT: B 46 ILE cc_start: 0.9764 (mp) cc_final: 0.9395 (tp) REVERT: B 67 ARG cc_start: 0.9456 (ttp-110) cc_final: 0.9225 (ttp-110) REVERT: B 84 MET cc_start: 0.9049 (tpp) cc_final: 0.8796 (tpp) REVERT: C 90 ASP cc_start: 0.8820 (t0) cc_final: 0.8453 (t70) REVERT: D 65 ASP cc_start: 0.9200 (t70) cc_final: 0.8561 (t0) REVERT: E 90 MET cc_start: 0.9351 (mmp) cc_final: 0.9046 (mmp) REVERT: E 97 GLU cc_start: 0.9323 (mt-10) cc_final: 0.8919 (mp0) REVERT: F 58 LEU cc_start: 0.9748 (tp) cc_final: 0.9500 (tt) REVERT: H 65 ASP cc_start: 0.9347 (t70) cc_final: 0.9065 (t0) REVERT: H 68 GLU cc_start: 0.9296 (tm-30) cc_final: 0.9062 (tm-30) REVERT: H 73 GLU cc_start: 0.9489 (mm-30) cc_final: 0.9195 (mm-30) REVERT: K 106 ASP cc_start: 0.9367 (m-30) cc_final: 0.9084 (m-30) REVERT: L 44 LYS cc_start: 0.9662 (mmpt) cc_final: 0.9419 (pttt) REVERT: L 84 MET cc_start: 0.9146 (tpp) cc_final: 0.8758 (tpp) REVERT: M 61 GLU cc_start: 0.9660 (tm-30) cc_final: 0.9153 (tm-30) REVERT: N 59 MET cc_start: 0.9765 (mmt) cc_final: 0.9475 (mmm) REVERT: N 67 PHE cc_start: 0.9734 (t80) cc_final: 0.9335 (t80) REVERT: N 68 GLU cc_start: 0.9612 (mt-10) cc_final: 0.9394 (mm-30) REVERT: N 73 GLU cc_start: 0.9659 (mm-30) cc_final: 0.9457 (mm-30) REVERT: O 97 GLU cc_start: 0.9275 (mm-30) cc_final: 0.9003 (mt-10) REVERT: O 106 ASP cc_start: 0.9413 (m-30) cc_final: 0.9110 (m-30) REVERT: O 130 ILE cc_start: 0.9747 (mm) cc_final: 0.9438 (tp) REVERT: P 63 GLU cc_start: 0.9575 (pt0) cc_final: 0.9358 (pp20) REVERT: Q 97 LEU cc_start: 0.9726 (tt) cc_final: 0.9427 (tt) REVERT: Q 98 LEU cc_start: 0.9298 (mm) cc_final: 0.9092 (mt) REVERT: R 56 GLU cc_start: 0.9614 (tt0) cc_final: 0.9198 (tt0) REVERT: S 127 PHE cc_start: 0.8844 (t80) cc_final: 0.8438 (p90) REVERT: T 132 ASN cc_start: 0.9210 (t0) cc_final: 0.8624 (m-40) REVERT: W 237 ARG cc_start: 0.8922 (ttm170) cc_final: 0.8660 (tpt170) REVERT: W 387 MET cc_start: 0.9368 (mtm) cc_final: 0.9137 (mtt) REVERT: W 403 MET cc_start: 0.9199 (mpp) cc_final: 0.8877 (mtm) outliers start: 2 outliers final: 2 residues processed: 209 average time/residue: 0.4921 time to fit residues: 164.3116 Evaluate side-chains 134 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 3.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 202 optimal weight: 30.0000 chunk 227 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 219 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 192 optimal weight: 30.0000 chunk 218 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 215 optimal weight: 0.5980 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN K 113 HIS ** O 68 GLN ** 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 222 HIS W 315 ASN ** W 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 530 ASN ** W 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.040374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.025116 restraints weight = 297040.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.025672 restraints weight = 180836.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.025813 restraints weight = 137980.199| |-----------------------------------------------------------------------------| r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 28073 Z= 0.303 Angle : 0.678 11.029 39946 Z= 0.400 Chirality : 0.038 0.153 4532 Planarity : 0.005 0.078 3427 Dihedral : 29.508 138.081 7522 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.17 % Allowed : 3.32 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.18), residues: 2060 helix: 1.32 (0.13), residues: 1395 sheet: -0.52 (0.53), residues: 88 loop : -0.61 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP W 507 HIS 0.012 0.002 HIS B 75 PHE 0.015 0.002 PHE M 25 TYR 0.016 0.002 TYR F 88 ARG 0.008 0.001 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.06700 ( 1691) hydrogen bonds : angle 4.26527 ( 4414) covalent geometry : bond 0.00655 (28072) covalent geometry : angle 0.67797 (39946) Misc. bond : bond 0.00074 ( 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 180 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 177 time to evaluate : 2.165 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 119 ILE cc_start: 0.9675 (pt) cc_final: 0.9268 (pt) REVERT: A 120 MET cc_start: 0.9159 (mmm) cc_final: 0.8743 (mmm) REVERT: B 67 ARG cc_start: 0.9424 (ttp-110) cc_final: 0.9107 (ttp-110) REVERT: B 84 MET cc_start: 0.9123 (tpp) cc_final: 0.8887 (tpp) REVERT: C 56 GLU cc_start: 0.9150 (pt0) cc_final: 0.8321 (pp20) REVERT: C 73 ASN cc_start: 0.9214 (t0) cc_final: 0.8910 (t0) REVERT: C 90 ASP cc_start: 0.8938 (t0) cc_final: 0.8563 (t70) REVERT: D 65 ASP cc_start: 0.9144 (t70) cc_final: 0.8619 (t0) REVERT: E 90 MET cc_start: 0.9305 (mmp) cc_final: 0.8929 (mmp) REVERT: E 94 GLU cc_start: 0.9301 (mm-30) cc_final: 0.8913 (mm-30) REVERT: E 97 GLU cc_start: 0.9359 (mt-10) cc_final: 0.8909 (mt-10) REVERT: E 120 MET cc_start: 0.9346 (mmp) cc_final: 0.8496 (mmm) REVERT: F 58 LEU cc_start: 0.9738 (tp) cc_final: 0.9499 (tt) REVERT: F 84 MET cc_start: 0.9009 (tpp) cc_final: 0.8714 (tpp) REVERT: K 106 ASP cc_start: 0.9295 (m-30) cc_final: 0.9089 (m-30) REVERT: L 44 LYS cc_start: 0.9637 (mmpt) cc_final: 0.9405 (pttt) REVERT: L 84 MET cc_start: 0.9162 (tpp) cc_final: 0.8739 (tpp) REVERT: M 61 GLU cc_start: 0.9416 (tm-30) cc_final: 0.9190 (tp30) REVERT: N 59 MET cc_start: 0.9745 (mmt) cc_final: 0.9486 (mmm) REVERT: O 97 GLU cc_start: 0.9321 (mm-30) cc_final: 0.9048 (mt-10) REVERT: O 106 ASP cc_start: 0.9447 (m-30) cc_final: 0.9241 (m-30) REVERT: O 130 ILE cc_start: 0.9761 (mm) cc_final: 0.9454 (tp) REVERT: P 25 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.8301 (m110) REVERT: Q 59 MET cc_start: 0.9895 (mmp) cc_final: 0.9675 (mmm) REVERT: Q 73 GLU cc_start: 0.9771 (mm-30) cc_final: 0.9536 (mm-30) REVERT: R 56 GLU cc_start: 0.9566 (tt0) cc_final: 0.9179 (tt0) REVERT: S 127 PHE cc_start: 0.8769 (t80) cc_final: 0.8296 (p90) REVERT: T 132 ASN cc_start: 0.9141 (t0) cc_final: 0.8523 (m-40) REVERT: W 237 ARG cc_start: 0.8966 (ttm170) cc_final: 0.8697 (tpt170) REVERT: W 387 MET cc_start: 0.9437 (mtm) cc_final: 0.9196 (mtt) REVERT: W 403 MET cc_start: 0.9159 (mpp) cc_final: 0.8350 (mpp) REVERT: W 697 MET cc_start: 0.8246 (mtm) cc_final: 0.8000 (ptp) REVERT: W 781 MET cc_start: 0.9144 (mmp) cc_final: 0.8814 (mmp) outliers start: 3 outliers final: 0 residues processed: 179 average time/residue: 0.3861 time to fit residues: 109.5520 Evaluate side-chains 121 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 184 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 242 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 200 optimal weight: 20.0000 chunk 161 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 796 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 = 0.3027 r_free = 0.3027 target = 0.040062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.024920 restraints weight = 306336.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.025471 restraints weight = 184793.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.025611 restraints weight = 140166.899| |-----------------------------------------------------------------------------| r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 28073 Z= 0.308 Angle : 0.666 12.598 39946 Z= 0.391 Chirality : 0.038 0.196 4532 Planarity : 0.005 0.066 3427 Dihedral : 29.717 132.821 7522 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.11 % Allowed : 4.26 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.18), residues: 2060 helix: 1.38 (0.14), residues: 1388 sheet: -0.34 (0.56), residues: 83 loop : -0.66 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP W 507 HIS 0.010 0.002 HIS B 75 PHE 0.023 0.002 PHE K 104 TYR 0.020 0.002 TYR R 39 ARG 0.009 0.001 ARG D 89 Details of bonding type rmsd hydrogen bonds : bond 0.06557 ( 1691) hydrogen bonds : angle 4.24478 ( 4414) covalent geometry : bond 0.00662 (28072) covalent geometry : angle 0.66579 (39946) Misc. bond : bond 0.00116 ( 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 164 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 2.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ILE cc_start: 0.9657 (pt) cc_final: 0.9278 (pt) REVERT: A 120 MET cc_start: 0.9159 (mmm) cc_final: 0.8749 (mmm) REVERT: B 67 ARG cc_start: 0.9340 (ttp-110) cc_final: 0.9025 (ttp-110) REVERT: C 73 ASN cc_start: 0.9312 (t0) cc_final: 0.8919 (t0) REVERT: C 90 ASP cc_start: 0.8965 (t0) cc_final: 0.8638 (t70) REVERT: E 90 MET cc_start: 0.9298 (mmp) cc_final: 0.8923 (mmp) REVERT: E 94 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8919 (mm-30) REVERT: E 97 GLU cc_start: 0.9351 (mt-10) cc_final: 0.8922 (mt-10) REVERT: E 120 MET cc_start: 0.9437 (mmp) cc_final: 0.8483 (mmm) REVERT: F 84 MET cc_start: 0.9064 (tpp) cc_final: 0.8772 (tpp) REVERT: H 65 ASP cc_start: 0.9469 (t0) cc_final: 0.9135 (t0) REVERT: L 44 LYS cc_start: 0.9640 (mmpt) cc_final: 0.9387 (pttt) REVERT: L 84 MET cc_start: 0.9075 (tpp) cc_final: 0.8623 (tpp) REVERT: M 61 GLU cc_start: 0.9412 (tm-30) cc_final: 0.9189 (tp30) REVERT: N 59 MET cc_start: 0.9745 (mmt) cc_final: 0.9471 (mmm) REVERT: N 73 GLU cc_start: 0.9656 (mm-30) cc_final: 0.9401 (mm-30) REVERT: O 97 GLU cc_start: 0.9309 (mm-30) cc_final: 0.9008 (mt-10) REVERT: O 106 ASP cc_start: 0.9498 (m-30) cc_final: 0.9108 (m-30) REVERT: P 63 GLU cc_start: 0.9648 (OUTLIER) cc_final: 0.9362 (pp20) REVERT: R 39 TYR cc_start: 0.9412 (m-10) cc_final: 0.9117 (m-10) REVERT: R 56 GLU cc_start: 0.9538 (tt0) cc_final: 0.9142 (tt0) REVERT: S 127 PHE cc_start: 0.8755 (t80) cc_final: 0.8157 (p90) REVERT: T 132 ASN cc_start: 0.9147 (t0) cc_final: 0.8545 (m-40) REVERT: W 387 MET cc_start: 0.9407 (mtm) cc_final: 0.9198 (mtt) REVERT: W 403 MET cc_start: 0.9082 (mpp) cc_final: 0.8293 (mpp) REVERT: W 697 MET cc_start: 0.8176 (mtm) cc_final: 0.7836 (mtm) REVERT: W 781 MET cc_start: 0.9080 (mmp) cc_final: 0.8535 (mmp) outliers start: 2 outliers final: 0 residues processed: 162 average time/residue: 0.3802 time to fit residues: 98.8450 Evaluate side-chains 113 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 109 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 246 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 156 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS D 92 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 796 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 = 0.3041 r_free = 0.3041 target = 0.040571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.025134 restraints weight = 294092.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.025676 restraints weight = 179738.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.025815 restraints weight = 136609.282| |-----------------------------------------------------------------------------| r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 28073 Z= 0.214 Angle : 0.609 11.533 39946 Z= 0.358 Chirality : 0.036 0.195 4532 Planarity : 0.004 0.066 3427 Dihedral : 29.596 131.176 7522 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.06 % Allowed : 2.16 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.18), residues: 2060 helix: 1.64 (0.14), residues: 1385 sheet: -0.62 (0.51), residues: 99 loop : -0.54 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 311 HIS 0.008 0.001 HIS B 75 PHE 0.022 0.002 PHE E 104 TYR 0.013 0.001 TYR R 39 ARG 0.007 0.000 ARG P 78 Details of bonding type rmsd hydrogen bonds : bond 0.04861 ( 1691) hydrogen bonds : angle 3.99582 ( 4414) covalent geometry : bond 0.00464 (28072) covalent geometry : angle 0.60867 (39946) Misc. bond : bond 0.00050 ( 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 168 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 2.073 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 120 MET cc_start: 0.9230 (mmm) cc_final: 0.8778 (mmm) REVERT: B 67 ARG cc_start: 0.9308 (ttp-110) cc_final: 0.8981 (ttp-110) REVERT: C 56 GLU cc_start: 0.9157 (pt0) cc_final: 0.8442 (pp20) REVERT: C 73 ASN cc_start: 0.9294 (t0) cc_final: 0.8923 (t0) REVERT: C 90 ASP cc_start: 0.8862 (t0) cc_final: 0.8561 (t70) REVERT: D 65 ASP cc_start: 0.9116 (t70) cc_final: 0.8570 (t0) REVERT: E 90 MET cc_start: 0.9259 (mmp) cc_final: 0.8895 (mmp) REVERT: E 94 GLU cc_start: 0.9272 (mm-30) cc_final: 0.8899 (mm-30) REVERT: E 97 GLU cc_start: 0.9313 (mt-10) cc_final: 0.8884 (mt-10) REVERT: E 120 MET cc_start: 0.9420 (mmp) cc_final: 0.8500 (mmm) REVERT: H 65 ASP cc_start: 0.9472 (t0) cc_final: 0.9211 (t0) REVERT: K 90 MET cc_start: 0.9037 (tmm) cc_final: 0.8751 (tmm) REVERT: L 44 LYS cc_start: 0.9646 (mmpt) cc_final: 0.9429 (pttt) REVERT: L 84 MET cc_start: 0.9014 (tpp) cc_final: 0.8542 (tpp) REVERT: M 61 GLU cc_start: 0.9423 (tm-30) cc_final: 0.9173 (tp30) REVERT: N 34 TYR cc_start: 0.9675 (m-80) cc_final: 0.9454 (m-10) REVERT: N 65 ASP cc_start: 0.9567 (t0) cc_final: 0.9352 (t0) REVERT: N 69 ARG cc_start: 0.9568 (mtp180) cc_final: 0.9048 (ttm110) REVERT: N 73 GLU cc_start: 0.9654 (mm-30) cc_final: 0.9408 (mm-30) REVERT: O 106 ASP cc_start: 0.9455 (m-30) cc_final: 0.9135 (m-30) REVERT: P 68 ASP cc_start: 0.9527 (m-30) cc_final: 0.9326 (m-30) REVERT: R 39 TYR cc_start: 0.9369 (m-10) cc_final: 0.9130 (m-80) REVERT: R 56 GLU cc_start: 0.9525 (tt0) cc_final: 0.9123 (tt0) REVERT: S 132 ASN cc_start: 0.6563 (p0) cc_final: 0.5965 (m-40) REVERT: T 132 ASN cc_start: 0.9144 (t0) cc_final: 0.8561 (m110) REVERT: W 387 MET cc_start: 0.9422 (mtm) cc_final: 0.9210 (mtt) REVERT: W 403 MET cc_start: 0.9012 (mpp) cc_final: 0.8479 (mpp) REVERT: W 697 MET cc_start: 0.8390 (mtm) cc_final: 0.7957 (mtm) REVERT: W 781 MET cc_start: 0.9087 (mmp) cc_final: 0.8494 (mmp) REVERT: W 802 MET cc_start: 0.9779 (ptp) cc_final: 0.9456 (ppp) outliers start: 1 outliers final: 1 residues processed: 167 average time/residue: 0.3784 time to fit residues: 102.9021 Evaluate side-chains 123 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 28 optimal weight: 5.9990 chunk 230 optimal weight: 0.4980 chunk 176 optimal weight: 20.0000 chunk 180 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 211 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 192 optimal weight: 50.0000 chunk 57 optimal weight: 5.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 93 GLN O 113 HIS P 93 GLN ** W 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.040033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.024954 restraints weight = 302504.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.025527 restraints weight = 181945.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.025683 restraints weight = 136848.896| |-----------------------------------------------------------------------------| r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 28073 Z= 0.265 Angle : 0.635 14.287 39946 Z= 0.372 Chirality : 0.037 0.197 4532 Planarity : 0.004 0.064 3427 Dihedral : 29.501 129.696 7522 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.18), residues: 2060 helix: 1.58 (0.14), residues: 1385 sheet: -0.72 (0.52), residues: 93 loop : -0.64 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 507 HIS 0.012 0.002 HIS W 661 PHE 0.020 0.002 PHE M 25 TYR 0.015 0.002 TYR R 39 ARG 0.009 0.000 ARG W 688 Details of bonding type rmsd hydrogen bonds : bond 0.06203 ( 1691) hydrogen bonds : angle 4.09105 ( 4414) covalent geometry : bond 0.00575 (28072) covalent geometry : angle 0.63523 (39946) Misc. bond : bond 0.00089 ( 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 159 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9134 (pm20) cc_final: 0.8667 (pm20) REVERT: A 119 ILE cc_start: 0.9662 (pt) cc_final: 0.9341 (pt) REVERT: A 120 MET cc_start: 0.9230 (mmm) cc_final: 0.8727 (mmm) REVERT: B 62 LEU cc_start: 0.9771 (mt) cc_final: 0.9562 (mt) REVERT: B 67 ARG cc_start: 0.9303 (ttp-110) cc_final: 0.8999 (ttp-110) REVERT: B 84 MET cc_start: 0.9019 (tpp) cc_final: 0.8808 (tpp) REVERT: C 56 GLU cc_start: 0.9191 (pt0) cc_final: 0.8442 (pp20) REVERT: C 73 ASN cc_start: 0.9415 (t0) cc_final: 0.9076 (t0) REVERT: C 90 ASP cc_start: 0.8720 (t0) cc_final: 0.8443 (t70) REVERT: D 65 ASP cc_start: 0.9218 (t70) cc_final: 0.8991 (t0) REVERT: E 90 MET cc_start: 0.9280 (mmp) cc_final: 0.8906 (mmp) REVERT: E 94 GLU cc_start: 0.9278 (mm-30) cc_final: 0.8906 (mm-30) REVERT: E 97 GLU cc_start: 0.9334 (mt-10) cc_final: 0.8916 (mt-10) REVERT: E 120 MET cc_start: 0.9466 (mmp) cc_final: 0.8650 (mmm) REVERT: F 63 GLU cc_start: 0.9463 (pt0) cc_final: 0.9219 (pp20) REVERT: F 84 MET cc_start: 0.8835 (tpp) cc_final: 0.8584 (tpp) REVERT: H 65 ASP cc_start: 0.9468 (t0) cc_final: 0.9187 (t0) REVERT: L 44 LYS cc_start: 0.9643 (mmpt) cc_final: 0.9380 (pttt) REVERT: L 84 MET cc_start: 0.9001 (tpp) cc_final: 0.8538 (tpp) REVERT: M 61 GLU cc_start: 0.9432 (tm-30) cc_final: 0.9184 (tp30) REVERT: N 34 TYR cc_start: 0.9706 (m-80) cc_final: 0.9485 (m-10) REVERT: N 59 MET cc_start: 0.9759 (mmp) cc_final: 0.9469 (mmm) REVERT: N 65 ASP cc_start: 0.9606 (t0) cc_final: 0.9386 (t0) REVERT: N 69 ARG cc_start: 0.9570 (mtp180) cc_final: 0.9012 (ttm110) REVERT: N 73 GLU cc_start: 0.9658 (mm-30) cc_final: 0.9396 (mm-30) REVERT: O 106 ASP cc_start: 0.9464 (m-30) cc_final: 0.9203 (m-30) REVERT: P 68 ASP cc_start: 0.9511 (m-30) cc_final: 0.9302 (m-30) REVERT: Q 59 MET cc_start: 0.9880 (mmp) cc_final: 0.9672 (mmm) REVERT: Q 73 GLU cc_start: 0.9703 (mm-30) cc_final: 0.9293 (tp30) REVERT: R 39 TYR cc_start: 0.9362 (m-10) cc_final: 0.9143 (m-10) REVERT: R 56 GLU cc_start: 0.9519 (tt0) cc_final: 0.9117 (tt0) REVERT: S 132 ASN cc_start: 0.6655 (p0) cc_final: 0.6086 (m-40) REVERT: T 132 ASN cc_start: 0.9151 (t0) cc_final: 0.8605 (m-40) REVERT: W 387 MET cc_start: 0.9458 (mtm) cc_final: 0.9218 (mtt) REVERT: W 403 MET cc_start: 0.8915 (mpp) cc_final: 0.8449 (mpp) REVERT: W 697 MET cc_start: 0.8598 (mtm) cc_final: 0.8189 (mtm) REVERT: W 781 MET cc_start: 0.9061 (mmp) cc_final: 0.8487 (mmp) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.3824 time to fit residues: 98.0574 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 : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 129 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 chunk 229 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 813 HIS ** 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 = 0.3030 r_free = 0.3030 target = 0.040179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.025335 restraints weight = 300388.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.025628 restraints weight = 182913.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.025775 restraints weight = 135013.261| |-----------------------------------------------------------------------------| r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 28073 Z= 0.235 Angle : 0.614 12.997 39946 Z= 0.360 Chirality : 0.036 0.200 4532 Planarity : 0.004 0.064 3427 Dihedral : 29.478 130.124 7522 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.06 % Allowed : 1.22 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.18), residues: 2060 helix: 1.67 (0.14), residues: 1385 sheet: -0.73 (0.53), residues: 93 loop : -0.65 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 507 HIS 0.010 0.001 HIS P 75 PHE 0.016 0.002 PHE K 104 TYR 0.023 0.001 TYR S 137 ARG 0.005 0.000 ARG P 39 Details of bonding type rmsd hydrogen bonds : bond 0.05096 ( 1691) hydrogen bonds : angle 4.03264 ( 4414) covalent geometry : bond 0.00507 (28072) covalent geometry : angle 0.61408 (39946) Misc. bond : bond 0.00061 ( 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 158 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 2.268 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 119 ILE cc_start: 0.9659 (pt) cc_final: 0.9347 (pt) REVERT: A 120 MET cc_start: 0.9274 (mmm) cc_final: 0.8737 (mmm) REVERT: B 62 LEU cc_start: 0.9768 (mt) cc_final: 0.9558 (mt) REVERT: C 56 GLU cc_start: 0.9156 (pt0) cc_final: 0.8445 (pp20) REVERT: C 73 ASN cc_start: 0.9428 (t0) cc_final: 0.9169 (t0) REVERT: C 90 ASP cc_start: 0.8756 (t0) cc_final: 0.8458 (t70) REVERT: D 65 ASP cc_start: 0.9217 (t70) cc_final: 0.9004 (t0) REVERT: E 90 MET cc_start: 0.9292 (mmp) cc_final: 0.8918 (mmp) REVERT: E 94 GLU cc_start: 0.9280 (mm-30) cc_final: 0.8895 (mm-30) REVERT: E 97 GLU cc_start: 0.9342 (mt-10) cc_final: 0.8903 (mt-10) REVERT: E 120 MET cc_start: 0.9442 (mmp) cc_final: 0.8761 (mmm) REVERT: F 84 MET cc_start: 0.8904 (tpp) cc_final: 0.8647 (tpp) REVERT: H 56 MET cc_start: 0.9363 (tpt) cc_final: 0.9158 (tpp) REVERT: H 65 ASP cc_start: 0.9217 (t0) cc_final: 0.8430 (t0) REVERT: H 68 GLU cc_start: 0.8949 (pp20) cc_final: 0.8731 (pp20) REVERT: L 44 LYS cc_start: 0.9641 (mmpt) cc_final: 0.9398 (pttt) REVERT: L 84 MET cc_start: 0.8959 (tpp) cc_final: 0.8474 (tpp) REVERT: M 61 GLU cc_start: 0.9455 (tm-30) cc_final: 0.9192 (tp30) REVERT: N 59 MET cc_start: 0.9789 (mmp) cc_final: 0.9443 (mmm) REVERT: N 68 GLU cc_start: 0.9426 (mp0) cc_final: 0.9220 (mp0) REVERT: N 73 GLU cc_start: 0.9669 (mm-30) cc_final: 0.9429 (mm-30) REVERT: O 106 ASP cc_start: 0.9392 (m-30) cc_final: 0.9120 (m-30) REVERT: P 68 ASP cc_start: 0.9524 (m-30) cc_final: 0.9310 (m-30) REVERT: Q 73 GLU cc_start: 0.9689 (mm-30) cc_final: 0.9296 (tp30) REVERT: R 39 TYR cc_start: 0.9380 (m-10) cc_final: 0.9112 (m-10) REVERT: R 56 GLU cc_start: 0.9521 (tt0) cc_final: 0.9182 (tt0) REVERT: S 132 ASN cc_start: 0.6860 (p0) cc_final: 0.6298 (m-40) REVERT: T 132 ASN cc_start: 0.9172 (t0) cc_final: 0.8636 (m-40) REVERT: W 387 MET cc_start: 0.9418 (mtm) cc_final: 0.9175 (mtt) REVERT: W 403 MET cc_start: 0.8830 (mpp) cc_final: 0.8352 (mpp) REVERT: W 697 MET cc_start: 0.8726 (mtm) cc_final: 0.8243 (mtm) REVERT: W 781 MET cc_start: 0.9055 (mmp) cc_final: 0.8504 (mmp) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.3574 time to fit residues: 92.6147 Evaluate side-chains 118 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 158 optimal weight: 0.4980 chunk 151 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 chunk 231 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 138 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 410 GLN ** W 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 813 HIS ** 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 = 0.3029 r_free = 0.3029 target = 0.039873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.025019 restraints weight = 305629.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.025276 restraints weight = 186264.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.025743 restraints weight = 150739.306| |-----------------------------------------------------------------------------| r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 28073 Z= 0.250 Angle : 0.621 13.771 39946 Z= 0.362 Chirality : 0.037 0.222 4532 Planarity : 0.004 0.063 3427 Dihedral : 29.439 129.038 7522 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.18), residues: 2060 helix: 1.67 (0.14), residues: 1385 sheet: -0.73 (0.52), residues: 93 loop : -0.63 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 507 HIS 0.007 0.001 HIS P 75 PHE 0.019 0.002 PHE K 104 TYR 0.014 0.001 TYR W 316 ARG 0.006 0.000 ARG P 78 Details of bonding type rmsd hydrogen bonds : bond 0.05729 ( 1691) hydrogen bonds : angle 4.06480 ( 4414) covalent geometry : bond 0.00540 (28072) covalent geometry : angle 0.62070 (39946) Misc. bond : bond 0.00055 ( 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 153 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 2.139 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: 0.9650 (pt) cc_final: 0.9339 (pt) REVERT: A 120 MET cc_start: 0.9277 (mmm) cc_final: 0.8745 (mmm) REVERT: B 62 LEU cc_start: 0.9772 (mt) cc_final: 0.9567 (mt) REVERT: C 56 GLU cc_start: 0.9174 (pt0) cc_final: 0.8493 (pp20) REVERT: C 73 ASN cc_start: 0.9460 (t0) cc_final: 0.9196 (t0) REVERT: C 90 ASP cc_start: 0.8813 (t0) cc_final: 0.8520 (t70) REVERT: D 65 ASP cc_start: 0.9210 (t70) cc_final: 0.9001 (t0) REVERT: E 90 MET cc_start: 0.9295 (mmp) cc_final: 0.8934 (mmp) REVERT: E 94 GLU cc_start: 0.9269 (mm-30) cc_final: 0.8883 (mm-30) REVERT: E 97 GLU cc_start: 0.9340 (mt-10) cc_final: 0.8908 (mt-10) REVERT: E 120 MET cc_start: 0.9466 (mmp) cc_final: 0.8798 (mmm) REVERT: F 63 GLU cc_start: 0.9510 (pt0) cc_final: 0.9295 (pp20) REVERT: F 84 MET cc_start: 0.8948 (tpp) cc_final: 0.8605 (tpp) REVERT: H 56 MET cc_start: 0.9426 (tpp) cc_final: 0.9208 (tpt) REVERT: H 65 ASP cc_start: 0.9218 (t0) cc_final: 0.8450 (t0) REVERT: L 84 MET cc_start: 0.8938 (tpp) cc_final: 0.8508 (tpp) REVERT: M 61 GLU cc_start: 0.9444 (tm-30) cc_final: 0.9169 (tp30) REVERT: N 59 MET cc_start: 0.9791 (mmp) cc_final: 0.9471 (mmm) REVERT: N 68 GLU cc_start: 0.9411 (mp0) cc_final: 0.9202 (mp0) REVERT: N 73 GLU cc_start: 0.9661 (mm-30) cc_final: 0.9393 (mm-30) REVERT: O 106 ASP cc_start: 0.9419 (m-30) cc_final: 0.9175 (m-30) REVERT: P 68 ASP cc_start: 0.9516 (m-30) cc_final: 0.9307 (m-30) REVERT: Q 73 GLU cc_start: 0.9693 (mm-30) cc_final: 0.9291 (tp30) REVERT: R 39 TYR cc_start: 0.9371 (m-10) cc_final: 0.9084 (m-10) REVERT: R 56 GLU cc_start: 0.9542 (tt0) cc_final: 0.9170 (tt0) REVERT: S 132 ASN cc_start: 0.6844 (p0) cc_final: 0.6338 (m-40) REVERT: T 132 ASN cc_start: 0.9250 (t0) cc_final: 0.8731 (m-40) REVERT: W 387 MET cc_start: 0.9428 (mtm) cc_final: 0.9172 (mtt) REVERT: W 403 MET cc_start: 0.8771 (mpp) cc_final: 0.8283 (mpp) REVERT: W 697 MET cc_start: 0.8816 (mtm) cc_final: 0.8341 (mtm) REVERT: W 781 MET cc_start: 0.9065 (mmp) cc_final: 0.8473 (mmp) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.3506 time to fit residues: 89.5232 Evaluate side-chains 116 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 27 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 241 optimal weight: 4.9990 chunk 247 optimal weight: 0.0370 chunk 173 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 546 GLN ** 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 = 0.3050 r_free = 0.3050 target = 0.040763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.026013 restraints weight = 298291.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.026138 restraints weight = 175920.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.026479 restraints weight = 134579.689| |-----------------------------------------------------------------------------| r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28073 Z= 0.164 Angle : 0.589 11.388 39946 Z= 0.343 Chirality : 0.036 0.189 4532 Planarity : 0.004 0.062 3427 Dihedral : 29.310 127.501 7522 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.18), residues: 2060 helix: 1.83 (0.14), residues: 1380 sheet: -0.66 (0.53), residues: 93 loop : -0.55 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP W 311 HIS 0.007 0.001 HIS P 75 PHE 0.017 0.001 PHE W 379 TYR 0.012 0.001 TYR W 245 ARG 0.008 0.000 ARG K 116 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 1691) hydrogen bonds : angle 3.84612 ( 4414) covalent geometry : bond 0.00352 (28072) covalent geometry : angle 0.58899 (39946) Misc. bond : bond 0.00001 ( 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 172 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 2.760 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 119 ILE cc_start: 0.9640 (pt) cc_final: 0.9359 (tp) REVERT: A 120 MET cc_start: 0.9311 (mmm) cc_final: 0.8727 (mmm) REVERT: C 56 GLU cc_start: 0.9081 (pt0) cc_final: 0.8488 (pp20) REVERT: C 73 ASN cc_start: 0.9406 (t0) cc_final: 0.9136 (t0) REVERT: C 90 ASP cc_start: 0.8639 (t0) cc_final: 0.8335 (t70) REVERT: C 95 LYS cc_start: 0.9415 (mtmm) cc_final: 0.9103 (mtmt) REVERT: D 65 ASP cc_start: 0.9159 (t70) cc_final: 0.8561 (t0) REVERT: E 50 GLU cc_start: 0.9557 (mp0) cc_final: 0.9093 (mp0) REVERT: E 90 MET cc_start: 0.9279 (mmp) cc_final: 0.8870 (mmp) REVERT: E 94 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8883 (mm-30) REVERT: E 97 GLU cc_start: 0.9311 (mt-10) cc_final: 0.8847 (mt-10) REVERT: E 120 MET cc_start: 0.9422 (mmp) cc_final: 0.8770 (mmm) REVERT: F 63 GLU cc_start: 0.9521 (pt0) cc_final: 0.9308 (pp20) REVERT: H 65 ASP cc_start: 0.9133 (t0) cc_final: 0.8654 (t0) REVERT: L 84 MET cc_start: 0.8918 (tpp) cc_final: 0.8616 (tpp) REVERT: L 85 ASP cc_start: 0.9251 (m-30) cc_final: 0.9005 (p0) REVERT: M 61 GLU cc_start: 0.9421 (tm-30) cc_final: 0.9136 (tp30) REVERT: M 89 ASN cc_start: 0.9464 (m-40) cc_final: 0.9130 (m110) REVERT: N 59 MET cc_start: 0.9769 (mmp) cc_final: 0.9425 (mmm) REVERT: O 106 ASP cc_start: 0.9387 (m-30) cc_final: 0.9146 (m-30) REVERT: P 68 ASP cc_start: 0.9507 (m-30) cc_final: 0.9294 (m-30) REVERT: Q 73 GLU cc_start: 0.9690 (mm-30) cc_final: 0.9279 (tp30) REVERT: R 39 TYR cc_start: 0.9345 (m-10) cc_final: 0.9081 (m-10) REVERT: R 56 GLU cc_start: 0.9513 (tt0) cc_final: 0.9139 (tt0) REVERT: S 132 ASN cc_start: 0.6892 (p0) cc_final: 0.6387 (m-40) REVERT: T 132 ASN cc_start: 0.9239 (t0) cc_final: 0.8753 (m110) REVERT: W 387 MET cc_start: 0.9433 (mtm) cc_final: 0.9182 (mtt) REVERT: W 403 MET cc_start: 0.8763 (mpp) cc_final: 0.8476 (mpp) REVERT: W 697 MET cc_start: 0.8915 (mtm) cc_final: 0.8463 (mtm) REVERT: W 781 MET cc_start: 0.9099 (mmp) cc_final: 0.8495 (mmp) REVERT: W 802 MET cc_start: 0.9767 (ptp) cc_final: 0.9463 (ppp) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.4085 time to fit residues: 115.7840 Evaluate side-chains 128 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 2.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 9 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 197 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 210 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 121 optimal weight: 0.0270 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 93 GLN W 385 ASN ** W 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 813 HIS ** 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 = 0.3068 r_free = 0.3068 target = 0.041232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.026298 restraints weight = 292983.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.026465 restraints weight = 179143.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.026611 restraints weight = 134739.984| |-----------------------------------------------------------------------------| r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28073 Z= 0.151 Angle : 0.601 9.797 39946 Z= 0.347 Chirality : 0.035 0.188 4532 Planarity : 0.004 0.063 3427 Dihedral : 29.099 125.008 7522 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.18), residues: 2060 helix: 1.77 (0.14), residues: 1388 sheet: -0.42 (0.55), residues: 88 loop : -0.55 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP W 311 HIS 0.006 0.001 HIS L 75 PHE 0.017 0.001 PHE W 379 TYR 0.012 0.001 TYR W 245 ARG 0.008 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 1691) hydrogen bonds : angle 3.79475 ( 4414) covalent geometry : bond 0.00317 (28072) covalent geometry : angle 0.60061 (39946) Misc. bond : bond 0.00014 ( 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 176 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 2.483 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: 0.9632 (pt) cc_final: 0.9328 (pt) REVERT: A 120 MET cc_start: 0.9307 (mmm) cc_final: 0.8809 (mmm) REVERT: C 56 GLU cc_start: 0.9038 (pt0) cc_final: 0.8478 (pp20) REVERT: C 73 ASN cc_start: 0.9354 (t0) cc_final: 0.9083 (t0) REVERT: C 90 ASP cc_start: 0.8566 (t0) cc_final: 0.8267 (t70) REVERT: C 95 LYS cc_start: 0.9401 (mtmm) cc_final: 0.9086 (mtmt) REVERT: D 65 ASP cc_start: 0.9146 (t70) cc_final: 0.8509 (t0) REVERT: E 50 GLU cc_start: 0.9544 (mp0) cc_final: 0.9090 (mp0) REVERT: E 90 MET cc_start: 0.9259 (mmp) cc_final: 0.8877 (mmp) REVERT: E 94 GLU cc_start: 0.9239 (mm-30) cc_final: 0.9032 (mm-30) REVERT: E 120 MET cc_start: 0.9400 (mmp) cc_final: 0.8759 (mmm) REVERT: F 63 GLU cc_start: 0.9503 (pt0) cc_final: 0.9294 (pp20) REVERT: H 56 MET cc_start: 0.9404 (tpp) cc_final: 0.9201 (tpp) REVERT: H 65 ASP cc_start: 0.9084 (t0) cc_final: 0.8596 (t0) REVERT: K 106 ASP cc_start: 0.9428 (m-30) cc_final: 0.9218 (m-30) REVERT: L 84 MET cc_start: 0.8881 (tpp) cc_final: 0.8574 (tpp) REVERT: L 85 ASP cc_start: 0.9257 (m-30) cc_final: 0.9020 (p0) REVERT: M 61 GLU cc_start: 0.9382 (tm-30) cc_final: 0.9079 (tp30) REVERT: M 84 GLN cc_start: 0.9500 (tp-100) cc_final: 0.9192 (tp40) REVERT: M 89 ASN cc_start: 0.9479 (m-40) cc_final: 0.9151 (m110) REVERT: N 59 MET cc_start: 0.9722 (mmp) cc_final: 0.9378 (mmm) REVERT: O 106 ASP cc_start: 0.9325 (m-30) cc_final: 0.9085 (m-30) REVERT: O 120 MET cc_start: 0.8569 (mmm) cc_final: 0.8147 (mmm) REVERT: P 68 ASP cc_start: 0.9475 (m-30) cc_final: 0.9268 (m-30) REVERT: Q 73 GLU cc_start: 0.9677 (mm-30) cc_final: 0.9052 (tp30) REVERT: R 39 TYR cc_start: 0.9354 (m-10) cc_final: 0.9107 (m-10) REVERT: R 56 GLU cc_start: 0.9509 (tt0) cc_final: 0.9114 (tt0) REVERT: S 132 ASN cc_start: 0.6898 (p0) cc_final: 0.6388 (m-40) REVERT: T 132 ASN cc_start: 0.9249 (t0) cc_final: 0.8824 (m110) REVERT: W 387 MET cc_start: 0.9459 (mtm) cc_final: 0.9211 (mtt) REVERT: W 403 MET cc_start: 0.8742 (mpp) cc_final: 0.8478 (mpp) REVERT: W 697 MET cc_start: 0.8981 (mtm) cc_final: 0.8552 (mtm) REVERT: W 781 MET cc_start: 0.9130 (mmp) cc_final: 0.8388 (mmp) REVERT: W 802 MET cc_start: 0.9748 (ptp) cc_final: 0.9395 (ppp) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.5468 time to fit residues: 159.8290 Evaluate side-chains 130 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 46 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 224 optimal weight: 3.9990 chunk 243 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 225 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 GLN ** W 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 796 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 = 0.3049 r_free = 0.3049 target = 0.040377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.025540 restraints weight = 299616.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.025700 restraints weight = 186055.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.025834 restraints weight = 142060.015| |-----------------------------------------------------------------------------| r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 28073 Z= 0.214 Angle : 0.614 10.623 39946 Z= 0.357 Chirality : 0.036 0.170 4532 Planarity : 0.004 0.061 3427 Dihedral : 29.117 125.176 7522 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.18), residues: 2060 helix: 1.76 (0.14), residues: 1397 sheet: -0.59 (0.53), residues: 93 loop : -0.55 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 311 HIS 0.006 0.001 HIS L 75 PHE 0.029 0.002 PHE O 104 TYR 0.012 0.001 TYR F 88 ARG 0.008 0.000 ARG P 92 Details of bonding type rmsd hydrogen bonds : bond 0.05058 ( 1691) hydrogen bonds : angle 3.90348 ( 4414) covalent geometry : bond 0.00461 (28072) covalent geometry : angle 0.61412 (39946) Misc. bond : bond 0.00029 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10495.08 seconds wall clock time: 188 minutes 16.40 seconds (11296.40 seconds total)