Starting phenix.real_space_refine on Sun Sep 13 05:00:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ftx_4318/09_2026/6ftx_4318_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ftx_4318/09_2026/6ftx_4318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ftx_4318/09_2026/6ftx_4318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ftx_4318/09_2026/6ftx_4318.map" model { file = "/net/cci-nas-00/data/ceres_data/6ftx_4318/09_2026/6ftx_4318_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ftx_4318/09_2026/6ftx_4318_neut.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians P 320 5.49 5 S 41 5.16 5 Be 1 3.05 5 C 12267 2.51 5 N 3844 2.21 5 O 4573 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21049 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" 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: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 866 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "F" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 686 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 90} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3238 Classifications: {'DNA': 159} Link IDs: {'rna3p': 158} Chain: "J" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3298 Classifications: {'DNA': 160} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 159} Chain: "N" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "O" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "W" Number of atoms: 7189 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 878, 7173 Classifications: {'peptide': 878} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 848} Chain breaks: 5 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 878, 7173 Classifications: {'peptide': 878} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 848} Chain breaks: 5 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 7294 Chain: "W" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.43, per 1000 atoms: 0.26 Number of scatterers: 21049 At special positions: 0 Unit cell: (152.6, 147, 173.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 41 16.00 P 320 15.00 F 3 9.00 O 4573 8.00 N 3844 7.00 C 12267 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS W 207 " - pdb=" SG CYS W 246 " distance=2.82 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 966.7 milliseconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3402 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 14 sheets defined 53.6% alpha, 5.6% beta 84 base pairs and 219 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 removed outlier: 3.670A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.580A pdb=" N GLN A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.541A pdb=" N ALA A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 4.006A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.832A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.627A pdb=" N ALA B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.927A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 4.032A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N HIS C 31 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 33 " --> pdb=" O ARG C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.758A pdb=" N LEU C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.586A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 removed outlier: 3.681A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 54 through 79 removed outlier: 3.602A pdb=" N GLU D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS D 79 " --> pdb=" O SER D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.939A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.752A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 57 removed outlier: 3.537A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 79 removed outlier: 3.801A pdb=" N ARG E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG E 72 " --> pdb=" O GLN E 68 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.850A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 132 removed outlier: 3.730A pdb=" N ALA E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.804A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 76 removed outlier: 3.745A pdb=" N TYR F 51 " --> pdb=" O SER F 47 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.709A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 34 Processing helix chain 'G' and resid 46 through 73 removed outlier: 4.232A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.850A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA G 86 " --> pdb=" O HIS G 82 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 98 removed outlier: 4.680A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.538A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS H 43 " --> pdb=" O TYR H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.661A pdb=" N ILE H 70 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 99 removed outlier: 3.524A pdb=" N ALA H 94 " --> pdb=" O GLU H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.736A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 31 removed outlier: 3.546A pdb=" N LYS N 29 " --> pdb=" O ASN N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 60 Processing helix chain 'O' and resid 22 through 35 Processing helix chain 'O' and resid 37 through 41 Processing helix chain 'O' and resid 56 through 60 Processing helix chain 'W' and resid 203 through 210 Processing helix chain 'W' and resid 239 through 255 removed outlier: 3.946A pdb=" N ASP W 243 " --> pdb=" O LEU W 239 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN W 244 " --> pdb=" O LYS W 240 " (cutoff:3.500A) Processing helix chain 'W' and resid 264 through 283 removed outlier: 3.614A pdb=" N GLU W 268 " --> pdb=" O ALA W 264 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG W 274 " --> pdb=" O MET W 270 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU W 283 " --> pdb=" O ASP W 279 " (cutoff:3.500A) Processing helix chain 'W' and resid 331 through 344 removed outlier: 3.687A pdb=" N VAL W 335 " --> pdb=" O ALA W 331 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU W 342 " --> pdb=" O PHE W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 383 through 388 Processing helix chain 'W' and resid 406 through 417 removed outlier: 3.514A pdb=" N THR W 411 " --> pdb=" O LYS W 407 " (cutoff:3.500A) Processing helix chain 'W' and resid 436 through 446 removed outlier: 3.651A pdb=" N TRP W 440 " --> pdb=" O THR W 436 " (cutoff:3.500A) Processing helix chain 'W' and resid 460 through 469 removed outlier: 3.682A pdb=" N ASP W 464 " --> pdb=" O GLN W 460 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG W 467 " --> pdb=" O ARG W 463 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR W 469 " --> pdb=" O THR W 465 " (cutoff:3.500A) Processing helix chain 'W' and resid 491 through 498 removed outlier: 3.814A pdb=" N LEU W 496 " --> pdb=" O TYR W 492 " (cutoff:3.500A) Processing helix chain 'W' and resid 498 through 505 removed outlier: 4.499A pdb=" N LEU W 502 " --> pdb=" O ASP W 498 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE W 505 " --> pdb=" O GLU W 501 " (cutoff:3.500A) Processing helix chain 'W' and resid 548 through 560 removed outlier: 4.023A pdb=" N LEU W 552 " --> pdb=" O ASN W 548 " (cutoff:3.500A) Processing helix chain 'W' and resid 578 through 591 removed outlier: 3.766A pdb=" N ARG W 588 " --> pdb=" O HIS W 584 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN W 591 " --> pdb=" O HIS W 587 " (cutoff:3.500A) Processing helix chain 'W' and resid 619 through 628 removed outlier: 3.540A pdb=" N THR W 623 " --> pdb=" O SER W 619 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU W 624 " --> pdb=" O ASP W 620 " (cutoff:3.500A) Processing helix chain 'W' and resid 629 through 631 No H-bonds generated for 'chain 'W' and resid 629 through 631' Processing helix chain 'W' and resid 639 through 653 removed outlier: 4.161A pdb=" N GLY W 644 " --> pdb=" O GLY W 640 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N HIS W 645 " --> pdb=" O ALA W 641 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE W 646 " --> pdb=" O LYS W 642 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU W 648 " --> pdb=" O GLY W 644 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU W 649 " --> pdb=" O HIS W 645 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE W 651 " --> pdb=" O SER W 647 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET W 652 " --> pdb=" O LEU W 648 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN W 653 " --> pdb=" O LEU W 649 " (cutoff:3.500A) Processing helix chain 'W' and resid 668 through 673 removed outlier: 3.878A pdb=" N VAL W 672 " --> pdb=" O ALA W 668 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU W 673 " --> pdb=" O GLU W 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 668 through 673' Processing helix chain 'W' and resid 683 through 693 removed outlier: 3.568A pdb=" N SER W 693 " --> pdb=" O GLY W 689 " (cutoff:3.500A) Processing helix chain 'W' and resid 694 through 709 removed outlier: 3.911A pdb=" N VAL W 698 " --> pdb=" O SER W 694 " (cutoff:3.500A) Processing helix chain 'W' and resid 720 through 732 removed outlier: 3.767A pdb=" N LEU W 724 " --> pdb=" O MET W 720 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP W 725 " --> pdb=" O VAL W 721 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER W 732 " --> pdb=" O GLY W 728 " (cutoff:3.500A) Processing helix chain 'W' and resid 746 through 759 removed outlier: 3.679A pdb=" N SER W 753 " --> pdb=" O GLN W 749 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE W 754 " --> pdb=" O ARG W 750 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP W 755 " --> pdb=" O ARG W 751 " (cutoff:3.500A) Processing helix chain 'W' and resid 796 through 802 Processing helix chain 'W' and resid 825 through 838 removed outlier: 3.986A pdb=" N VAL W 829 " --> pdb=" O VAL W 825 " (cutoff:3.500A) Processing helix chain 'W' and resid 1010 through 1025 removed outlier: 3.835A pdb=" N LYS W1019 " --> pdb=" O ARG W1015 " (cutoff:3.500A) Processing helix chain 'W' and resid 1030 through 1037 removed outlier: 3.778A pdb=" N LEU W1034 " --> pdb=" O ILE W1030 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE W1035 " --> pdb=" O LEU W1031 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP W1037 " --> pdb=" O GLU W1033 " (cutoff:3.500A) Processing helix chain 'W' and resid 1044 through 1091 removed outlier: 3.943A pdb=" N TYR W1048 " --> pdb=" O SER W1044 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY W1049 " --> pdb=" O PHE W1045 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR W1051 " --> pdb=" O LYS W1047 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET W1056 " --> pdb=" O TYR W1052 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP W1061 " --> pdb=" O GLU W1057 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS W1062 " --> pdb=" O ALA W1058 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL W1063 " --> pdb=" O ALA W1059 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS W1076 " --> pdb=" O GLU W1072 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA W1083 " --> pdb=" O LYS W1079 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS W1087 " --> pdb=" O ALA W1083 " (cutoff:3.500A) Processing helix chain 'W' and resid 1102 through 1112 removed outlier: 3.610A pdb=" N ARG W1106 " --> pdb=" O ASN W1102 " (cutoff:3.500A) Processing helix chain 'W' and resid 1129 through 1148 removed outlier: 3.512A pdb=" N LEU W1133 " --> pdb=" O ALA W1129 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU W1137 " --> pdb=" O LEU W1133 " (cutoff:3.500A) Processing helix chain 'W' and resid 1153 through 1157 removed outlier: 3.774A pdb=" N LYS W1156 " --> pdb=" O ASP W1153 " (cutoff:3.500A) Processing helix chain 'W' and resid 1175 through 1190 removed outlier: 3.668A pdb=" N ASP W1179 " --> pdb=" O THR W1175 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE W1184 " --> pdb=" O GLU W1180 " (cutoff:3.500A) Processing helix chain 'W' and resid 1194 through 1200 Processing helix chain 'W' and resid 1248 through 1265 removed outlier: 3.761A pdb=" N ASP W1257 " --> pdb=" O GLY W1253 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR W1258 " --> pdb=" O ARG W1254 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG W1264 " --> pdb=" O LEU W1260 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.770A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.510A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.395A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.583A pdb=" N LEU N 15 " --> pdb=" O ILE N 3 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL N 5 " --> pdb=" O ILE N 13 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE N 13 " --> pdb=" O VAL N 5 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 48 through 49 Processing sheet with id=AA9, first strand: chain 'O' and resid 12 through 16 Processing sheet with id=AB1, first strand: chain 'W' and resid 179 through 187 removed outlier: 5.740A pdb=" N VAL W 182 " --> pdb=" O LYS W 216 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS W 216 " --> pdb=" O VAL W 182 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN W 184 " --> pdb=" O LEU W 214 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE W 213 " --> pdb=" O GLU W 228 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'W' and resid 287 through 297 removed outlier: 6.867A pdb=" N LYS W 310 " --> pdb=" O GLU W 288 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE W 290 " --> pdb=" O LEU W 308 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU W 308 " --> pdb=" O ILE W 290 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASP W 292 " --> pdb=" O GLN W 306 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLN W 306 " --> pdb=" O ASP W 292 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN W 294 " --> pdb=" O GLN W 304 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLN W 304 " --> pdb=" O GLN W 294 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'W' and resid 397 through 399 removed outlier: 3.952A pdb=" N LEU W 539 " --> pdb=" O GLY W 397 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE W 540 " --> pdb=" O VAL W 512 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE W 430 " --> pdb=" O THR W 490 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'W' and resid 612 through 613 removed outlier: 6.449A pdb=" N LEU W 715 " --> pdb=" O VAL W 787 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL W 714 " --> pdb=" O PHE W 767 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU W 769 " --> pdb=" O VAL W 714 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE W 716 " --> pdb=" O LEU W 769 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'W' and resid 1118 through 1119 609 hydrogen bonds defined for protein. 1771 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 196 hydrogen bonds 380 hydrogen bond angles 0 basepair planarities 84 basepair parallelities 219 stacking parallelities Total time for adding SS restraints: 6.18 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.26: 2383 1.26 - 1.43: 7265 1.43 - 1.59: 11902 1.59 - 1.76: 452 1.76 - 1.92: 75 Bond restraints: 22077 Sorted by residual: bond pdb=" F2 BEF W1301 " pdb="BE BEF W1301 " ideal model delta sigma weight residual 1.476 1.823 -0.347 2.00e-02 2.50e+03 3.01e+02 bond pdb=" F3 BEF W1301 " pdb="BE BEF W1301 " ideal model delta sigma weight residual 1.476 1.783 -0.307 2.00e-02 2.50e+03 2.35e+02 bond pdb=" C4' DC I -2 " pdb=" O4' DC I -2 " ideal model delta sigma weight residual 1.446 1.593 -0.147 1.00e-02 1.00e+04 2.17e+02 bond pdb=" F1 BEF W1301 " pdb="BE BEF W1301 " ideal model delta sigma weight residual 1.476 1.744 -0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C ILE C 102 " pdb=" O ILE C 102 " ideal model delta sigma weight residual 1.236 1.356 -0.120 1.00e-02 1.00e+04 1.45e+02 ... (remaining 22072 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 28870 4.37 - 8.73: 2100 8.73 - 13.10: 172 13.10 - 17.47: 23 17.47 - 21.83: 3 Bond angle restraints: 31168 Sorted by residual: angle pdb=" CA ALA G 47 " pdb=" C ALA G 47 " pdb=" N PRO G 48 " ideal model delta sigma weight residual 120.52 109.66 10.86 8.30e-01 1.45e+00 1.71e+02 angle pdb=" O5' DG J -42 " pdb=" C5' DG J -42 " pdb=" C4' DG J -42 " ideal model delta sigma weight residual 109.40 118.76 -9.36 8.00e-01 1.56e+00 1.37e+02 angle pdb=" O5' DC J -27 " pdb=" C5' DC J -27 " pdb=" C4' DC J -27 " ideal model delta sigma weight residual 109.40 117.69 -8.29 8.00e-01 1.56e+00 1.07e+02 angle pdb=" N TYR C 39 " pdb=" CA TYR C 39 " pdb=" C TYR C 39 " ideal model delta sigma weight residual 110.97 121.99 -11.02 1.09e+00 8.42e-01 1.02e+02 angle pdb=" CB GLU O 64 " pdb=" CG GLU O 64 " pdb=" CD GLU O 64 " ideal model delta sigma weight residual 112.60 128.89 -16.29 1.70e+00 3.46e-01 9.18e+01 ... (remaining 31163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 10784 35.12 - 70.24: 1671 70.24 - 105.36: 67 105.36 - 140.49: 4 140.49 - 175.61: 1 Dihedral angle restraints: 12527 sinusoidal: 7266 harmonic: 5261 Sorted by residual: dihedral pdb=" CD ARG D 30 " pdb=" NE ARG D 30 " pdb=" CZ ARG D 30 " pdb=" NH1 ARG D 30 " ideal model delta sinusoidal sigma weight residual 0.00 87.52 -87.52 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CD ARG G 77 " pdb=" NE ARG G 77 " pdb=" CZ ARG G 77 " pdb=" NH1 ARG G 77 " ideal model delta sinusoidal sigma weight residual 0.00 87.05 -87.05 1 1.00e+01 1.00e-02 9.11e+01 dihedral pdb=" C ASN D 81 " pdb=" N ASN D 81 " pdb=" CA ASN D 81 " pdb=" CB ASN D 81 " ideal model delta harmonic sigma weight residual -122.60 -144.97 22.37 0 2.50e+00 1.60e-01 8.01e+01 ... (remaining 12524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 2911 0.157 - 0.314: 516 0.314 - 0.471: 62 0.471 - 0.628: 17 0.628 - 0.784: 2 Chirality restraints: 3508 Sorted by residual: chirality pdb=" CA ASN D 81 " pdb=" N ASN D 81 " pdb=" C ASN D 81 " pdb=" CB ASN D 81 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" C3' DG I -52 " pdb=" C4' DG I -52 " pdb=" O3' DG I -52 " pdb=" C2' DG I -52 " both_signs ideal model delta sigma weight residual False -2.73 -1.96 -0.77 2.00e-01 2.50e+01 1.47e+01 chirality pdb=" C3' DC I -29 " pdb=" C4' DC I -29 " pdb=" O3' DC I -29 " pdb=" C2' DC I -29 " both_signs ideal model delta sigma weight residual False -2.73 -2.12 -0.61 2.00e-01 2.50e+01 9.24e+00 ... (remaining 3505 not shown) Planarity restraints: 2863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 30 " 1.099 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG D 30 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG D 30 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG D 30 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG D 30 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 77 " 1.098 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG G 77 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG G 77 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG G 77 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG G 77 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J -19 " -0.149 2.00e-02 2.50e+03 6.23e-02 1.16e+02 pdb=" N9 DG J -19 " 0.038 2.00e-02 2.50e+03 pdb=" C8 DG J -19 " 0.027 2.00e-02 2.50e+03 pdb=" N7 DG J -19 " 0.034 2.00e-02 2.50e+03 pdb=" C5 DG J -19 " 0.027 2.00e-02 2.50e+03 pdb=" C6 DG J -19 " -0.050 2.00e-02 2.50e+03 pdb=" O6 DG J -19 " -0.046 2.00e-02 2.50e+03 pdb=" N1 DG J -19 " -0.049 2.00e-02 2.50e+03 pdb=" C2 DG J -19 " 0.049 2.00e-02 2.50e+03 pdb=" N2 DG J -19 " -0.024 2.00e-02 2.50e+03 pdb=" N3 DG J -19 " 0.073 2.00e-02 2.50e+03 pdb=" C4 DG J -19 " 0.070 2.00e-02 2.50e+03 ... (remaining 2860 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 158 2.37 - 3.00: 11667 3.00 - 3.63: 33685 3.63 - 4.27: 50954 4.27 - 4.90: 74033 Nonbonded interactions: 170497 Sorted by model distance: nonbonded pdb=" NH1 ARG E 63 " pdb=" C5' DA I 17 " model vdw 1.732 3.520 nonbonded pdb=" OE2 GLU A 59 " pdb=" O LEU A 60 " model vdw 1.840 3.040 nonbonded pdb=" O2 DC I 22 " pdb=" N1 DG J -21 " model vdw 1.851 2.496 nonbonded pdb=" O2 DT I 62 " pdb=" N1 DA J -62 " model vdw 1.868 2.496 nonbonded pdb=" NE ARG C 17 " pdb=" OP1 DT I -43 " model vdw 1.868 3.120 ... (remaining 170492 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' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and ((resid 20 through 24 and (name N or name CA or name C or name O \ or name CB )) or resid 25 through 102)) selection = (chain 'F' and resid 20 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } ncs_group { reference = chain 'N' selection = chain 'O' } 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=0.19 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: 1.580 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 24.020 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 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 : 0.021 0.832 22080 Z= 1.595 Angle : 2.396 46.817 31170 Z= 1.562 Chirality : 0.127 0.784 3508 Planarity : 0.039 0.492 2863 Dihedral : 26.058 175.606 9122 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 68.71 Ramachandran Plot: Outliers : 1.63 % Allowed : 8.11 % Favored : 90.26 % Rotamer: Outliers : 3.23 % Allowed : 10.85 % Favored : 85.92 % Cbeta Deviations : 0.82 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.16), residues: 1778 helix: -1.38 (0.14), residues: 885 sheet: -0.70 (0.49), residues: 96 loop : -2.77 (0.18), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.080 0.006 ARG B 40 TYR 0.143 0.020 TYR H 34 PHE 0.098 0.016 PHE A 67 TRP 0.053 0.016 TRP W 447 HIS 0.036 0.008 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.01968 / 1.44 (22077) covalent geometry : angle 2.38167 / 1.56 (31168) SS BOND : bond 0.79175 / 52.78 ( 1) SS BOND : angle 33.25421 / 17.57 ( 2) hydrogen bonds : bond 0.30032 / 20.31 ( 805) hydrogen bonds : angle 11.32447 / 8.05 ( 2151) Misc. bond : bond 0.67397 / 45.72 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 389 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.8554 (m-80) cc_final: 0.8209 (m-80) REVERT: A 107 THR cc_start: 0.7686 (m) cc_final: 0.7038 (p) REVERT: C 36 LYS cc_start: 0.9568 (mmtm) cc_final: 0.9283 (mtmt) REVERT: C 38 ASN cc_start: 0.9311 (m-40) cc_final: 0.9025 (m-40) REVERT: C 71 ARG cc_start: 0.7346 (mmt-90) cc_final: 0.6961 (mmt-90) REVERT: D 48 ASP cc_start: 0.9288 (m-30) cc_final: 0.9035 (m-30) REVERT: D 86 ILE cc_start: 0.7983 (mp) cc_final: 0.7730 (mt) REVERT: E 120 MET cc_start: 0.2022 (mmm) cc_final: 0.1540 (mmt) REVERT: G 15 LYS cc_start: 0.6591 (tttt) cc_final: 0.6164 (mmtp) REVERT: G 92 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8240 (pt0) REVERT: H 51 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7230 (pt) REVERT: H 56 MET cc_start: 0.8524 (ttm) cc_final: 0.8042 (tmm) REVERT: W 305 LEU cc_start: 0.7616 (tp) cc_final: 0.7405 (tp) REVERT: W 322 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.6194 (mm-30) REVERT: W 376 LEU cc_start: 0.7258 (mt) cc_final: 0.6376 (mp) REVERT: W 379 PHE cc_start: 0.8831 (t80) cc_final: 0.8181 (t80) REVERT: W 463 ARG cc_start: 0.9171 (ttp-170) cc_final: 0.8514 (ttm-80) REVERT: W 467 ARG cc_start: 0.9676 (mtt180) cc_final: 0.9435 (mtm180) REVERT: W 495 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.6973 (mp) REVERT: W 594 ILE cc_start: 0.8875 (mm) cc_final: 0.8580 (mm) REVERT: W 637 LEU cc_start: 0.8843 (tt) cc_final: 0.8560 (mt) REVERT: W 670 GLU cc_start: 0.9330 (mp0) cc_final: 0.9046 (tp30) REVERT: W 741 LEU cc_start: 0.9370 (tt) cc_final: 0.9158 (tt) REVERT: W 817 TYR cc_start: 0.9381 (m-80) cc_final: 0.8959 (m-80) REVERT: W 832 ARG cc_start: 0.9312 (mtp180) cc_final: 0.8999 (ptm-80) REVERT: W 1053 ASP cc_start: 0.9121 (t70) cc_final: 0.8908 (m-30) REVERT: W 1255 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.6805 (tpm170) REVERT: W 1259 LEU cc_start: 0.8590 (mt) cc_final: 0.7316 (mt) outliers start: 50 outliers final: 13 residues processed: 428 average time/residue: 0.1720 time to fit residues: 108.2309 Evaluate side-chains 263 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 245 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 30.0000 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 ASN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN N 2 GLN N 40 GLN ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 474 ASN ** W 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 579 GLN W 645 HIS ** W 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 739 GLN W 756 HIS W 813 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.112249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.078231 restraints weight = 209312.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.080961 restraints weight = 115925.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.083132 restraints weight = 78456.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.084063 restraints weight = 61709.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.084859 restraints weight = 53984.961| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3977 r_free = 0.3977 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3977 r_free = 0.3977 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 22080 Z= 0.224 Angle : 0.973 11.301 31170 Z= 0.517 Chirality : 0.059 0.338 3508 Planarity : 0.008 0.159 2863 Dihedral : 29.551 167.833 5475 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.22 % Favored : 95.27 % Rotamer: Outliers : 0.26 % Allowed : 3.68 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.18), residues: 1778 helix: -0.31 (0.15), residues: 910 sheet: -0.87 (0.49), residues: 96 loop : -2.28 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 63 TYR 0.034 0.003 TYR B 88 PHE 0.032 0.003 PHE A 104 TRP 0.023 0.003 TRP W1194 HIS 0.015 0.002 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.22 (22077) covalent geometry : angle 0.97139 / 0.52 (31168) SS BOND : bond 0.00361 / 0.24 ( 1) SS BOND : angle 7.19832 / 3.96 ( 2) hydrogen bonds : bond 0.11075 / 7.45 ( 805) hydrogen bonds : angle 5.42805 / 3.86 ( 2151) Misc. bond : bond 0.01831 / 1.29 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 333 time to evaluate : 0.567 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: 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 77 ASP cc_start: 0.8953 (m-30) cc_final: 0.8714 (m-30) REVERT: A 110 CYS cc_start: 0.8863 (m) cc_final: 0.8562 (t) REVERT: B 59 LYS cc_start: 0.9787 (mtmt) cc_final: 0.9490 (mmmt) REVERT: C 35 ARG cc_start: 0.8623 (ptp90) cc_final: 0.8357 (ptp90) REVERT: C 36 LYS cc_start: 0.8992 (mmtm) cc_final: 0.8502 (mttt) REVERT: C 110 ASN cc_start: 0.9063 (t0) cc_final: 0.8704 (t0) REVERT: D 54 LYS cc_start: 0.7476 (pttm) cc_final: 0.7153 (pttm) REVERT: D 82 LYS cc_start: 0.9528 (mmmt) cc_final: 0.9232 (mppt) REVERT: D 86 ILE cc_start: 0.7979 (mp) cc_final: 0.7666 (mt) REVERT: D 105 LYS cc_start: 0.9139 (ptpp) cc_final: 0.8936 (ptpp) REVERT: E 50 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8460 (mt-10) REVERT: E 67 PHE cc_start: 0.8218 (t80) cc_final: 0.7953 (t80) REVERT: E 104 PHE cc_start: 0.9694 (m-10) cc_final: 0.9448 (m-10) REVERT: E 120 MET cc_start: -0.1474 (mmm) cc_final: -0.1683 (mmt) REVERT: G 15 LYS cc_start: 0.6636 (ttpt) cc_final: 0.6020 (mmtp) REVERT: G 23 LEU cc_start: 0.8282 (mt) cc_final: 0.7985 (mt) REVERT: G 90 ASP cc_start: 0.9225 (t0) cc_final: 0.8939 (t70) REVERT: G 97 LEU cc_start: 0.8869 (mp) cc_final: 0.8545 (tt) REVERT: G 100 VAL cc_start: 0.7059 (OUTLIER) cc_final: 0.5987 (m) REVERT: H 56 MET cc_start: 0.8565 (ttm) cc_final: 0.8018 (tpp) REVERT: H 81 ASN cc_start: 0.9657 (t0) cc_final: 0.9256 (t0) REVERT: H 96 ARG cc_start: 0.8852 (ttm110) cc_final: 0.8248 (tpm170) REVERT: H 118 TYR cc_start: 0.9011 (t80) cc_final: 0.8797 (t80) REVERT: W 270 MET cc_start: 0.7974 (mmp) cc_final: 0.7585 (mtm) REVERT: W 379 PHE cc_start: 0.7964 (t80) cc_final: 0.7178 (t80) REVERT: W 423 ARG cc_start: 0.9667 (mtt-85) cc_final: 0.9462 (mmm160) REVERT: W 429 ILE cc_start: 0.8942 (tp) cc_final: 0.8468 (tp) REVERT: W 483 MET cc_start: 0.8045 (mmp) cc_final: 0.7729 (mmm) REVERT: W 560 MET cc_start: 0.8671 (mtp) cc_final: 0.8353 (ptm) REVERT: W 723 MET cc_start: 0.8216 (tmm) cc_final: 0.7858 (tmm) REVERT: W 794 ASN cc_start: 0.8232 (t0) cc_final: 0.7440 (p0) REVERT: W 802 MET cc_start: 0.7682 (ppp) cc_final: 0.7212 (ppp) REVERT: W 832 ARG cc_start: 0.8654 (mtp180) cc_final: 0.8145 (ptm-80) outliers start: 4 outliers final: 1 residues processed: 335 average time/residue: 0.1510 time to fit residues: 75.9306 Evaluate side-chains 239 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 237 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 157 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 187 optimal weight: 4.9990 chunk 198 optimal weight: 6.9990 chunk 200 optimal weight: 20.0000 chunk 189 optimal weight: 6.9990 chunk 113 optimal weight: 40.0000 chunk 53 optimal weight: 7.9990 chunk 92 optimal weight: 30.0000 chunk 66 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.096937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.062614 restraints weight = 183072.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.064833 restraints weight = 105198.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.066345 restraints weight = 73290.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.067454 restraints weight = 58833.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.067955 restraints weight = 51157.010| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3857 r_free = 0.3857 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3857 r_free = 0.3857 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 22080 Z= 0.261 Angle : 0.892 18.736 31170 Z= 0.481 Chirality : 0.053 0.363 3508 Planarity : 0.007 0.125 2863 Dihedral : 29.300 161.078 5475 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 22.96 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.17 % Favored : 95.50 % Rotamer: Outliers : 0.26 % Allowed : 3.55 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.18), residues: 1778 helix: -0.31 (0.15), residues: 928 sheet: -1.09 (0.47), residues: 108 loop : -2.07 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 39 TYR 0.026 0.003 TYR E 54 PHE 0.036 0.003 PHE G 25 TRP 0.052 0.003 TRP W1194 HIS 0.009 0.002 HIS W 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.26 (22077) covalent geometry : angle 0.89151 / 0.48 (31168) SS BOND : bond 0.00622 / 0.41 ( 1) SS BOND : angle 3.52294 / 1.93 ( 2) hydrogen bonds : bond 0.10976 / 7.42 ( 805) hydrogen bonds : angle 5.30267 / 3.78 ( 2151) Misc. bond : bond 0.00593 / 0.42 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 284 time to evaluate : 0.497 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: 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 77 ASP cc_start: 0.9003 (m-30) cc_final: 0.8791 (m-30) REVERT: B 74 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8965 (pp20) REVERT: C 35 ARG cc_start: 0.8756 (ptp90) cc_final: 0.8498 (ttp80) REVERT: D 82 LYS cc_start: 0.9572 (mmmt) cc_final: 0.9343 (mppt) REVERT: E 60 LEU cc_start: 0.7625 (mp) cc_final: 0.7331 (pt) REVERT: E 67 PHE cc_start: 0.8457 (t80) cc_final: 0.8052 (t80) REVERT: E 97 GLU cc_start: 0.9544 (OUTLIER) cc_final: 0.9234 (mt-10) REVERT: E 104 PHE cc_start: 0.9793 (m-10) cc_final: 0.9414 (m-10) REVERT: E 110 CYS cc_start: 0.8880 (t) cc_final: 0.8573 (t) REVERT: E 120 MET cc_start: -0.1353 (mmm) cc_final: -0.1558 (mmt) REVERT: G 15 LYS cc_start: 0.5994 (ttpt) cc_final: 0.5235 (mmtp) REVERT: G 56 GLU cc_start: 0.9365 (tm-30) cc_final: 0.9125 (tm-30) REVERT: G 97 LEU cc_start: 0.8876 (mp) cc_final: 0.8484 (tt) REVERT: H 56 MET cc_start: 0.8616 (ttm) cc_final: 0.7867 (tmm) REVERT: H 81 ASN cc_start: 0.9660 (t0) cc_final: 0.9379 (t0) REVERT: H 118 TYR cc_start: 0.9138 (t80) cc_final: 0.8723 (t80) REVERT: W 230 TYR cc_start: 0.8405 (m-80) cc_final: 0.7693 (m-80) REVERT: W 367 GLN cc_start: 0.8954 (pt0) cc_final: 0.8433 (pt0) REVERT: W 379 PHE cc_start: 0.8153 (t80) cc_final: 0.7494 (t80) REVERT: W 395 ASP cc_start: 0.8380 (t0) cc_final: 0.7673 (p0) REVERT: W 423 ARG cc_start: 0.9692 (mtt-85) cc_final: 0.9474 (mmm160) REVERT: W 429 ILE cc_start: 0.9228 (tp) cc_final: 0.8812 (tp) REVERT: W 518 LEU cc_start: 0.8777 (pp) cc_final: 0.8232 (mt) REVERT: W 534 VAL cc_start: 0.7416 (m) cc_final: 0.6923 (t) REVERT: W 560 MET cc_start: 0.8754 (mtp) cc_final: 0.8478 (ptm) REVERT: W 595 LEU cc_start: 0.8856 (tt) cc_final: 0.8520 (tt) REVERT: W 723 MET cc_start: 0.8744 (tmm) cc_final: 0.8098 (tmm) REVERT: W 794 ASN cc_start: 0.8250 (t0) cc_final: 0.7785 (t0) REVERT: W 802 MET cc_start: 0.8004 (ppp) cc_final: 0.7597 (ppp) REVERT: W 832 ARG cc_start: 0.8758 (mtp180) cc_final: 0.8219 (ptp-170) REVERT: W 1055 MET cc_start: 0.0919 (ptm) cc_final: 0.0396 (ptp) outliers start: 4 outliers final: 0 residues processed: 286 average time/residue: 0.1650 time to fit residues: 70.9746 Evaluate side-chains 210 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 45 optimal weight: 0.0770 chunk 35 optimal weight: 0.9990 chunk 9 optimal weight: 0.0170 chunk 123 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 145 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 536 ASN W 685 ASN ** W 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.109410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.075148 restraints weight = 225944.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.077882 restraints weight = 123966.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.080017 restraints weight = 82553.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.081624 restraints weight = 64231.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.082634 restraints weight = 55422.187| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3929 r_free = 0.3929 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3929 r_free = 0.3929 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 22080 Z= 0.164 Angle : 0.771 9.276 31170 Z= 0.414 Chirality : 0.049 0.430 3508 Planarity : 0.005 0.062 2863 Dihedral : 29.124 167.881 5475 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.17 % Favored : 95.61 % Rotamer: Outliers : 0.19 % Allowed : 2.58 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.18), residues: 1778 helix: -0.07 (0.16), residues: 923 sheet: -0.70 (0.51), residues: 94 loop : -1.99 (0.20), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 76 TYR 0.024 0.002 TYR H 37 PHE 0.046 0.003 PHE W1119 TRP 0.027 0.002 TRP W1194 HIS 0.010 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (22077) covalent geometry : angle 0.77062 / 0.41 (31168) SS BOND : bond 0.00397 / 0.26 ( 1) SS BOND : angle 2.08838 / 1.13 ( 2) hydrogen bonds : bond 0.08444 / 5.64 ( 805) hydrogen bonds : angle 4.81812 / 3.44 ( 2151) Misc. bond : bond 0.00059 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 283 time to evaluate : 0.741 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: 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 77 ASP cc_start: 0.9028 (m-30) cc_final: 0.8808 (m-30) REVERT: A 90 MET cc_start: 0.6826 (mmp) cc_final: 0.6621 (mmm) REVERT: D 42 LEU cc_start: 0.9272 (tp) cc_final: 0.9026 (tp) REVERT: D 45 VAL cc_start: 0.8191 (m) cc_final: 0.7860 (m) REVERT: D 51 ILE cc_start: 0.9027 (pt) cc_final: 0.8663 (mm) REVERT: D 82 LYS cc_start: 0.9491 (mmmt) cc_final: 0.9162 (mppt) REVERT: D 105 LYS cc_start: 0.9172 (ptpp) cc_final: 0.8971 (ptpp) REVERT: E 67 PHE cc_start: 0.8196 (t80) cc_final: 0.7879 (t80) REVERT: E 104 PHE cc_start: 0.9733 (m-10) cc_final: 0.9435 (m-10) REVERT: E 110 CYS cc_start: 0.8774 (t) cc_final: 0.8513 (t) REVERT: E 120 MET cc_start: -0.1053 (mmm) cc_final: -0.1363 (mmt) REVERT: G 90 ASP cc_start: 0.9182 (t0) cc_final: 0.8957 (t0) REVERT: G 97 LEU cc_start: 0.8859 (mp) cc_final: 0.8444 (tt) REVERT: H 56 MET cc_start: 0.8838 (ttm) cc_final: 0.8543 (tpp) REVERT: H 81 ASN cc_start: 0.9568 (t0) cc_final: 0.9297 (t0) REVERT: H 96 ARG cc_start: 0.8773 (mtm180) cc_final: 0.8257 (mtm180) REVERT: H 118 TYR cc_start: 0.9179 (t80) cc_final: 0.8744 (t80) REVERT: W 282 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8566 (pp20) REVERT: W 370 PHE cc_start: 0.9387 (m-80) cc_final: 0.9157 (t80) REVERT: W 379 PHE cc_start: 0.8213 (t80) cc_final: 0.7520 (t80) REVERT: W 423 ARG cc_start: 0.9698 (mtt-85) cc_final: 0.9462 (mmm160) REVERT: W 463 ARG cc_start: 0.8373 (ttp-170) cc_final: 0.7765 (ttm170) REVERT: W 518 LEU cc_start: 0.8889 (pp) cc_final: 0.8385 (mt) REVERT: W 555 LEU cc_start: 0.9179 (mp) cc_final: 0.8961 (mp) REVERT: W 595 LEU cc_start: 0.8508 (tt) cc_final: 0.8288 (tt) REVERT: W 723 MET cc_start: 0.8801 (tmm) cc_final: 0.8261 (tmm) REVERT: W 794 ASN cc_start: 0.8605 (t0) cc_final: 0.8126 (t0) REVERT: W 802 MET cc_start: 0.8153 (ppp) cc_final: 0.7896 (ppp) outliers start: 3 outliers final: 0 residues processed: 283 average time/residue: 0.1579 time to fit residues: 68.4160 Evaluate side-chains 216 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 7 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 204 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 195 optimal weight: 30.0000 chunk 194 optimal weight: 5.9990 chunk 65 optimal weight: 0.0770 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 367 GLN ** W 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W1161 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.096163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.060276 restraints weight = 208390.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.062839 restraints weight = 114527.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.064611 restraints weight = 79619.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.065714 restraints weight = 63270.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.066345 restraints weight = 54913.531| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3834 r_free = 0.3834 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3834 r_free = 0.3834 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 22080 Z= 0.201 Angle : 0.773 10.898 31170 Z= 0.420 Chirality : 0.048 0.377 3508 Planarity : 0.006 0.064 2863 Dihedral : 28.821 178.674 5475 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.17 % Favored : 95.61 % Rotamer: Outliers : 0.26 % Allowed : 2.20 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.18), residues: 1778 helix: -0.10 (0.16), residues: 928 sheet: -0.67 (0.51), residues: 94 loop : -1.87 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 45 TYR 0.024 0.002 TYR D 118 PHE 0.041 0.003 PHE G 25 TRP 0.015 0.002 TRP W 386 HIS 0.010 0.002 HIS W 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.20 (22077) covalent geometry : angle 0.77251 / 0.42 (31168) SS BOND : bond 0.00030 / 0.02 ( 1) SS BOND : angle 1.28811 / 0.68 ( 2) hydrogen bonds : bond 0.09609 / 6.48 ( 805) hydrogen bonds : angle 4.87466 / 3.45 ( 2151) Misc. bond : bond 0.00069 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 267 time to evaluate : 0.639 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: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7871 (m-80) cc_final: 0.7323 (m-10) REVERT: A 77 ASP cc_start: 0.8871 (m-30) cc_final: 0.8654 (m-30) REVERT: B 63 GLU cc_start: 0.9330 (OUTLIER) cc_final: 0.9009 (pp20) REVERT: B 84 MET cc_start: 0.7252 (ttp) cc_final: 0.6837 (tmm) REVERT: D 38 VAL cc_start: 0.8664 (t) cc_final: 0.8401 (t) REVERT: D 39 TYR cc_start: 0.8288 (t80) cc_final: 0.7986 (t80) REVERT: D 42 LEU cc_start: 0.9297 (tp) cc_final: 0.9079 (tp) REVERT: D 51 ILE cc_start: 0.9116 (pt) cc_final: 0.8749 (mm) REVERT: D 82 LYS cc_start: 0.9548 (mmmt) cc_final: 0.9300 (mppt) REVERT: E 67 PHE cc_start: 0.8247 (t80) cc_final: 0.7719 (t80) REVERT: E 104 PHE cc_start: 0.9755 (m-10) cc_final: 0.9429 (m-10) REVERT: E 110 CYS cc_start: 0.8752 (t) cc_final: 0.8504 (t) REVERT: G 15 LYS cc_start: 0.6274 (ttpt) cc_final: 0.5376 (mmtp) REVERT: H 56 MET cc_start: 0.8897 (ttm) cc_final: 0.8165 (tmm) REVERT: H 96 ARG cc_start: 0.8804 (mtm180) cc_final: 0.8293 (mtm180) REVERT: H 118 TYR cc_start: 0.9211 (t80) cc_final: 0.8826 (t80) REVERT: W 334 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7839 (mt0) REVERT: W 379 PHE cc_start: 0.8399 (t80) cc_final: 0.7665 (t80) REVERT: W 398 ILE cc_start: 0.8725 (mp) cc_final: 0.8470 (mp) REVERT: W 423 ARG cc_start: 0.9717 (mtt-85) cc_final: 0.9461 (mmm160) REVERT: W 429 ILE cc_start: 0.9111 (tp) cc_final: 0.8908 (tp) REVERT: W 463 ARG cc_start: 0.8373 (ttp-170) cc_final: 0.7911 (ttm170) REVERT: W 518 LEU cc_start: 0.8828 (pp) cc_final: 0.8280 (mt) REVERT: W 555 LEU cc_start: 0.9272 (mp) cc_final: 0.9024 (mp) REVERT: W 723 MET cc_start: 0.8922 (tmm) cc_final: 0.8339 (tmm) REVERT: W 794 ASN cc_start: 0.8468 (t0) cc_final: 0.8154 (t0) REVERT: W 802 MET cc_start: 0.8213 (ppp) cc_final: 0.7907 (ppp) outliers start: 4 outliers final: 0 residues processed: 269 average time/residue: 0.1526 time to fit residues: 62.7462 Evaluate side-chains 218 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 112 optimal weight: 30.0000 chunk 136 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 26 optimal weight: 0.0020 chunk 138 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 chunk 75 optimal weight: 50.0000 chunk 158 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 166 optimal weight: 0.0570 chunk 95 optimal weight: 20.0000 overall best weight: 2.4112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 294 GLN W 367 GLN ** W 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.105629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.072620 restraints weight = 221512.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.074776 restraints weight = 124135.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.076105 restraints weight = 85839.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.077929 restraints weight = 68562.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.078482 restraints weight = 59381.504| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3857 r_free = 0.3857 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3857 r_free = 0.3857 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22080 Z= 0.170 Angle : 0.710 9.139 31170 Z= 0.389 Chirality : 0.046 0.346 3508 Planarity : 0.005 0.065 2863 Dihedral : 28.738 172.050 5475 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.11 % Favored : 95.66 % Rotamer: Outliers : 0.13 % Allowed : 1.74 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.19), residues: 1778 helix: 0.10 (0.16), residues: 923 sheet: -0.33 (0.53), residues: 93 loop : -1.80 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 42 TYR 0.020 0.002 TYR D 118 PHE 0.031 0.002 PHE G 25 TRP 0.014 0.001 TRP W1194 HIS 0.009 0.001 HIS W 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (22077) covalent geometry : angle 0.71019 / 0.39 (31168) SS BOND : bond 0.00078 / 0.05 ( 1) SS BOND : angle 0.85917 / 0.46 ( 2) hydrogen bonds : bond 0.08040 / 5.40 ( 805) hydrogen bonds : angle 4.67564 / 3.32 ( 2151) Misc. bond : bond 0.00017 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 276 time to evaluate : 0.413 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8882 (m-30) cc_final: 0.8656 (m-30) REVERT: B 84 MET cc_start: 0.7296 (ttp) cc_final: 0.6843 (tmm) REVERT: C 35 ARG cc_start: 0.9469 (ttp80) cc_final: 0.9207 (ttp80) REVERT: C 104 GLN cc_start: 0.7564 (mt0) cc_final: 0.7106 (mp10) REVERT: C 112 GLN cc_start: 0.8330 (pm20) cc_final: 0.8100 (pm20) REVERT: D 39 TYR cc_start: 0.8381 (t80) cc_final: 0.8121 (t80) REVERT: D 51 ILE cc_start: 0.9105 (pt) cc_final: 0.8855 (tp) REVERT: D 82 LYS cc_start: 0.9495 (mmmt) cc_final: 0.9203 (mppt) REVERT: D 105 LYS cc_start: 0.9069 (ptpp) cc_final: 0.8815 (ptpp) REVERT: E 67 PHE cc_start: 0.8170 (t80) cc_final: 0.7571 (t80) REVERT: E 92 LEU cc_start: 0.9729 (tp) cc_final: 0.9482 (tt) REVERT: E 104 PHE cc_start: 0.9723 (m-10) cc_final: 0.9453 (m-10) REVERT: E 110 CYS cc_start: 0.8607 (t) cc_final: 0.8390 (t) REVERT: F 97 LEU cc_start: 0.8264 (tt) cc_final: 0.8061 (tt) REVERT: H 56 MET cc_start: 0.8955 (ttm) cc_final: 0.8186 (tmm) REVERT: H 96 ARG cc_start: 0.8799 (mtm180) cc_final: 0.8276 (mtm180) REVERT: H 118 TYR cc_start: 0.9208 (t80) cc_final: 0.8836 (t80) REVERT: W 379 PHE cc_start: 0.8271 (t80) cc_final: 0.7712 (t80) REVERT: W 423 ARG cc_start: 0.9713 (mtt-85) cc_final: 0.9357 (mmm160) REVERT: W 463 ARG cc_start: 0.8355 (ttp-170) cc_final: 0.7909 (ttm170) REVERT: W 518 LEU cc_start: 0.8791 (pp) cc_final: 0.8138 (mt) REVERT: W 794 ASN cc_start: 0.8486 (t0) cc_final: 0.7783 (p0) REVERT: W 802 MET cc_start: 0.8273 (ppp) cc_final: 0.7957 (ppp) outliers start: 2 outliers final: 1 residues processed: 278 average time/residue: 0.1517 time to fit residues: 64.7148 Evaluate side-chains 212 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 14 optimal weight: 10.0000 chunk 136 optimal weight: 0.7980 chunk 198 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 97 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 203 optimal weight: 0.3980 chunk 179 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS D 46 HIS ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 806 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 = 0.4151 r_free = 0.4151 target = 0.094999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.060430 restraints weight = 190971.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.062405 restraints weight = 111908.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.063907 restraints weight = 79550.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.064350 restraints weight = 64562.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.065399 restraints weight = 58764.245| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3818 r_free = 0.3818 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3818 r_free = 0.3818 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 22080 Z= 0.189 Angle : 0.735 12.187 31170 Z= 0.404 Chirality : 0.046 0.301 3508 Planarity : 0.005 0.052 2863 Dihedral : 28.646 166.036 5475 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.28 % Favored : 95.50 % Rotamer: Outliers : 0.06 % Allowed : 1.74 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.19), residues: 1778 helix: -0.01 (0.16), residues: 928 sheet: -0.29 (0.52), residues: 93 loop : -1.72 (0.21), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG W 597 TYR 0.021 0.002 TYR D 118 PHE 0.041 0.003 PHE C 25 TRP 0.032 0.002 TRP W1174 HIS 0.011 0.002 HIS W 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.19 (22077) covalent geometry : angle 0.73493 / 0.40 (31168) SS BOND : bond 0.00210 / 0.14 ( 1) SS BOND : angle 0.66310 / 0.39 ( 2) hydrogen bonds : bond 0.08555 / 5.73 ( 805) hydrogen bonds : angle 4.80381 / 3.42 ( 2151) Misc. bond : bond 0.00530 / 0.35 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 0.640 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: 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 77 ASP cc_start: 0.8896 (m-30) cc_final: 0.8685 (m-30) REVERT: C 36 LYS cc_start: 0.9172 (mmtm) cc_final: 0.8569 (mttt) REVERT: C 104 GLN cc_start: 0.7632 (mt0) cc_final: 0.7105 (mp10) REVERT: D 39 TYR cc_start: 0.8354 (t80) cc_final: 0.8034 (t80) REVERT: D 42 LEU cc_start: 0.9193 (tp) cc_final: 0.8979 (tp) REVERT: D 82 LYS cc_start: 0.9499 (mmmt) cc_final: 0.9283 (mppt) REVERT: D 105 LYS cc_start: 0.9126 (ptpp) cc_final: 0.8918 (ptpp) REVERT: E 67 PHE cc_start: 0.8324 (t80) cc_final: 0.7624 (t80) REVERT: E 92 LEU cc_start: 0.9681 (tp) cc_final: 0.9451 (tp) REVERT: E 93 GLN cc_start: 0.9156 (pm20) cc_final: 0.8743 (pm20) REVERT: E 104 PHE cc_start: 0.9736 (m-10) cc_final: 0.9435 (m-10) REVERT: E 110 CYS cc_start: 0.8527 (t) cc_final: 0.8284 (t) REVERT: G 41 GLU cc_start: 0.6940 (tm-30) cc_final: 0.6645 (tm-30) REVERT: H 56 MET cc_start: 0.8850 (ttm) cc_final: 0.8239 (tmm) REVERT: H 96 ARG cc_start: 0.8773 (mtm180) cc_final: 0.8293 (mtm180) REVERT: H 118 TYR cc_start: 0.9241 (t80) cc_final: 0.8877 (t80) REVERT: W 379 PHE cc_start: 0.8535 (t80) cc_final: 0.7735 (t80) REVERT: W 463 ARG cc_start: 0.8359 (ttp-170) cc_final: 0.7911 (ttm170) REVERT: W 518 LEU cc_start: 0.8880 (pp) cc_final: 0.8298 (mt) REVERT: W 555 LEU cc_start: 0.9260 (mp) cc_final: 0.9056 (mp) REVERT: W 723 MET cc_start: 0.8557 (tmm) cc_final: 0.8312 (ppp) REVERT: W 794 ASN cc_start: 0.8535 (t0) cc_final: 0.7810 (p0) REVERT: W 802 MET cc_start: 0.8277 (ppp) cc_final: 0.7976 (ppp) outliers start: 1 outliers final: 0 residues processed: 262 average time/residue: 0.1531 time to fit residues: 61.4445 Evaluate side-chains 211 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 93 optimal weight: 20.0000 chunk 136 optimal weight: 0.6980 chunk 115 optimal weight: 30.0000 chunk 57 optimal weight: 0.6980 chunk 18 optimal weight: 0.0980 chunk 84 optimal weight: 20.0000 chunk 150 optimal weight: 0.9980 chunk 198 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS D 92 GLN G 68 ASN ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.097897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.063096 restraints weight = 220505.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 80)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.064302 restraints weight = 121904.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.065926 restraints weight = 82836.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.067151 restraints weight = 65180.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.067650 restraints weight = 56120.323| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3856 r_free = 0.3856 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3856 r_free = 0.3856 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22080 Z= 0.145 Angle : 0.699 8.828 31170 Z= 0.382 Chirality : 0.045 0.320 3508 Planarity : 0.005 0.052 2863 Dihedral : 28.584 170.600 5475 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.17 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.19), residues: 1778 helix: 0.11 (0.16), residues: 920 sheet: 0.36 (0.51), residues: 104 loop : -1.67 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG W 537 TYR 0.019 0.002 TYR H 37 PHE 0.032 0.002 PHE W 509 TRP 0.043 0.002 TRP W 391 HIS 0.007 0.001 HIS W 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 (22077) covalent geometry : angle 0.69867 / 0.38 (31168) SS BOND : bond 0.00009 / 0.01 ( 1) SS BOND : angle 0.75301 / 0.41 ( 2) hydrogen bonds : bond 0.07184 / 4.79 ( 805) hydrogen bonds : angle 4.55665 / 3.26 ( 2151) Misc. bond : bond 0.00032 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.634 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: A 77 ASP cc_start: 0.8844 (m-30) cc_final: 0.8642 (m-30) REVERT: C 36 LYS cc_start: 0.9060 (mmtm) cc_final: 0.8534 (mttt) REVERT: C 38 ASN cc_start: 0.8789 (m-40) cc_final: 0.8553 (m110) REVERT: C 104 GLN cc_start: 0.7687 (mt0) cc_final: 0.7118 (pm20) REVERT: D 82 LYS cc_start: 0.9497 (mmmt) cc_final: 0.9252 (mppt) REVERT: E 50 GLU cc_start: 0.8522 (mt-10) cc_final: 0.7640 (mt-10) REVERT: E 53 ARG cc_start: 0.9072 (pmt-80) cc_final: 0.8775 (pmt-80) REVERT: E 54 TYR cc_start: 0.8996 (m-10) cc_final: 0.8760 (m-10) REVERT: E 67 PHE cc_start: 0.8156 (t80) cc_final: 0.7491 (t80) REVERT: E 104 PHE cc_start: 0.9685 (m-10) cc_final: 0.9368 (m-10) REVERT: E 110 CYS cc_start: 0.8542 (t) cc_final: 0.8292 (t) REVERT: F 88 TYR cc_start: 0.9086 (m-10) cc_final: 0.8840 (m-80) REVERT: G 63 LEU cc_start: 0.9796 (mt) cc_final: 0.9551 (pp) REVERT: H 56 MET cc_start: 0.8814 (ttm) cc_final: 0.8234 (tmm) REVERT: H 96 ARG cc_start: 0.8672 (mtm180) cc_final: 0.8178 (mtm180) REVERT: H 118 TYR cc_start: 0.9195 (t80) cc_final: 0.8825 (t80) REVERT: W 379 PHE cc_start: 0.8345 (t80) cc_final: 0.7762 (t80) REVERT: W 396 ASN cc_start: 0.9154 (m-40) cc_final: 0.8795 (m-40) REVERT: W 423 ARG cc_start: 0.9723 (mtt-85) cc_final: 0.9403 (mmm160) REVERT: W 463 ARG cc_start: 0.8332 (ttp-170) cc_final: 0.7906 (ttm170) REVERT: W 518 LEU cc_start: 0.8782 (pp) cc_final: 0.8180 (mt) REVERT: W 538 MET cc_start: 0.8681 (mmp) cc_final: 0.7917 (mpp) REVERT: W 723 MET cc_start: 0.8560 (tmm) cc_final: 0.8308 (ppp) REVERT: W 794 ASN cc_start: 0.8449 (t0) cc_final: 0.7938 (p0) REVERT: W 802 MET cc_start: 0.8154 (ppp) cc_final: 0.7863 (ppp) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.1587 time to fit residues: 65.9339 Evaluate side-chains 215 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 20.0000 chunk 199 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 114 optimal weight: 50.0000 chunk 159 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 174 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 339 GLN W 367 GLN ** W 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 536 ASN ** W 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.090851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.057872 restraints weight = 170379.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.059847 restraints weight = 105049.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.061129 restraints weight = 77685.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.061958 restraints weight = 64337.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.062339 restraints weight = 57288.823| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3737 r_free = 0.3737 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3737 r_free = 0.3737 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.6400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 22080 Z= 0.248 Angle : 0.809 9.831 31170 Z= 0.444 Chirality : 0.048 0.256 3508 Planarity : 0.006 0.057 2863 Dihedral : 28.555 167.181 5475 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 26.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.24 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.18), residues: 1778 helix: -0.36 (0.16), residues: 940 sheet: 0.40 (0.46), residues: 112 loop : -1.69 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 45 TYR 0.025 0.002 TYR D 118 PHE 0.032 0.003 PHE G 25 TRP 0.029 0.003 TRP W 391 HIS 0.012 0.002 HIS W 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.25 (22077) covalent geometry : angle 0.80916 / 0.44 (31168) SS BOND : bond 0.00471 / 0.31 ( 1) SS BOND : angle 0.72450 / 0.51 ( 2) hydrogen bonds : bond 0.10275 / 6.88 ( 805) hydrogen bonds : angle 5.00880 / 3.57 ( 2151) Misc. bond : bond 0.00088 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.568 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: C 36 LYS cc_start: 0.9183 (mmtm) cc_final: 0.8637 (mttt) REVERT: C 104 GLN cc_start: 0.7786 (mt0) cc_final: 0.7186 (mp10) REVERT: C 112 GLN cc_start: 0.8446 (pm20) cc_final: 0.8100 (pm20) REVERT: D 105 LYS cc_start: 0.9139 (ptpp) cc_final: 0.8925 (ptpp) REVERT: E 67 PHE cc_start: 0.8395 (t80) cc_final: 0.7742 (t80) REVERT: E 100 LEU cc_start: 0.9835 (mt) cc_final: 0.9584 (mt) REVERT: E 104 PHE cc_start: 0.9695 (m-10) cc_final: 0.9422 (m-80) REVERT: E 110 CYS cc_start: 0.8572 (t) cc_final: 0.8213 (t) REVERT: F 88 TYR cc_start: 0.9281 (m-10) cc_final: 0.8974 (m-80) REVERT: G 36 LYS cc_start: 0.9693 (tttt) cc_final: 0.9486 (tmmt) REVERT: H 56 MET cc_start: 0.8894 (ttm) cc_final: 0.8222 (tmm) REVERT: H 96 ARG cc_start: 0.8697 (mtm180) cc_final: 0.8019 (mtm180) REVERT: H 118 TYR cc_start: 0.9288 (t80) cc_final: 0.8960 (t80) REVERT: W 379 PHE cc_start: 0.8821 (t80) cc_final: 0.8040 (t80) REVERT: W 423 ARG cc_start: 0.9719 (mtt-85) cc_final: 0.9474 (mmm160) REVERT: W 463 ARG cc_start: 0.8334 (ttp-170) cc_final: 0.7858 (ttm170) REVERT: W 518 LEU cc_start: 0.8845 (pp) cc_final: 0.8194 (mt) REVERT: W 595 LEU cc_start: 0.7998 (tp) cc_final: 0.7649 (tp) REVERT: W 794 ASN cc_start: 0.8506 (t0) cc_final: 0.7801 (p0) REVERT: W 802 MET cc_start: 0.8407 (ppp) cc_final: 0.8089 (ppp) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.1528 time to fit residues: 58.5604 Evaluate side-chains 191 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 65 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 87 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 192 optimal weight: 7.9990 chunk 163 optimal weight: 0.6980 chunk 75 optimal weight: 50.0000 chunk 95 optimal weight: 20.0000 chunk 166 optimal weight: 10.0000 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 685 ASN ** 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 = 0.4132 r_free = 0.4132 target = 0.093402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.059458 restraints weight = 155138.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.061352 restraints weight = 97101.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.062616 restraints weight = 72893.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.063018 restraints weight = 61051.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.063593 restraints weight = 56220.155| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.6571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 22080 Z= 0.175 Angle : 0.740 11.948 31170 Z= 0.408 Chirality : 0.046 0.266 3508 Planarity : 0.005 0.085 2863 Dihedral : 28.673 170.657 5475 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.79 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.19), residues: 1778 helix: -0.22 (0.16), residues: 940 sheet: 0.39 (0.49), residues: 106 loop : -1.56 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 55 TYR 0.019 0.002 TYR H 37 PHE 0.026 0.002 PHE G 25 TRP 0.020 0.002 TRP W 391 HIS 0.005 0.001 HIS W 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (22077) covalent geometry : angle 0.74023 / 0.41 (31168) SS BOND : bond 0.00225 / 0.15 ( 1) SS BOND : angle 0.60887 / 0.40 ( 2) hydrogen bonds : bond 0.07645 / 5.10 ( 805) hydrogen bonds : angle 4.80537 / 3.42 ( 2151) Misc. bond : bond 0.00013 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.658 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: C 24 GLN cc_start: 0.8683 (pm20) cc_final: 0.7330 (tp-100) REVERT: C 36 LYS cc_start: 0.9126 (mmtm) cc_final: 0.8561 (mttt) REVERT: C 104 GLN cc_start: 0.7696 (mt0) cc_final: 0.7143 (mp10) REVERT: C 112 GLN cc_start: 0.8420 (pm20) cc_final: 0.8096 (pm20) REVERT: D 42 LEU cc_start: 0.9324 (tp) cc_final: 0.9063 (tp) REVERT: D 86 ILE cc_start: 0.8282 (mt) cc_final: 0.8052 (mt) REVERT: D 102 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8705 (mp0) REVERT: E 100 LEU cc_start: 0.9836 (mt) cc_final: 0.9574 (mt) REVERT: E 104 PHE cc_start: 0.9595 (m-10) cc_final: 0.9366 (m-80) REVERT: E 110 CYS cc_start: 0.8562 (t) cc_final: 0.8359 (t) REVERT: F 88 TYR cc_start: 0.9180 (m-10) cc_final: 0.8946 (m-80) REVERT: G 99 ARG cc_start: 0.7869 (mmt180) cc_final: 0.7499 (ptp-170) REVERT: H 56 MET cc_start: 0.8869 (ttm) cc_final: 0.8196 (tmm) REVERT: H 118 TYR cc_start: 0.9246 (t80) cc_final: 0.8905 (t80) REVERT: W 379 PHE cc_start: 0.8655 (t80) cc_final: 0.8081 (t80) REVERT: W 396 ASN cc_start: 0.9393 (m-40) cc_final: 0.8807 (m-40) REVERT: W 423 ARG cc_start: 0.9728 (mtt-85) cc_final: 0.9408 (mmm160) REVERT: W 463 ARG cc_start: 0.8319 (ttp-170) cc_final: 0.7858 (ttm170) REVERT: W 518 LEU cc_start: 0.8784 (pp) cc_final: 0.8150 (mt) REVERT: W 538 MET cc_start: 0.9222 (mmp) cc_final: 0.8922 (mmt) REVERT: W 794 ASN cc_start: 0.8582 (t0) cc_final: 0.7927 (p0) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.1497 time to fit residues: 59.2529 Evaluate side-chains 199 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 60 optimal weight: 0.9980 chunk 110 optimal weight: 0.0870 chunk 135 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 78 optimal weight: 30.0000 chunk 122 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN G 68 ASN ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 285 HIS ** W 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.094060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.058970 restraints weight = 222623.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.061432 restraints weight = 120194.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.062905 restraints weight = 82032.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.064108 restraints weight = 65523.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.064450 restraints weight = 56764.694| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3782 r_free = 0.3782 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3782 r_free = 0.3782 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.6739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22080 Z= 0.153 Angle : 0.715 10.471 31170 Z= 0.393 Chirality : 0.046 0.286 3508 Planarity : 0.005 0.052 2863 Dihedral : 28.612 171.894 5475 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.62 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.19), residues: 1778 helix: -0.12 (0.16), residues: 930 sheet: 0.24 (0.49), residues: 115 loop : -1.51 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 35 TYR 0.022 0.002 TYR W1189 PHE 0.017 0.002 PHE W 646 TRP 0.019 0.002 TRP W 386 HIS 0.012 0.001 HIS W 813 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (22077) covalent geometry : angle 0.71504 / 0.39 (31168) SS BOND : bond 0.00158 / 0.11 ( 1) SS BOND : angle 0.56964 / 0.35 ( 2) hydrogen bonds : bond 0.07077 / 4.73 ( 805) hydrogen bonds : angle 4.72265 / 3.36 ( 2151) Misc. bond : bond 0.00011 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6314.87 seconds wall clock time: 109 minutes 14.63 seconds (6554.63 seconds total)