Starting phenix.real_space_refine on Wed Nov 19 05:00:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ftx_4318/11_2025/6ftx_4318_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ftx_4318/11_2025/6ftx_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_4318/11_2025/6ftx_4318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ftx_4318/11_2025/6ftx_4318.map" model { file = "/net/cci-nas-00/data/ceres_data/6ftx_4318/11_2025/6ftx_4318_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ftx_4318/11_2025/6ftx_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-2.0-5881/lib/python3.9/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: 6.26, per 1000 atoms: 0.30 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: 1.82 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 2.97 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: 5.77 Time building geometry restraints manager: 2.44 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=" 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 bond pdb=" C THR D 87 " pdb=" O THR D 87 " ideal model delta sigma weight residual 1.234 1.097 0.137 1.16e-02 7.43e+03 1.39e+02 ... (remaining 22072 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 28872 4.37 - 8.73: 2102 8.73 - 13.10: 174 13.10 - 17.47: 17 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=" 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 angle pdb=" NE ARG B 40 " pdb=" CZ ARG B 40 " pdb=" NH1 ARG B 40 " ideal model delta sigma weight residual 121.50 112.46 9.04 1.00e+00 1.00e+00 8.18e+01 angle pdb=" CA ARG G 17 " pdb=" C ARG G 17 " pdb=" O ARG G 17 " ideal model delta sigma weight residual 120.82 111.56 9.26 1.05e+00 9.07e-01 7.78e+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: 2942 0.157 - 0.314: 505 0.314 - 0.471: 50 0.471 - 0.628: 9 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 -2.66 -1.96 -0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA LEU O 71 " pdb=" N LEU O 71 " pdb=" C LEU O 71 " pdb=" CB LEU O 71 " both_signs ideal model delta sigma weight residual False 2.51 3.11 -0.60 2.00e-01 2.50e+01 8.92e+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: 0.770 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: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 25.400 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 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= 1.498 Angle : 2.402 46.817 31170 Z= 1.550 Chirality : 0.121 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 covalent geometry : bond 0.01974 (22077) covalent geometry : angle 2.38694 (31168) SS BOND : bond 0.79175 ( 1) SS BOND : angle 33.25421 ( 2) hydrogen bonds : bond 0.30032 ( 805) hydrogen bonds : angle 11.32447 ( 2151) Misc. bond : bond 0.67397 ( 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 : 0.661 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.8554 (m-80) cc_final: 0.8288 (m-80) REVERT: A 107 THR cc_start: 0.7686 (m) cc_final: 0.7039 (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: 0.6965 (mmt-90) REVERT: D 48 ASP cc_start: 0.9288 (m-30) cc_final: 0.9029 (m-30) REVERT: D 86 ILE cc_start: 0.7982 (mp) cc_final: 0.7730 (mt) REVERT: E 120 MET cc_start: 0.2022 (mmm) cc_final: 0.1515 (mmt) REVERT: G 15 LYS cc_start: 0.6591 (tttt) cc_final: 0.6097 (mmtp) REVERT: G 92 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8239 (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: 0.7403 (tp) REVERT: W 322 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.6190 (mm-30) REVERT: W 376 LEU cc_start: 0.7258 (mt) cc_final: 0.6374 (mp) REVERT: W 379 PHE cc_start: 0.8831 (t80) cc_final: 0.8180 (t80) REVERT: W 463 ARG cc_start: 0.9171 (ttp-170) cc_final: 0.8514 (ttm-80) REVERT: W 467 ARG cc_start: 0.9677 (mtt180) cc_final: 0.9435 (mtm180) REVERT: W 495 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.6957 (mp) REVERT: W 594 ILE cc_start: 0.8875 (mm) cc_final: 0.8579 (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: 0.9047 (tp30) REVERT: W 741 LEU cc_start: 0.9370 (tt) cc_final: 0.9143 (tt) REVERT: W 817 TYR cc_start: 0.9381 (m-80) cc_final: 0.8961 (m-80) REVERT: W 832 ARG cc_start: 0.9312 (mtp180) cc_final: 0.8980 (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: 0.6807 (tpm170) REVERT: W 1259 LEU cc_start: 0.8589 (mt) cc_final: 0.7316 (mt) outliers start: 50 outliers final: 13 residues processed: 428 average time/residue: 0.1893 time to fit residues: 117.6354 Evaluate side-chains 265 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 247 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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: 0.8980 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN E 68 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN N 2 GLN N 40 GLN ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 285 HIS ** 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 339 GLN ** W 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 579 GLN W 645 HIS ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.106191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.072400 restraints weight = 218244.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.074951 restraints weight = 122437.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.076336 restraints weight = 83411.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.077419 restraints weight = 66817.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.078964 restraints weight = 58655.609| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3835 r_free = 0.3835 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 22080 Z= 0.299 Angle : 0.901 11.376 31170 Z= 0.496 Chirality : 0.050 0.231 3508 Planarity : 0.007 0.076 2863 Dihedral : 29.523 176.495 5475 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.05 % Favored : 95.44 % Rotamer: Outliers : 0.32 % Allowed : 3.94 % Favored : 95.74 % 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: -1.60 (0.18), residues: 1778 helix: -0.21 (0.16), residues: 933 sheet: -0.84 (0.48), residues: 106 loop : -2.20 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 89 TYR 0.030 0.003 TYR B 72 PHE 0.032 0.003 PHE W 646 TRP 0.026 0.004 TRP W1194 HIS 0.013 0.003 HIS W 661 Details of bonding type rmsd covalent geometry : bond 0.00651 (22077) covalent geometry : angle 0.90087 (31168) SS BOND : bond 0.01713 ( 1) SS BOND : angle 3.53169 ( 2) hydrogen bonds : bond 0.09900 ( 805) hydrogen bonds : angle 5.21625 ( 2151) Misc. bond : bond 0.00180 ( 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 325 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 320 time to evaluate : 0.667 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: A 41 TYR cc_start: 0.8156 (m-80) cc_final: 0.7635 (m-10) REVERT: A 50 GLU cc_start: 0.9585 (mt-10) cc_final: 0.9330 (pt0) REVERT: A 77 ASP cc_start: 0.9023 (m-30) cc_final: 0.8790 (m-30) REVERT: C 17 ARG cc_start: 0.8309 (mtt-85) cc_final: 0.7909 (mmt180) REVERT: D 86 ILE cc_start: 0.8011 (mp) cc_final: 0.7781 (mt) REVERT: E 54 TYR cc_start: 0.9472 (m-80) cc_final: 0.9039 (m-80) REVERT: E 67 PHE cc_start: 0.8277 (t80) cc_final: 0.8062 (t80) REVERT: E 94 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8964 (mt-10) REVERT: E 104 PHE cc_start: 0.9711 (m-10) cc_final: 0.9509 (m-10) REVERT: E 105 GLU cc_start: 0.9512 (tt0) cc_final: 0.9271 (mt-10) REVERT: E 120 MET cc_start: -0.1072 (mmm) cc_final: -0.2039 (mmt) REVERT: E 126 LEU cc_start: 0.3195 (OUTLIER) cc_final: 0.2484 (mp) REVERT: G 15 LYS cc_start: 0.6549 (ttpt) cc_final: 0.5779 (mmtp) REVERT: G 50 TYR cc_start: 0.9117 (t80) cc_final: 0.8809 (t80) REVERT: G 90 ASP cc_start: 0.9196 (t0) cc_final: 0.8956 (t70) REVERT: G 97 LEU cc_start: 0.8885 (mp) cc_final: 0.8488 (tt) REVERT: H 56 MET cc_start: 0.8794 (ttm) cc_final: 0.8367 (tpp) REVERT: H 92 GLN cc_start: 0.9038 (tt0) cc_final: 0.7678 (tp-100) REVERT: H 118 TYR cc_start: 0.9236 (t80) cc_final: 0.8794 (t80) REVERT: W 230 TYR cc_start: 0.8314 (m-80) cc_final: 0.7634 (m-80) REVERT: W 367 GLN cc_start: 0.8985 (pt0) cc_final: 0.8515 (pt0) REVERT: W 376 LEU cc_start: 0.7286 (mt) cc_final: 0.6855 (mp) REVERT: W 379 PHE cc_start: 0.8369 (t80) cc_final: 0.7610 (t80) REVERT: W 398 ILE cc_start: 0.9081 (mp) cc_final: 0.8858 (mp) REVERT: W 423 ARG cc_start: 0.9706 (mtt-85) cc_final: 0.9483 (mmm160) REVERT: W 429 ILE cc_start: 0.9093 (tp) cc_final: 0.8698 (tp) REVERT: W 457 MET cc_start: 0.7945 (ppp) cc_final: 0.7517 (ppp) REVERT: W 467 ARG cc_start: 0.9391 (mtt180) cc_final: 0.8850 (mmt180) REVERT: W 520 ASN cc_start: 0.9039 (t0) cc_final: 0.8577 (m110) REVERT: W 723 MET cc_start: 0.8627 (tmm) cc_final: 0.8289 (tmm) REVERT: W 794 ASN cc_start: 0.8514 (t0) cc_final: 0.7696 (p0) REVERT: W 802 MET cc_start: 0.8225 (ppp) cc_final: 0.7833 (ppp) outliers start: 5 outliers final: 0 residues processed: 322 average time/residue: 0.1865 time to fit residues: 87.3822 Evaluate side-chains 231 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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: 0.5980 chunk 3 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 187 optimal weight: 10.0000 chunk 198 optimal weight: 9.9990 chunk 200 optimal weight: 0.0570 chunk 189 optimal weight: 0.9980 chunk 113 optimal weight: 50.0000 chunk 53 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS H 60 ASN ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 294 GLN W 357 GLN W 536 ASN W 685 ASN ** W 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.100166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.063385 restraints weight = 182506.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.066093 restraints weight = 100494.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.067873 restraints weight = 69691.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.069248 restraints weight = 55566.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.069942 restraints weight = 48216.330| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3906 r_free = 0.3906 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3906 r_free = 0.3906 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 22080 Z= 0.174 Angle : 0.705 10.385 31170 Z= 0.387 Chirality : 0.041 0.196 3508 Planarity : 0.005 0.053 2863 Dihedral : 28.887 175.624 5475 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.32 % Favored : 96.28 % Rotamer: Outliers : 0.32 % Allowed : 2.45 % 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: -1.10 (0.18), residues: 1778 helix: 0.19 (0.16), residues: 933 sheet: -0.83 (0.49), residues: 105 loop : -1.89 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 36 TYR 0.029 0.002 TYR F 88 PHE 0.027 0.002 PHE G 25 TRP 0.017 0.002 TRP W1194 HIS 0.008 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00375 (22077) covalent geometry : angle 0.70523 (31168) SS BOND : bond 0.00601 ( 1) SS BOND : angle 2.20798 ( 2) hydrogen bonds : bond 0.07508 ( 805) hydrogen bonds : angle 4.54700 ( 2151) Misc. bond : bond 0.00034 ( 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 308 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 303 time to evaluate : 0.736 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 41 TYR cc_start: 0.8326 (m-80) cc_final: 0.7681 (m-80) REVERT: A 50 GLU cc_start: 0.9562 (mt-10) cc_final: 0.9307 (pt0) REVERT: C 88 ARG cc_start: 0.8278 (tpt90) cc_final: 0.8059 (ptp-170) REVERT: D 86 ILE cc_start: 0.7881 (mp) cc_final: 0.7601 (mt) REVERT: E 50 GLU cc_start: 0.8542 (mt-10) cc_final: 0.7876 (pt0) REVERT: E 54 TYR cc_start: 0.9087 (m-80) cc_final: 0.8851 (m-10) REVERT: E 67 PHE cc_start: 0.8196 (t80) cc_final: 0.7862 (t80) REVERT: E 93 GLN cc_start: 0.9441 (OUTLIER) cc_final: 0.8996 (pm20) REVERT: E 94 GLU cc_start: 0.9240 (mt-10) cc_final: 0.9019 (mt-10) REVERT: E 104 PHE cc_start: 0.9770 (m-10) cc_final: 0.9565 (m-10) REVERT: E 105 GLU cc_start: 0.9616 (tt0) cc_final: 0.9364 (mt-10) REVERT: E 120 MET cc_start: -0.1495 (mmm) cc_final: -0.1703 (mmt) REVERT: F 88 TYR cc_start: 0.9552 (m-80) cc_final: 0.8938 (m-80) REVERT: G 97 LEU cc_start: 0.8989 (mp) cc_final: 0.8659 (tt) REVERT: H 56 MET cc_start: 0.8791 (ttm) cc_final: 0.8077 (tmm) REVERT: H 115 VAL cc_start: 0.8301 (t) cc_final: 0.7938 (t) REVERT: H 118 TYR cc_start: 0.9148 (t80) cc_final: 0.8750 (t80) REVERT: W 282 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8556 (pp20) REVERT: W 379 PHE cc_start: 0.8307 (t80) cc_final: 0.7532 (t80) REVERT: W 423 ARG cc_start: 0.9701 (mtt-85) cc_final: 0.9478 (mmm160) REVERT: W 457 MET cc_start: 0.7685 (ppp) cc_final: 0.7317 (ppp) REVERT: W 518 LEU cc_start: 0.9001 (pp) cc_final: 0.8598 (mt) REVERT: W 533 LYS cc_start: 0.9392 (mtmm) cc_final: 0.9155 (mtmm) REVERT: W 723 MET cc_start: 0.8663 (tmm) cc_final: 0.8255 (tmm) REVERT: W 794 ASN cc_start: 0.8335 (t0) cc_final: 0.7834 (t0) REVERT: W 1055 MET cc_start: -0.0630 (ptt) cc_final: -0.1157 (ptt) outliers start: 5 outliers final: 0 residues processed: 306 average time/residue: 0.1785 time to fit residues: 80.3400 Evaluate side-chains 216 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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: 3.9990 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 0.0040 chunk 123 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 127 optimal weight: 9.9990 chunk 189 optimal weight: 7.9990 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 367 GLN ** W 685 ASN ** 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 = 0.4222 r_free = 0.4222 target = 0.098553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.061762 restraints weight = 195622.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.064479 restraints weight = 107512.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.066290 restraints weight = 74037.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.067115 restraints weight = 59288.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.067475 restraints weight = 52057.692| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3859 r_free = 0.3859 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3859 r_free = 0.3859 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22080 Z= 0.163 Angle : 0.663 8.792 31170 Z= 0.366 Chirality : 0.039 0.199 3508 Planarity : 0.005 0.053 2863 Dihedral : 28.415 173.928 5475 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.77 % Favored : 95.95 % Rotamer: Outliers : 0.06 % Allowed : 2.84 % Favored : 97.09 % 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: -0.72 (0.19), residues: 1778 helix: 0.47 (0.16), residues: 923 sheet: -0.56 (0.50), residues: 101 loop : -1.66 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 35 TYR 0.023 0.002 TYR D 118 PHE 0.035 0.002 PHE C 25 TRP 0.016 0.002 TRP W1194 HIS 0.006 0.001 HIS W 222 Details of bonding type rmsd covalent geometry : bond 0.00353 (22077) covalent geometry : angle 0.66292 (31168) SS BOND : bond 0.00027 ( 1) SS BOND : angle 1.13240 ( 2) hydrogen bonds : bond 0.06924 ( 805) hydrogen bonds : angle 4.30788 ( 2151) Misc. bond : bond 0.00011 ( 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 281 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 280 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8313 (m-80) cc_final: 0.7547 (m-10) REVERT: A 50 GLU cc_start: 0.9566 (mt-10) cc_final: 0.9365 (mt-10) REVERT: B 36 ARG cc_start: 0.8023 (mtm180) cc_final: 0.7476 (mmp80) REVERT: C 35 ARG cc_start: 0.9425 (ttp80) cc_final: 0.9218 (ttp80) REVERT: D 51 ILE cc_start: 0.8932 (pt) cc_final: 0.8708 (tp) REVERT: D 86 ILE cc_start: 0.7890 (mp) cc_final: 0.7635 (mt) REVERT: D 105 LYS cc_start: 0.9106 (ptpp) cc_final: 0.8880 (ptpp) REVERT: E 49 ARG cc_start: 0.9279 (ptt90) cc_final: 0.8880 (ttp80) REVERT: E 50 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8469 (mm-30) REVERT: E 53 ARG cc_start: 0.9273 (ptm-80) cc_final: 0.9066 (ptt90) REVERT: E 67 PHE cc_start: 0.8344 (t80) cc_final: 0.7873 (t80) REVERT: E 94 GLU cc_start: 0.9288 (mt-10) cc_final: 0.9046 (mt-10) REVERT: E 97 GLU cc_start: 0.9484 (mm-30) cc_final: 0.9189 (mm-30) REVERT: E 120 MET cc_start: -0.1089 (mmm) cc_final: -0.1429 (mmt) REVERT: F 88 TYR cc_start: 0.9629 (m-80) cc_final: 0.9369 (m-10) REVERT: G 25 PHE cc_start: 0.9221 (m-80) cc_final: 0.8888 (m-10) REVERT: G 38 ASN cc_start: 0.8281 (m-40) cc_final: 0.7687 (t0) REVERT: G 56 GLU cc_start: 0.9354 (tm-30) cc_final: 0.9122 (tm-30) REVERT: H 96 ARG cc_start: 0.8523 (mtm180) cc_final: 0.8105 (mtm180) REVERT: H 118 TYR cc_start: 0.9179 (t80) cc_final: 0.8788 (t80) REVERT: W 370 PHE cc_start: 0.9563 (m-80) cc_final: 0.9349 (m-80) REVERT: W 379 PHE cc_start: 0.8228 (t80) cc_final: 0.7487 (t80) REVERT: W 396 ASN cc_start: 0.9301 (m-40) cc_final: 0.8620 (m-40) REVERT: W 398 ILE cc_start: 0.7738 (mp) cc_final: 0.7398 (mp) REVERT: W 423 ARG cc_start: 0.9703 (mtt-85) cc_final: 0.9482 (mmm160) REVERT: W 518 LEU cc_start: 0.8843 (pp) cc_final: 0.8089 (mt) REVERT: W 520 ASN cc_start: 0.8871 (t0) cc_final: 0.8350 (p0) REVERT: W 538 MET cc_start: 0.8468 (mmt) cc_final: 0.8193 (mmt) REVERT: W 555 LEU cc_start: 0.9207 (mp) cc_final: 0.9001 (mp) REVERT: W 595 LEU cc_start: 0.7452 (tp) cc_final: 0.7230 (tp) REVERT: W 723 MET cc_start: 0.8760 (tmm) cc_final: 0.8319 (tmm) REVERT: W 794 ASN cc_start: 0.8296 (t0) cc_final: 0.7938 (t0) outliers start: 1 outliers final: 0 residues processed: 281 average time/residue: 0.1754 time to fit residues: 73.0511 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 : 0.690 ------------------------------------------------------------------------------- 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: 6.9990 chunk 79 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 109 optimal weight: 0.3980 chunk 204 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 195 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 285 HIS ** W 685 ASN ** 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 = 0.4187 r_free = 0.4187 target = 0.096890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.060540 restraints weight = 209725.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.062984 restraints weight = 116436.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.064457 restraints weight = 80219.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.065575 restraints weight = 64792.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.066000 restraints weight = 56467.239| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 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 = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22080 Z= 0.168 Angle : 0.652 12.762 31170 Z= 0.356 Chirality : 0.038 0.256 3508 Planarity : 0.005 0.070 2863 Dihedral : 28.141 179.680 5475 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.77 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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: -0.54 (0.19), residues: 1778 helix: 0.47 (0.16), residues: 940 sheet: 0.31 (0.49), residues: 104 loop : -1.52 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 29 TYR 0.019 0.002 TYR W 841 PHE 0.024 0.002 PHE C 25 TRP 0.022 0.002 TRP W1194 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00363 (22077) covalent geometry : angle 0.65242 (31168) SS BOND : bond 0.00049 ( 1) SS BOND : angle 0.75061 ( 2) hydrogen bonds : bond 0.06874 ( 805) hydrogen bonds : angle 4.28535 ( 2151) Misc. bond : bond 0.00029 ( 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 278 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.688 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: A 41 TYR cc_start: 0.8366 (m-80) cc_final: 0.7545 (m-10) REVERT: B 36 ARG cc_start: 0.8084 (mtm180) cc_final: 0.7438 (mmp80) REVERT: B 84 MET cc_start: 0.7230 (ttp) cc_final: 0.6985 (tmm) REVERT: C 36 LYS cc_start: 0.9063 (mmtm) cc_final: 0.8522 (mttt) REVERT: D 32 GLU cc_start: 0.7068 (tm-30) cc_final: 0.6836 (tm-30) REVERT: D 48 ASP cc_start: 0.9474 (m-30) cc_final: 0.8974 (p0) REVERT: E 46 VAL cc_start: 0.8521 (t) cc_final: 0.7953 (t) REVERT: E 49 ARG cc_start: 0.9365 (ptt90) cc_final: 0.8846 (ttp80) REVERT: E 50 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8643 (mm-30) REVERT: E 67 PHE cc_start: 0.8493 (t80) cc_final: 0.7863 (t80) REVERT: E 94 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8978 (mt-10) REVERT: E 97 GLU cc_start: 0.9449 (mm-30) cc_final: 0.9139 (mm-30) REVERT: E 100 LEU cc_start: 0.9850 (mt) cc_final: 0.9582 (mt) REVERT: E 104 PHE cc_start: 0.9686 (m-10) cc_final: 0.9360 (m-80) REVERT: E 110 CYS cc_start: 0.9039 (t) cc_final: 0.8666 (t) REVERT: F 88 TYR cc_start: 0.9373 (m-80) cc_final: 0.8973 (m-10) REVERT: G 38 ASN cc_start: 0.8311 (m-40) cc_final: 0.7723 (t0) REVERT: G 56 GLU cc_start: 0.9252 (tm-30) cc_final: 0.8976 (tm-30) REVERT: H 96 ARG cc_start: 0.8535 (mtm180) cc_final: 0.8146 (mtm180) REVERT: H 118 TYR cc_start: 0.9212 (t80) cc_final: 0.8857 (t80) REVERT: W 370 PHE cc_start: 0.9562 (m-80) cc_final: 0.9337 (m-80) REVERT: W 379 PHE cc_start: 0.8298 (t80) cc_final: 0.7741 (t80) REVERT: W 396 ASN cc_start: 0.9271 (m-40) cc_final: 0.8448 (m-40) REVERT: W 398 ILE cc_start: 0.7521 (mp) cc_final: 0.7202 (mp) REVERT: W 423 ARG cc_start: 0.9714 (mtt-85) cc_final: 0.9480 (mmm160) REVERT: W 463 ARG cc_start: 0.8345 (ttp-170) cc_final: 0.7801 (ttm170) REVERT: W 518 LEU cc_start: 0.8770 (pp) cc_final: 0.7930 (mt) REVERT: W 520 ASN cc_start: 0.8929 (t0) cc_final: 0.8432 (p0) REVERT: W 538 MET cc_start: 0.8611 (mmt) cc_final: 0.8154 (mmt) REVERT: W 555 LEU cc_start: 0.9257 (mp) cc_final: 0.9043 (mp) REVERT: W 595 LEU cc_start: 0.7952 (tp) cc_final: 0.7741 (tp) REVERT: W 723 MET cc_start: 0.8823 (tmm) cc_final: 0.8437 (tmm) REVERT: W 781 MET cc_start: 0.8325 (mmp) cc_final: 0.8067 (mmp) REVERT: W 794 ASN cc_start: 0.8431 (t0) cc_final: 0.8056 (p0) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.1703 time to fit residues: 70.8192 Evaluate side-chains 222 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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: 0.1980 chunk 136 optimal weight: 0.0030 chunk 22 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 138 optimal weight: 0.1980 chunk 91 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 158 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN W 177 HIS ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 334 GLN W 367 GLN ** W 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.097772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.063033 restraints weight = 183708.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.065512 restraints weight = 103764.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.066867 restraints weight = 72675.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 14)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.067346 restraints weight = 59251.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.068184 restraints weight = 53643.103| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3872 r_free = 0.3872 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 = 0.3872 r_free = 0.3872 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22080 Z= 0.143 Angle : 0.624 9.739 31170 Z= 0.341 Chirality : 0.038 0.198 3508 Planarity : 0.004 0.052 2863 Dihedral : 28.093 176.768 5475 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.55 % Favored : 96.23 % Rotamer: Outliers : 0.26 % Allowed : 1.74 % Favored : 98.00 % 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: -0.38 (0.19), residues: 1778 helix: 0.55 (0.17), residues: 938 sheet: 0.31 (0.49), residues: 112 loop : -1.37 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.016 0.001 TYR H 37 PHE 0.019 0.001 PHE C 25 TRP 0.031 0.002 TRP W1194 HIS 0.016 0.001 HIS W1251 Details of bonding type rmsd covalent geometry : bond 0.00308 (22077) covalent geometry : angle 0.62406 (31168) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.63800 ( 2) hydrogen bonds : bond 0.06051 ( 805) hydrogen bonds : angle 4.16182 ( 2151) Misc. bond : bond 0.00013 ( 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 291 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 287 time to evaluate : 0.728 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: B 36 ARG cc_start: 0.8033 (mtm180) cc_final: 0.7435 (mmp80) REVERT: B 84 MET cc_start: 0.7331 (ttp) cc_final: 0.7094 (tmm) REVERT: C 36 LYS cc_start: 0.9015 (mmtm) cc_final: 0.8474 (mttt) REVERT: D 48 ASP cc_start: 0.9460 (m-30) cc_final: 0.8965 (p0) REVERT: D 105 LYS cc_start: 0.9482 (ptpp) cc_final: 0.9239 (ptpp) REVERT: E 49 ARG cc_start: 0.9330 (ptt90) cc_final: 0.9080 (ttp80) REVERT: E 50 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8531 (pt0) REVERT: E 67 PHE cc_start: 0.8511 (t80) cc_final: 0.7836 (t80) REVERT: E 100 LEU cc_start: 0.9840 (mt) cc_final: 0.9371 (pp) REVERT: E 104 PHE cc_start: 0.9685 (m-10) cc_final: 0.9336 (m-80) REVERT: F 88 TYR cc_start: 0.9191 (m-80) cc_final: 0.8949 (m-10) REVERT: G 25 PHE cc_start: 0.8696 (m-10) cc_final: 0.7869 (m-10) REVERT: G 36 LYS cc_start: 0.8194 (pptt) cc_final: 0.7843 (pptt) REVERT: G 38 ASN cc_start: 0.7954 (m-40) cc_final: 0.7402 (t0) REVERT: H 96 ARG cc_start: 0.8494 (mtm180) cc_final: 0.8240 (mtm180) REVERT: H 118 TYR cc_start: 0.9182 (t80) cc_final: 0.8820 (t80) REVERT: W 271 ASP cc_start: 0.8669 (m-30) cc_final: 0.8102 (p0) REVERT: W 370 PHE cc_start: 0.9555 (m-80) cc_final: 0.9308 (m-80) REVERT: W 375 GLU cc_start: 0.9705 (mm-30) cc_final: 0.9411 (mm-30) REVERT: W 379 PHE cc_start: 0.8388 (t80) cc_final: 0.7857 (t80) REVERT: W 396 ASN cc_start: 0.9026 (m-40) cc_final: 0.8464 (m-40) REVERT: W 423 ARG cc_start: 0.9700 (mtt-85) cc_final: 0.9428 (mmm160) REVERT: W 463 ARG cc_start: 0.8312 (ttp-170) cc_final: 0.7793 (ttm170) REVERT: W 518 LEU cc_start: 0.8655 (pp) cc_final: 0.7739 (mt) REVERT: W 519 LYS cc_start: 0.7766 (tttp) cc_final: 0.7559 (tmtt) REVERT: W 520 ASN cc_start: 0.8912 (t0) cc_final: 0.8340 (p0) REVERT: W 538 MET cc_start: 0.8549 (mmt) cc_final: 0.8111 (mmt) REVERT: W 666 ASP cc_start: 0.9155 (m-30) cc_final: 0.8576 (p0) REVERT: W 692 MET cc_start: 0.8909 (ptp) cc_final: 0.8377 (ppp) REVERT: W 723 MET cc_start: 0.8791 (tmm) cc_final: 0.8555 (tmm) REVERT: W 781 MET cc_start: 0.8392 (mmp) cc_final: 0.8133 (mmp) REVERT: W 794 ASN cc_start: 0.8026 (t0) cc_final: 0.7816 (p0) outliers start: 4 outliers final: 1 residues processed: 289 average time/residue: 0.1717 time to fit residues: 74.0668 Evaluate side-chains 232 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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: 5.9990 chunk 136 optimal weight: 0.1980 chunk 198 optimal weight: 6.9990 chunk 155 optimal weight: 0.0020 chunk 21 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 203 optimal weight: 10.0000 chunk 179 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 367 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 = 0.4205 r_free = 0.4205 target = 0.096500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.061801 restraints weight = 188958.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.064003 restraints weight = 106468.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.065720 restraints weight = 76875.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.066542 restraints weight = 61682.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.067222 restraints weight = 54436.985| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3852 r_free = 0.3852 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 = 0.3852 r_free = 0.3852 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.6746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22080 Z= 0.151 Angle : 0.615 7.999 31170 Z= 0.339 Chirality : 0.037 0.233 3508 Planarity : 0.004 0.054 2863 Dihedral : 27.990 176.249 5475 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.66 % Favored : 96.11 % 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: -0.39 (0.19), residues: 1778 helix: 0.47 (0.17), residues: 941 sheet: 0.38 (0.48), residues: 117 loop : -1.30 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 76 TYR 0.013 0.001 TYR F 88 PHE 0.015 0.001 PHE H 62 TRP 0.026 0.001 TRP W1194 HIS 0.007 0.001 HIS W 177 Details of bonding type rmsd covalent geometry : bond 0.00324 (22077) covalent geometry : angle 0.61503 (31168) SS BOND : bond 0.00090 ( 1) SS BOND : angle 0.59386 ( 2) hydrogen bonds : bond 0.06215 ( 805) hydrogen bonds : angle 4.22368 ( 2151) Misc. bond : bond 0.00036 ( 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 275 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.613 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: B 36 ARG cc_start: 0.8012 (mtm180) cc_final: 0.7445 (mmp80) REVERT: C 17 ARG cc_start: 0.8445 (mtt-85) cc_final: 0.7942 (mtt-85) REVERT: C 36 LYS cc_start: 0.9036 (mmtm) cc_final: 0.8498 (mttt) REVERT: D 48 ASP cc_start: 0.9480 (m-30) cc_final: 0.9020 (p0) REVERT: D 105 LYS cc_start: 0.9463 (ptpp) cc_final: 0.9225 (ptpp) REVERT: E 49 ARG cc_start: 0.9330 (ptt90) cc_final: 0.9114 (ttp80) REVERT: E 60 LEU cc_start: 0.8456 (pt) cc_final: 0.8235 (pt) REVERT: E 100 LEU cc_start: 0.9820 (mt) cc_final: 0.9598 (mt) REVERT: E 104 PHE cc_start: 0.9591 (m-10) cc_final: 0.9271 (m-80) REVERT: F 88 TYR cc_start: 0.9158 (m-80) cc_final: 0.8866 (m-10) REVERT: G 36 LYS cc_start: 0.8408 (pptt) cc_final: 0.8052 (pptt) REVERT: G 38 ASN cc_start: 0.7969 (m-40) cc_final: 0.7285 (t0) REVERT: G 63 LEU cc_start: 0.9677 (mt) cc_final: 0.9327 (pp) REVERT: H 118 TYR cc_start: 0.9254 (t80) cc_final: 0.8925 (t80) REVERT: W 271 ASP cc_start: 0.8694 (m-30) cc_final: 0.8086 (p0) REVERT: W 334 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8719 (mt0) REVERT: W 370 PHE cc_start: 0.9554 (m-80) cc_final: 0.9297 (m-80) REVERT: W 379 PHE cc_start: 0.8486 (t80) cc_final: 0.7956 (t80) REVERT: W 396 ASN cc_start: 0.9151 (m-40) cc_final: 0.8530 (m-40) REVERT: W 423 ARG cc_start: 0.9702 (mtt-85) cc_final: 0.9441 (mmm160) REVERT: W 463 ARG cc_start: 0.8272 (ttp-170) cc_final: 0.7751 (ttm170) REVERT: W 518 LEU cc_start: 0.8694 (pp) cc_final: 0.7822 (mt) REVERT: W 520 ASN cc_start: 0.8952 (t0) cc_final: 0.8483 (p0) REVERT: W 538 MET cc_start: 0.8557 (mmt) cc_final: 0.8102 (mmt) REVERT: W 666 ASP cc_start: 0.9159 (m-30) cc_final: 0.8568 (p0) REVERT: W 781 MET cc_start: 0.8433 (mmp) cc_final: 0.8154 (mmp) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.1581 time to fit residues: 66.0075 Evaluate side-chains 222 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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: 6.9990 chunk 136 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 198 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 187 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN H 60 ASN O 68 HIS ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 367 GLN W 587 HIS ** W 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.091133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.056402 restraints weight = 232289.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.058556 restraints weight = 125896.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.059838 restraints weight = 86422.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.060884 restraints weight = 69685.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.061702 restraints weight = 60579.729| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.7244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 22080 Z= 0.240 Angle : 0.723 15.476 31170 Z= 0.398 Chirality : 0.042 0.287 3508 Planarity : 0.005 0.055 2863 Dihedral : 28.251 175.123 5475 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.34 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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: -0.72 (0.19), residues: 1778 helix: 0.10 (0.16), residues: 940 sheet: 0.32 (0.46), residues: 129 loop : -1.34 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 76 TYR 0.025 0.002 TYR W 526 PHE 0.026 0.002 PHE A 104 TRP 0.017 0.002 TRP W1194 HIS 0.009 0.002 HIS W 661 Details of bonding type rmsd covalent geometry : bond 0.00528 (22077) covalent geometry : angle 0.72265 (31168) SS BOND : bond 0.00449 ( 1) SS BOND : angle 0.84219 ( 2) hydrogen bonds : bond 0.08385 ( 805) hydrogen bonds : angle 4.68964 ( 2151) Misc. bond : bond 0.00052 ( 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 259 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.669 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: B 36 ARG cc_start: 0.8125 (mtm180) cc_final: 0.7557 (mmp80) REVERT: C 36 LYS cc_start: 0.9148 (mmtm) cc_final: 0.8596 (mttt) REVERT: C 104 GLN cc_start: 0.7825 (mt0) cc_final: 0.7222 (mp10) REVERT: D 105 LYS cc_start: 0.9469 (ptpp) cc_final: 0.9248 (ptpp) REVERT: E 67 PHE cc_start: 0.8639 (t80) cc_final: 0.8080 (t80) REVERT: E 100 LEU cc_start: 0.9846 (mt) cc_final: 0.9572 (mt) REVERT: E 104 PHE cc_start: 0.9534 (m-10) cc_final: 0.9247 (m-80) REVERT: E 110 CYS cc_start: 0.8798 (t) cc_final: 0.8378 (t) REVERT: F 88 TYR cc_start: 0.8963 (m-80) cc_final: 0.8714 (m-10) REVERT: G 15 LYS cc_start: 0.6678 (ttpt) cc_final: 0.5866 (mmtp) REVERT: G 38 ASN cc_start: 0.8275 (m-40) cc_final: 0.7707 (t0) REVERT: H 115 VAL cc_start: 0.8568 (t) cc_final: 0.8229 (t) REVERT: H 118 TYR cc_start: 0.9303 (t80) cc_final: 0.8991 (t80) REVERT: N 1 MET cc_start: 0.6376 (tpt) cc_final: 0.6152 (tpt) REVERT: W 315 ASN cc_start: 0.8250 (p0) cc_final: 0.8033 (p0) REVERT: W 334 GLN cc_start: 0.8969 (mm-40) cc_final: 0.8758 (mt0) REVERT: W 379 PHE cc_start: 0.8797 (t80) cc_final: 0.8223 (t80) REVERT: W 396 ASN cc_start: 0.9270 (m-40) cc_final: 0.8700 (m-40) REVERT: W 423 ARG cc_start: 0.9722 (mtt-85) cc_final: 0.9478 (mmm160) REVERT: W 463 ARG cc_start: 0.8359 (ttp-170) cc_final: 0.7872 (ttm170) REVERT: W 518 LEU cc_start: 0.8884 (pp) cc_final: 0.8068 (mt) REVERT: W 520 ASN cc_start: 0.9165 (t0) cc_final: 0.8651 (p0) REVERT: W 538 MET cc_start: 0.8566 (mmt) cc_final: 0.8039 (mmp) REVERT: W 652 MET cc_start: 0.7965 (tpp) cc_final: 0.7718 (tpt) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.1633 time to fit residues: 64.2698 Evaluate side-chains 209 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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: 4.9990 chunk 199 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 chunk 159 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 172 optimal weight: 0.6980 chunk 174 optimal weight: 0.4980 chunk 157 optimal weight: 0.8980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 112 GLN ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 685 ASN ** 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 = 0.4137 r_free = 0.4137 target = 0.093182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.059314 restraints weight = 169619.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.061387 restraints weight = 102158.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.062796 restraints weight = 74676.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.063516 restraints weight = 61744.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.064058 restraints weight = 55169.321| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3786 r_free = 0.3786 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 = 0.3786 r_free = 0.3786 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.7445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22080 Z= 0.164 Angle : 0.647 11.632 31170 Z= 0.355 Chirality : 0.038 0.208 3508 Planarity : 0.005 0.076 2863 Dihedral : 28.347 177.475 5475 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.83 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: -0.46 (0.19), residues: 1778 helix: 0.30 (0.16), residues: 938 sheet: 0.48 (0.47), residues: 123 loop : -1.19 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 53 TYR 0.012 0.002 TYR W1018 PHE 0.017 0.001 PHE H 62 TRP 0.018 0.001 TRP W1194 HIS 0.004 0.001 HIS W 177 Details of bonding type rmsd covalent geometry : bond 0.00355 (22077) covalent geometry : angle 0.64667 (31168) SS BOND : bond 0.00193 ( 1) SS BOND : angle 0.49737 ( 2) hydrogen bonds : bond 0.06159 ( 805) hydrogen bonds : angle 4.42447 ( 2151) Misc. bond : bond 0.00045 ( 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 261 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.782 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: B 36 ARG cc_start: 0.7992 (mtm180) cc_final: 0.7439 (mmp80) REVERT: C 36 LYS cc_start: 0.9098 (mmtm) cc_final: 0.8490 (mttt) REVERT: D 105 LYS cc_start: 0.9479 (ptpp) cc_final: 0.9249 (ptpp) REVERT: E 60 LEU cc_start: 0.8867 (pt) cc_final: 0.8652 (pt) REVERT: E 67 PHE cc_start: 0.8528 (t80) cc_final: 0.7919 (t80) REVERT: E 100 LEU cc_start: 0.9826 (mt) cc_final: 0.9603 (mt) REVERT: E 104 PHE cc_start: 0.9477 (m-10) cc_final: 0.9215 (m-80) REVERT: E 110 CYS cc_start: 0.9086 (t) cc_final: 0.8680 (t) REVERT: F 88 TYR cc_start: 0.8868 (m-80) cc_final: 0.8652 (m-10) REVERT: G 38 ASN cc_start: 0.8079 (m-40) cc_final: 0.7488 (t0) REVERT: G 50 TYR cc_start: 0.9185 (t80) cc_final: 0.8873 (t80) REVERT: G 99 ARG cc_start: 0.7506 (mmt180) cc_final: 0.7121 (ptp-170) REVERT: H 115 VAL cc_start: 0.8170 (t) cc_final: 0.7778 (t) REVERT: H 118 TYR cc_start: 0.9262 (t80) cc_final: 0.8938 (t80) REVERT: W 334 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8726 (mt0) REVERT: W 379 PHE cc_start: 0.8876 (t80) cc_final: 0.8427 (t80) REVERT: W 396 ASN cc_start: 0.9272 (m-40) cc_final: 0.8667 (m-40) REVERT: W 423 ARG cc_start: 0.9720 (mtt-85) cc_final: 0.9477 (mmm160) REVERT: W 463 ARG cc_start: 0.8396 (ttp-170) cc_final: 0.7999 (ttm170) REVERT: W 518 LEU cc_start: 0.8767 (pp) cc_final: 0.7985 (mt) REVERT: W 520 ASN cc_start: 0.9132 (t0) cc_final: 0.8600 (p0) REVERT: W 538 MET cc_start: 0.8687 (mmt) cc_final: 0.8262 (mmt) REVERT: W 652 MET cc_start: 0.7786 (tpp) cc_final: 0.7547 (tpt) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.1682 time to fit residues: 66.4869 Evaluate side-chains 212 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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: 10.0000 chunk 122 optimal weight: 0.3980 chunk 200 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 166 optimal weight: 0.0570 overall best weight: 3.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 104 GLN C 112 GLN ** W 206 ASN ** 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 = 0.4066 r_free = 0.4066 target = 0.089309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.056069 restraints weight = 165616.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.057908 restraints weight = 103600.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.059143 restraints weight = 77521.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.059704 restraints weight = 64762.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.060361 restraints weight = 58915.334| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.7915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 22080 Z= 0.238 Angle : 0.726 12.079 31170 Z= 0.400 Chirality : 0.041 0.215 3508 Planarity : 0.006 0.059 2863 Dihedral : 28.486 177.524 5475 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.62 % Favored : 95.21 % Rotamer: Outliers : 0.06 % Allowed : 0.45 % 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: -0.82 (0.19), residues: 1778 helix: -0.08 (0.16), residues: 929 sheet: 0.12 (0.45), residues: 131 loop : -1.17 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 76 TYR 0.024 0.002 TYR W 526 PHE 0.028 0.002 PHE A 104 TRP 0.016 0.002 TRP W1194 HIS 0.008 0.002 HIS W 661 Details of bonding type rmsd covalent geometry : bond 0.00519 (22077) covalent geometry : angle 0.72600 (31168) SS BOND : bond 0.00444 ( 1) SS BOND : angle 0.93698 ( 2) hydrogen bonds : bond 0.08318 ( 805) hydrogen bonds : angle 4.74704 ( 2151) Misc. bond : bond 0.00078 ( 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 247 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 246 time to evaluate : 0.660 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: B 36 ARG cc_start: 0.8112 (mtm180) cc_final: 0.7528 (mmp80) REVERT: C 36 LYS cc_start: 0.9152 (mmtm) cc_final: 0.8525 (mttt) REVERT: C 88 ARG cc_start: 0.8231 (tpp-160) cc_final: 0.7662 (ttp80) REVERT: E 60 LEU cc_start: 0.8728 (pt) cc_final: 0.8414 (pp) REVERT: E 61 LEU cc_start: 0.8803 (mt) cc_final: 0.8529 (mt) REVERT: E 67 PHE cc_start: 0.8777 (t80) cc_final: 0.8230 (t80) REVERT: E 100 LEU cc_start: 0.9837 (mt) cc_final: 0.9587 (mt) REVERT: E 104 PHE cc_start: 0.9474 (m-10) cc_final: 0.9236 (m-80) REVERT: E 110 CYS cc_start: 0.9024 (t) cc_final: 0.8693 (t) REVERT: F 84 MET cc_start: 0.9158 (ptp) cc_final: 0.8868 (ptp) REVERT: F 88 TYR cc_start: 0.8762 (m-80) cc_final: 0.8456 (m-10) REVERT: H 59 MET cc_start: 0.9586 (mmp) cc_final: 0.9360 (mmp) REVERT: H 118 TYR cc_start: 0.9307 (t80) cc_final: 0.9021 (t80) REVERT: W 334 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8727 (mt0) REVERT: W 379 PHE cc_start: 0.9070 (t80) cc_final: 0.8670 (t80) REVERT: W 396 ASN cc_start: 0.9294 (m-40) cc_final: 0.8740 (m-40) REVERT: W 423 ARG cc_start: 0.9722 (mtt-85) cc_final: 0.9403 (mmm160) REVERT: W 518 LEU cc_start: 0.8956 (pp) cc_final: 0.8347 (mt) REVERT: W 520 ASN cc_start: 0.9277 (t0) cc_final: 0.8800 (p0) REVERT: W 538 MET cc_start: 0.8571 (mmt) cc_final: 0.8068 (mmp) REVERT: W 652 MET cc_start: 0.8042 (tpp) cc_final: 0.7737 (tpt) REVERT: W 802 MET cc_start: 0.7809 (ppp) cc_final: 0.7365 (ppp) REVERT: W 812 ASN cc_start: 0.9281 (t0) cc_final: 0.8928 (m-40) outliers start: 1 outliers final: 0 residues processed: 247 average time/residue: 0.1633 time to fit residues: 61.6092 Evaluate side-chains 194 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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: 0.7980 chunk 110 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 158 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN C 112 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.091973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.057261 restraints weight = 227382.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.059639 restraints weight = 120927.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.061167 restraints weight = 83401.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.062280 restraints weight = 66261.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.062858 restraints weight = 57188.290| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 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 = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.8066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22080 Z= 0.160 Angle : 0.668 12.764 31170 Z= 0.365 Chirality : 0.039 0.220 3508 Planarity : 0.005 0.059 2863 Dihedral : 28.467 179.119 5475 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.77 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -0.58 (0.19), residues: 1778 helix: 0.16 (0.16), residues: 937 sheet: 0.36 (0.47), residues: 123 loop : -1.15 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 53 TYR 0.014 0.001 TYR D 118 PHE 0.021 0.002 PHE F 61 TRP 0.013 0.001 TRP W1194 HIS 0.004 0.001 HIS W 177 Details of bonding type rmsd covalent geometry : bond 0.00343 (22077) covalent geometry : angle 0.66762 (31168) SS BOND : bond 0.00140 ( 1) SS BOND : angle 0.47040 ( 2) hydrogen bonds : bond 0.06095 ( 805) hydrogen bonds : angle 4.43621 ( 2151) Misc. bond : bond 0.00045 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6737.77 seconds wall clock time: 115 minutes 35.97 seconds (6935.97 seconds total)