Starting phenix.real_space_refine on Thu Mar 5 01:13:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o7e_0640/03_2026/6o7e_0640_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o7e_0640/03_2026/6o7e_0640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6o7e_0640/03_2026/6o7e_0640_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o7e_0640/03_2026/6o7e_0640_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6o7e_0640/03_2026/6o7e_0640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o7e_0640/03_2026/6o7e_0640.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 Mn 3 7.51 5 Zn 3 6.06 5 P 51 5.49 5 S 49 5.16 5 C 11025 2.51 5 N 3090 2.21 5 O 3385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17606 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 6150 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 35, 'TRANS': 735} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1128 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'GLN:plan1': 2, 'TRP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2214 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 265} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2262 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2261 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 20, 'TRANS': 265} Chain: "G" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 589 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 4, 'rna3p_pur': 10, 'rna3p_pyr': 4} Link IDs: {'rna2p': 12, 'rna3p': 14} Chain: "H" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 398 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 6, 'rna3p_pyr': 8} Link IDs: {'rna2p': 5, 'rna3p': 13} Chain: "Y" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 313 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Chain: "Y" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2223 Classifications: {'peptide': 322} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 106} Link IDs: {'PTRANS': 12, 'TRANS': 309} Chain breaks: 10 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'UNK:plan-1': 93, 'GLN:plan1': 1, 'PHE:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 146 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {' MN': 3, ' ZN': 1, 'ANP': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3074 SG CYS A 389 37.892 75.781 90.435 1.00 31.85 S ATOM 3094 SG CYS A 392 37.312 71.986 89.324 1.00 29.62 S ATOM 3249 SG CYS A 413 36.293 73.674 92.950 1.00 39.63 S ATOM 3269 SG CYS A 416 39.468 72.026 92.600 1.00 40.77 S ATOM 8105 SG CYS C 113 35.937 101.845 73.782 1.00 32.07 S ATOM 8172 SG CYS C 122 37.047 103.593 70.619 1.00 24.93 S ATOM 8192 SG CYS C 125 37.319 98.974 71.753 1.00 28.16 S ATOM 10367 SG CYS D 113 69.676 102.898 77.101 1.00 44.46 S ATOM 10434 SG CYS D 122 71.311 105.673 74.810 1.00 40.17 S ATOM 10454 SG CYS D 125 69.883 101.685 73.673 1.00 35.09 S Time building chain proxies: 3.77, per 1000 atoms: 0.21 Number of scatterers: 17606 At special positions: 0 Unit cell: (133.947, 132.858, 137.214, 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) Zn 3 29.99 Mn 3 24.99 S 49 16.00 P 51 15.00 O 3385 8.00 N 3090 7.00 C 11025 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " UNK Y 40 " - " ARG Y 39 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 724.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 389 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 416 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 413 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 392 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 111 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 125 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 122 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 113 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 111 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 122 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 125 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 113 " Number of angles added : 12 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3894 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 24 sheets defined 39.5% alpha, 12.7% beta 9 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 removed outlier: 3.507A pdb=" N ALA A 8 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 9 " --> pdb=" O GLU A 5 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 12 " --> pdb=" O ALA A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 22 Processing helix chain 'A' and resid 30 through 44 removed outlier: 3.502A pdb=" N ALA A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A 43 " --> pdb=" O ARG A 39 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 78 removed outlier: 4.314A pdb=" N GLU A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 104 removed outlier: 3.640A pdb=" N LEU A 91 " --> pdb=" O MET A 87 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 167 removed outlier: 3.734A pdb=" N GLU A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER A 166 " --> pdb=" O TRP A 162 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 183 removed outlier: 3.504A pdb=" N LEU A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.560A pdb=" N TYR A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 204 through 216 removed outlier: 3.591A pdb=" N ILE A 208 " --> pdb=" O MET A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.749A pdb=" N TYR A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 282 removed outlier: 3.986A pdb=" N SER A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 303 through 325 removed outlier: 3.722A pdb=" N GLU A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 368 removed outlier: 3.621A pdb=" N LYS A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 375 removed outlier: 3.688A pdb=" N ILE A 374 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS A 375 " --> pdb=" O GLY A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 371 through 375' Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 416 through 425 removed outlier: 3.616A pdb=" N VAL A 420 " --> pdb=" O CYS A 416 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 removed outlier: 3.886A pdb=" N SER A 506 " --> pdb=" O PHE A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 529 removed outlier: 3.680A pdb=" N PHE A 528 " --> pdb=" O ARG A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 551 removed outlier: 3.567A pdb=" N ARG A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 558 removed outlier: 3.609A pdb=" N ILE A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 Processing helix chain 'A' and resid 596 through 614 removed outlier: 3.719A pdb=" N PHE A 600 " --> pdb=" O TRP A 596 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU A 601 " --> pdb=" O ASP A 597 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 607 " --> pdb=" O ALA A 603 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 608 " --> pdb=" O PHE A 604 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 612 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 647 removed outlier: 3.677A pdb=" N ASP A 638 " --> pdb=" O TYR A 634 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL A 640 " --> pdb=" O MET A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 689 removed outlier: 3.553A pdb=" N ARG A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Proline residue: A 686 - end of helix Processing helix chain 'A' and resid 702 through 719 removed outlier: 4.236A pdb=" N LEU A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 708 " --> pdb=" O GLY A 704 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU A 711 " --> pdb=" O TRP A 707 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 733 removed outlier: 4.340A pdb=" N TYR A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 728 " --> pdb=" O ARG A 724 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 746 removed outlier: 3.920A pdb=" N LEU A 745 " --> pdb=" O PHE A 742 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL A 746 " --> pdb=" O PRO A 743 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 742 through 746' Processing helix chain 'A' and resid 749 through 756 removed outlier: 3.848A pdb=" N VAL A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 754 " --> pdb=" O THR A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 774 removed outlier: 4.283A pdb=" N ILE A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 771 " --> pdb=" O VAL A 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.635A pdb=" N LYS B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 36 through 41' Processing helix chain 'B' and resid 48 through 63 removed outlier: 3.944A pdb=" N ILE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Proline residue: B 54 - end of helix Processing helix chain 'B' and resid 72 through 87 removed outlier: 3.684A pdb=" N THR B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 108 removed outlier: 4.548A pdb=" N LYS B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE B 98 " --> pdb=" O GLN B 94 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 134 removed outlier: 3.806A pdb=" N VAL B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 156 removed outlier: 3.639A pdb=" N ALA B 144 " --> pdb=" O TYR B 140 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP B 150 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Proline residue: B 151 - end of helix removed outlier: 3.595A pdb=" N VAL B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 removed outlier: 3.788A pdb=" N VAL B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 69 removed outlier: 3.858A pdb=" N ARG C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 149 through 158 removed outlier: 3.578A pdb=" N LYS C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 223 removed outlier: 3.729A pdb=" N ASP C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 254 removed outlier: 3.573A pdb=" N TYR C 251 " --> pdb=" O PRO C 247 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 280 removed outlier: 3.544A pdb=" N PHE C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 287 removed outlier: 3.521A pdb=" N LYS C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 69 removed outlier: 4.119A pdb=" N ARG D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 149 through 151 No H-bonds generated for 'chain 'D' and resid 149 through 151' Processing helix chain 'D' and resid 152 through 159 Processing helix chain 'D' and resid 206 through 223 removed outlier: 3.595A pdb=" N ASP D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 removed outlier: 3.767A pdb=" N GLY D 232 " --> pdb=" O GLY D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 254 removed outlier: 3.893A pdb=" N TYR D 251 " --> pdb=" O PRO D 247 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 280 Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.726A pdb=" N GLU D 284 " --> pdb=" O PHE D 280 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 280 through 285' Processing helix chain 'E' and resid 21 through 36 removed outlier: 3.932A pdb=" N ALA E 27 " --> pdb=" O THR E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 51 removed outlier: 3.758A pdb=" N VAL E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU E 42 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.788A pdb=" N VAL E 73 " --> pdb=" O PRO E 70 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU E 74 " --> pdb=" O LEU E 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 74' Processing helix chain 'E' and resid 76 through 81 removed outlier: 3.865A pdb=" N LEU E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 98 Processing helix chain 'E' and resid 103 through 111 removed outlier: 3.565A pdb=" N GLU E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 171 removed outlier: 3.727A pdb=" N PHE E 168 " --> pdb=" O PRO E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 179 removed outlier: 3.901A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'Y' and resid 21 through 25 removed outlier: 3.523A pdb=" N ILE Y 25 " --> pdb=" O PRO Y 22 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 44 No H-bonds generated for 'chain 'Y' and resid 36 through 44' Processing helix chain 'Y' and resid 52 through 60 removed outlier: 3.621A pdb=" N UNK Y 57 " --> pdb=" O UNK Y 53 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N UNK Y 58 " --> pdb=" O UNK Y 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 61 through 62 No H-bonds generated for 'chain 'Y' and resid 61 through 62' Processing helix chain 'Y' and resid 65 through 67 No H-bonds generated for 'chain 'Y' and resid 65 through 67' Processing helix chain 'Y' and resid 113 through 133 removed outlier: 3.934A pdb=" N GLY Y 119 " --> pdb=" O SER Y 115 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA Y 120 " --> pdb=" O SER Y 116 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE Y 121 " --> pdb=" O LEU Y 117 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA Y 124 " --> pdb=" O ALA Y 120 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N CYS Y 133 " --> pdb=" O ALA Y 129 " (cutoff:3.500A) Processing helix chain 'Y' and resid 160 through 169 Processing helix chain 'Y' and resid 204 through 207 removed outlier: 3.704A pdb=" N LYS Y 207 " --> pdb=" O ASP Y 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 204 through 207' Processing helix chain 'Y' and resid 218 through 220 No H-bonds generated for 'chain 'Y' and resid 218 through 220' Processing helix chain 'Y' and resid 258 through 263 removed outlier: 3.886A pdb=" N LEU Y 262 " --> pdb=" O GLU Y 258 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN Y 263 " --> pdb=" O ALA Y 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 258 through 263' Processing helix chain 'Y' and resid 284 through 294 Processing helix chain 'Y' and resid 317 through 323 Processing helix chain 'Y' and resid 345 through 349 removed outlier: 4.045A pdb=" N LEU Y 348 " --> pdb=" O THR Y 345 " (cutoff:3.500A) Processing helix chain 'Y' and resid 354 through 365 removed outlier: 3.631A pdb=" N VAL Y 360 " --> pdb=" O LYS Y 356 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS Y 363 " --> pdb=" O ASN Y 359 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 288 through 291 removed outlier: 6.675A pdb=" N MET A 297 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASN A 291 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N HIS A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 386 through 388 Processing sheet with id=AA3, first strand: chain 'A' and resid 402 through 403 Processing sheet with id=AA4, first strand: chain 'A' and resid 444 through 445 removed outlier: 3.969A pdb=" N VAL A 444 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A 464 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 580 through 586 removed outlier: 6.934A pdb=" N ILE A 580 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ALA A 595 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL A 582 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 593 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 589 " --> pdb=" O GLY A 586 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AA7, first strand: chain 'C' and resid 147 through 148 removed outlier: 4.040A pdb=" N PHE C 147 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY C 13 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY C 7 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL C 10 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE C 243 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LYS C 12 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 85 through 88 removed outlier: 4.603A pdb=" N SER C 85 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N PHE C 101 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N GLY C 87 " --> pdb=" O PHE C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 103 through 104 Processing sheet with id=AB1, first strand: chain 'C' and resid 163 through 168 removed outlier: 3.554A pdb=" N ARG C 185 " --> pdb=" O GLU C 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 141 through 143 removed outlier: 3.760A pdb=" N GLY D 7 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL D 10 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE D 243 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LYS D 12 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP D 241 " --> pdb=" O LYS D 12 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 85 through 88 removed outlier: 7.093A pdb=" N SER D 85 " --> pdb=" O PHE D 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 163 through 169 Processing sheet with id=AB5, first strand: chain 'E' and resid 54 through 61 removed outlier: 5.977A pdb=" N SER E 56 " --> pdb=" O LEU E 160 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU E 160 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N SER E 155 " --> pdb=" O PRO E 11 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET E 202 " --> pdb=" O PHE E 4 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 67 through 68 Processing sheet with id=AB7, first strand: chain 'E' and resid 124 through 132 Processing sheet with id=AB8, first strand: chain 'E' and resid 252 through 253 Processing sheet with id=AB9, first strand: chain 'E' and resid 229 through 232 Processing sheet with id=AC1, first strand: chain 'E' and resid 235 through 236 Processing sheet with id=AC2, first strand: chain 'E' and resid 261 through 263 Processing sheet with id=AC3, first strand: chain 'Y' and resid 248 through 251 removed outlier: 3.582A pdb=" N VAL Y 251 " --> pdb=" O ARG Y 4 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Y' and resid 19 through 20 removed outlier: 3.859A pdb=" N ILE Y 100 " --> pdb=" O LEU Y 20 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Y' and resid 209 through 211 removed outlier: 3.577A pdb=" N HIS Y 254 " --> pdb=" O ILE Y 210 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Y' and resid 236 through 243 removed outlier: 3.817A pdb=" N ILE Y 236 " --> pdb=" O VAL Y 229 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU Y 385 " --> pdb=" O GLU Y 228 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1512 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4501 1.33 - 1.45: 3620 1.45 - 1.57: 9768 1.57 - 1.69: 100 1.69 - 1.81: 81 Bond restraints: 18070 Sorted by residual: bond pdb=" O3A ANP A 803 " pdb=" PB ANP A 803 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.22e+01 bond pdb=" O3A ANP A 802 " pdb=" PB ANP A 802 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.02e+01 bond pdb=" C ALA A 685 " pdb=" N PRO A 686 " ideal model delta sigma weight residual 1.334 1.385 -0.052 8.40e-03 1.42e+04 3.78e+01 bond pdb=" N3B ANP A 802 " pdb=" PG ANP A 802 " ideal model delta sigma weight residual 1.795 1.687 0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" N3B ANP A 803 " pdb=" PG ANP A 803 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.59e+01 ... (remaining 18065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 24420 3.59 - 7.17: 206 7.17 - 10.76: 23 10.76 - 14.34: 2 14.34 - 17.93: 2 Bond angle restraints: 24653 Sorted by residual: angle pdb=" C ARG E 53 " pdb=" N ILE E 54 " pdb=" CA ILE E 54 " ideal model delta sigma weight residual 122.27 128.82 -6.55 1.07e+00 8.73e-01 3.75e+01 angle pdb=" PB ANP A 802 " pdb=" N3B ANP A 802 " pdb=" PG ANP A 802 " ideal model delta sigma weight residual 126.95 109.02 17.93 3.00e+00 1.11e-01 3.57e+01 angle pdb=" PB ANP A 803 " pdb=" N3B ANP A 803 " pdb=" PG ANP A 803 " ideal model delta sigma weight residual 126.95 111.23 15.72 3.00e+00 1.11e-01 2.75e+01 angle pdb=" N GLY A 399 " pdb=" CA GLY A 399 " pdb=" C GLY A 399 " ideal model delta sigma weight residual 113.79 107.82 5.97 1.17e+00 7.31e-01 2.61e+01 angle pdb=" C GLU C 95 " pdb=" N ASN C 96 " pdb=" CA ASN C 96 " ideal model delta sigma weight residual 121.54 130.65 -9.11 1.91e+00 2.74e-01 2.28e+01 ... (remaining 24648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 10637 35.22 - 70.45: 211 70.45 - 105.67: 34 105.67 - 140.89: 0 140.89 - 176.11: 4 Dihedral angle restraints: 10886 sinusoidal: 4794 harmonic: 6092 Sorted by residual: dihedral pdb=" O4' C G 11 " pdb=" C1' C G 11 " pdb=" N1 C G 11 " pdb=" C2 C G 11 " ideal model delta sinusoidal sigma weight residual -128.00 48.11 -176.11 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C G 5 " pdb=" C1' C G 5 " pdb=" N1 C G 5 " pdb=" C2 C G 5 " ideal model delta sinusoidal sigma weight residual -128.00 43.10 -171.10 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" CA VAL A 775 " pdb=" C VAL A 775 " pdb=" N ARG A 776 " pdb=" CA ARG A 776 " ideal model delta harmonic sigma weight residual -180.00 -151.79 -28.21 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 10883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2129 0.059 - 0.117: 476 0.117 - 0.176: 95 0.176 - 0.235: 8 0.235 - 0.294: 6 Chirality restraints: 2714 Sorted by residual: chirality pdb=" C3' ANP A 802 " pdb=" C2' ANP A 802 " pdb=" C4' ANP A 802 " pdb=" O3' ANP A 802 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB ILE E 122 " pdb=" CA ILE E 122 " pdb=" CG1 ILE E 122 " pdb=" CG2 ILE E 122 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C1' C G 5 " pdb=" O4' C G 5 " pdb=" C2' C G 5 " pdb=" N1 C G 5 " both_signs ideal model delta sigma weight residual False 2.45 2.19 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2711 not shown) Planarity restraints: 3007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 494 " 0.041 5.00e-02 4.00e+02 6.19e-02 6.14e+00 pdb=" N PRO A 495 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 495 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 495 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 652 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.88e+00 pdb=" C ARG A 652 " -0.042 2.00e-02 2.50e+03 pdb=" O ARG A 652 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN A 653 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA E 173 " -0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO E 174 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO E 174 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 174 " -0.033 5.00e-02 4.00e+02 ... (remaining 3004 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 80 2.50 - 3.10: 10884 3.10 - 3.70: 26779 3.70 - 4.30: 39396 4.30 - 4.90: 64691 Nonbonded interactions: 141830 Sorted by model distance: nonbonded pdb=" O2G ANP A 802 " pdb="MN MN A 805 " model vdw 1.896 2.320 nonbonded pdb=" OD1 ASP A 239 " pdb="MN MN A 806 " model vdw 1.943 2.320 nonbonded pdb=" OD2 ASP A 239 " pdb="MN MN A 806 " model vdw 1.957 2.320 nonbonded pdb=" O2A ANP A 802 " pdb="MN MN A 804 " model vdw 2.022 2.320 nonbonded pdb=" OD1 ASP A 588 " pdb="MN MN A 804 " model vdw 2.198 2.320 ... (remaining 141825 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 'C' selection = (chain 'D' and (resid 4 through 27 or resid 34 through 301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.980 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.181 18083 Z= 0.276 Angle : 0.987 41.426 24668 Z= 0.492 Chirality : 0.052 0.294 2714 Planarity : 0.007 0.062 3006 Dihedral : 14.310 176.113 6989 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.24 % Allowed : 3.90 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.14 (0.14), residues: 2018 helix: -4.40 (0.08), residues: 721 sheet: -2.62 (0.27), residues: 287 loop : -2.82 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 177 TYR 0.020 0.002 TYR A 634 PHE 0.025 0.002 PHE C 194 TRP 0.025 0.002 TRP A 131 HIS 0.006 0.001 HIS D 22 Details of bonding type rmsd covalent geometry : bond 0.00494 (18070) covalent geometry : angle 0.90362 (24653) hydrogen bonds : bond 0.29667 ( 551) hydrogen bonds : angle 10.65251 ( 1558) metal coordination : bond 0.15037 ( 12) metal coordination : angle 18.04787 ( 12) link_TRANS : bond 0.00190 ( 1) link_TRANS : angle 0.28408 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 428 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7884 (tm130) cc_final: 0.7560 (tm-30) REVERT: A 41 LEU cc_start: 0.8942 (tp) cc_final: 0.8740 (tp) REVERT: A 386 LEU cc_start: 0.8472 (mp) cc_final: 0.8054 (mt) REVERT: A 507 MET cc_start: 0.7325 (mmm) cc_final: 0.6920 (mmm) REVERT: A 545 MET cc_start: 0.8252 (tpp) cc_final: 0.7799 (tpp) REVERT: A 571 LEU cc_start: 0.7573 (mm) cc_final: 0.7313 (mt) REVERT: B 178 TYR cc_start: 0.7070 (m-80) cc_final: 0.6614 (m-80) REVERT: C 47 LEU cc_start: 0.8667 (mt) cc_final: 0.8385 (mt) REVERT: D 133 LYS cc_start: 0.7103 (mppt) cc_final: 0.6769 (mtpp) REVERT: E 145 PHE cc_start: 0.8723 (m-80) cc_final: 0.8410 (m-80) REVERT: E 148 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6525 (mt-10) REVERT: E 176 MET cc_start: 0.8996 (mmm) cc_final: 0.8761 (mmt) REVERT: E 244 MET cc_start: 0.8080 (mtp) cc_final: 0.7573 (mtm) outliers start: 4 outliers final: 2 residues processed: 432 average time/residue: 0.1923 time to fit residues: 112.2602 Evaluate side-chains 215 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 213 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain E residue 53 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.0670 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 201 HIS A 456 GLN A 653 ASN A 668 HIS A 676 HIS B 72 ASN B 77 ASN B 179 HIS C 136 ASN C 179 ASN D 183 ASN Y 18 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.190136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.141451 restraints weight = 22947.970| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.56 r_work: 0.3251 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18083 Z= 0.128 Angle : 0.615 10.158 24668 Z= 0.313 Chirality : 0.043 0.280 2714 Planarity : 0.006 0.049 3006 Dihedral : 16.442 173.225 3145 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.28 % Allowed : 8.76 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.62 (0.16), residues: 2018 helix: -2.65 (0.14), residues: 757 sheet: -1.95 (0.29), residues: 275 loop : -2.25 (0.17), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 157 TYR 0.013 0.001 TYR A 716 PHE 0.027 0.001 PHE A 147 TRP 0.012 0.001 TRP A 320 HIS 0.003 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00273 (18070) covalent geometry : angle 0.60714 (24653) hydrogen bonds : bond 0.04861 ( 551) hydrogen bonds : angle 5.52194 ( 1558) metal coordination : bond 0.00789 ( 12) metal coordination : angle 4.56855 ( 12) link_TRANS : bond 0.00027 ( 1) link_TRANS : angle 0.09216 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 249 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8808 (tt0) cc_final: 0.8454 (tp30) REVERT: A 21 GLN cc_start: 0.8249 (tm130) cc_final: 0.7824 (tm-30) REVERT: A 26 TYR cc_start: 0.7610 (m-80) cc_final: 0.7321 (m-80) REVERT: A 58 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8480 (tm-30) REVERT: A 91 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8718 (tp) REVERT: A 160 ARG cc_start: 0.7625 (mtm180) cc_final: 0.7420 (mtt180) REVERT: A 545 MET cc_start: 0.8673 (tpp) cc_final: 0.8388 (tpp) REVERT: A 571 LEU cc_start: 0.7962 (mm) cc_final: 0.7603 (mt) REVERT: B 152 MET cc_start: 0.7313 (mtm) cc_final: 0.6311 (ttm) REVERT: B 178 TYR cc_start: 0.7037 (m-80) cc_final: 0.6617 (m-80) REVERT: C 66 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8691 (tt) REVERT: D 21 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8413 (tp) REVERT: D 64 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7919 (mt-10) REVERT: D 103 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7893 (ttm170) REVERT: D 263 ASP cc_start: 0.6289 (m-30) cc_final: 0.5779 (m-30) REVERT: E 145 PHE cc_start: 0.9099 (m-80) cc_final: 0.8755 (m-80) REVERT: Y 101 LYS cc_start: 0.4006 (mtpp) cc_final: 0.3713 (mtpt) REVERT: Y 126 LEU cc_start: 0.7481 (tp) cc_final: 0.7251 (tp) REVERT: Y 221 HIS cc_start: 0.6338 (m-70) cc_final: 0.6075 (m170) outliers start: 38 outliers final: 15 residues processed: 272 average time/residue: 0.1575 time to fit residues: 62.0520 Evaluate side-chains 217 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 198 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain Y residue 215 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 75 optimal weight: 0.0050 chunk 133 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 124 ASN A 438 ASN A 456 GLN B 93 ASN C 94 GLN D 22 HIS E 106 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.183603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.133410 restraints weight = 23062.092| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.80 r_work: 0.3150 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 18083 Z= 0.192 Angle : 0.624 8.814 24668 Z= 0.316 Chirality : 0.045 0.237 2714 Planarity : 0.005 0.053 3006 Dihedral : 16.109 174.179 3145 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.70 % Allowed : 11.04 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.17), residues: 2018 helix: -1.55 (0.17), residues: 762 sheet: -1.76 (0.28), residues: 295 loop : -1.98 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 20 TYR 0.025 0.002 TYR E 90 PHE 0.021 0.002 PHE E 15 TRP 0.017 0.002 TRP A 674 HIS 0.006 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00452 (18070) covalent geometry : angle 0.61909 (24653) hydrogen bonds : bond 0.04563 ( 551) hydrogen bonds : angle 4.96023 ( 1558) metal coordination : bond 0.01215 ( 12) metal coordination : angle 3.77010 ( 12) link_TRANS : bond 0.00023 ( 1) link_TRANS : angle 0.10158 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 207 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8341 (tm130) cc_final: 0.7929 (tm-30) REVERT: A 91 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8789 (tp) REVERT: A 124 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7911 (m110) REVERT: A 545 MET cc_start: 0.8769 (tpp) cc_final: 0.8363 (tpp) REVERT: B 152 MET cc_start: 0.7214 (mtm) cc_final: 0.6304 (ttm) REVERT: B 178 TYR cc_start: 0.7042 (m-80) cc_final: 0.6594 (m-80) REVERT: C 66 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8727 (tt) REVERT: C 185 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8568 (ptt180) REVERT: C 195 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7541 (tp30) REVERT: D 21 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8495 (tp) REVERT: D 64 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8082 (mt-10) REVERT: D 103 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.8008 (ttm170) REVERT: D 107 ARG cc_start: 0.6865 (mtt90) cc_final: 0.6647 (mtt90) REVERT: D 133 LYS cc_start: 0.7853 (mppt) cc_final: 0.7205 (mtpp) REVERT: E 145 PHE cc_start: 0.9128 (m-80) cc_final: 0.8761 (m-80) REVERT: E 148 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7113 (mt-10) REVERT: E 228 ARG cc_start: 0.8095 (ttm110) cc_final: 0.7839 (ttm170) REVERT: E 255 ASN cc_start: 0.8796 (t0) cc_final: 0.8181 (t0) REVERT: Y 101 LYS cc_start: 0.4151 (mtpp) cc_final: 0.3900 (mtpt) REVERT: Y 221 HIS cc_start: 0.6400 (m-70) cc_final: 0.6161 (m170) outliers start: 45 outliers final: 30 residues processed: 237 average time/residue: 0.1592 time to fit residues: 54.6422 Evaluate side-chains 218 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 181 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 185 ARG Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain Y residue 12 LEU Chi-restraints excluded: chain Y residue 215 LYS Chi-restraints excluded: chain Y residue 289 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 97 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 76 optimal weight: 0.2980 chunk 106 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 102 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN E 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.186210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.138849 restraints weight = 22917.922| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.56 r_work: 0.3188 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18083 Z= 0.122 Angle : 0.546 8.102 24668 Z= 0.279 Chirality : 0.042 0.214 2714 Planarity : 0.004 0.069 3006 Dihedral : 15.890 173.830 3145 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.10 % Allowed : 12.42 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.18), residues: 2018 helix: -0.84 (0.19), residues: 755 sheet: -1.58 (0.29), residues: 281 loop : -1.82 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 114 TYR 0.019 0.001 TYR E 90 PHE 0.014 0.001 PHE E 159 TRP 0.009 0.001 TRP Y 393 HIS 0.003 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00277 (18070) covalent geometry : angle 0.54294 (24653) hydrogen bonds : bond 0.03728 ( 551) hydrogen bonds : angle 4.63973 ( 1558) metal coordination : bond 0.00588 ( 12) metal coordination : angle 2.88036 ( 12) link_TRANS : bond 0.00020 ( 1) link_TRANS : angle 0.10634 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8337 (tm130) cc_final: 0.7897 (tm-30) REVERT: A 26 TYR cc_start: 0.7621 (m-80) cc_final: 0.7322 (m-80) REVERT: A 545 MET cc_start: 0.8635 (tpp) cc_final: 0.8364 (tpp) REVERT: B 152 MET cc_start: 0.7212 (mtm) cc_final: 0.6213 (ttm) REVERT: B 178 TYR cc_start: 0.6997 (m-80) cc_final: 0.6579 (m-80) REVERT: C 66 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8689 (tt) REVERT: C 84 TYR cc_start: 0.9279 (m-80) cc_final: 0.8931 (m-80) REVERT: C 195 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7530 (tp30) REVERT: D 1 MET cc_start: 0.6939 (ttp) cc_final: 0.6699 (ttt) REVERT: D 21 LEU cc_start: 0.8705 (tm) cc_final: 0.8441 (tp) REVERT: D 133 LYS cc_start: 0.7750 (mppt) cc_final: 0.7034 (mtpp) REVERT: E 145 PHE cc_start: 0.9131 (m-80) cc_final: 0.8834 (m-80) REVERT: E 148 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7061 (mt-10) REVERT: E 255 ASN cc_start: 0.8839 (t0) cc_final: 0.8191 (t0) REVERT: Y 101 LYS cc_start: 0.4063 (mtpp) cc_final: 0.3784 (mtpt) REVERT: Y 105 LYS cc_start: 0.7019 (mtmm) cc_final: 0.6749 (mtmm) REVERT: Y 221 HIS cc_start: 0.6349 (m-70) cc_final: 0.5970 (m170) outliers start: 35 outliers final: 22 residues processed: 221 average time/residue: 0.1599 time to fit residues: 51.5651 Evaluate side-chains 201 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain Y residue 106 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 170 optimal weight: 0.8980 chunk 132 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 27 optimal weight: 0.0970 chunk 134 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 ASN E 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.185228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.136028 restraints weight = 22830.885| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.73 r_work: 0.3173 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18083 Z= 0.123 Angle : 0.529 8.230 24668 Z= 0.271 Chirality : 0.042 0.222 2714 Planarity : 0.004 0.066 3006 Dihedral : 15.798 174.316 3145 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.04 % Allowed : 12.48 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.18), residues: 2018 helix: -0.38 (0.19), residues: 754 sheet: -1.44 (0.30), residues: 276 loop : -1.70 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 319 TYR 0.017 0.001 TYR E 90 PHE 0.014 0.001 PHE E 159 TRP 0.012 0.001 TRP A 131 HIS 0.004 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00281 (18070) covalent geometry : angle 0.52555 (24653) hydrogen bonds : bond 0.03536 ( 551) hydrogen bonds : angle 4.47369 ( 1558) metal coordination : bond 0.00713 ( 12) metal coordination : angle 2.72640 ( 12) link_TRANS : bond 0.00020 ( 1) link_TRANS : angle 0.10577 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8444 (tm130) cc_final: 0.8004 (tm-30) REVERT: A 26 TYR cc_start: 0.7644 (m-80) cc_final: 0.7259 (m-80) REVERT: A 545 MET cc_start: 0.8642 (tpp) cc_final: 0.8334 (tpp) REVERT: B 152 MET cc_start: 0.7213 (mtm) cc_final: 0.6227 (ttm) REVERT: B 178 TYR cc_start: 0.6984 (m-80) cc_final: 0.6568 (m-80) REVERT: C 66 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8691 (tt) REVERT: C 84 TYR cc_start: 0.9255 (m-80) cc_final: 0.8948 (m-80) REVERT: C 195 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7499 (tp30) REVERT: D 1 MET cc_start: 0.6987 (ttp) cc_final: 0.6703 (ttt) REVERT: D 21 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8421 (tp) REVERT: D 133 LYS cc_start: 0.7805 (mppt) cc_final: 0.6964 (mtpp) REVERT: D 181 ARG cc_start: 0.7524 (ptt-90) cc_final: 0.7315 (ptt-90) REVERT: E 145 PHE cc_start: 0.9133 (m-80) cc_final: 0.8844 (m-80) REVERT: E 148 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7025 (mt-10) REVERT: E 255 ASN cc_start: 0.8873 (t0) cc_final: 0.8188 (t0) REVERT: Y 101 LYS cc_start: 0.3909 (mtpp) cc_final: 0.3599 (mtpt) REVERT: Y 105 LYS cc_start: 0.7220 (mtmm) cc_final: 0.6909 (mtmm) REVERT: Y 221 HIS cc_start: 0.6362 (m-70) cc_final: 0.5992 (m170) outliers start: 34 outliers final: 25 residues processed: 221 average time/residue: 0.1588 time to fit residues: 51.4328 Evaluate side-chains 212 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain Y residue 106 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 172 optimal weight: 0.8980 chunk 170 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 154 optimal weight: 0.0980 chunk 149 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 ASN E 38 GLN E 200 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.184843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.138027 restraints weight = 22707.032| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.60 r_work: 0.3199 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18083 Z= 0.110 Angle : 0.514 8.814 24668 Z= 0.262 Chirality : 0.041 0.190 2714 Planarity : 0.004 0.076 3006 Dihedral : 15.742 174.830 3145 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.16 % Allowed : 13.03 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.18), residues: 2018 helix: -0.03 (0.20), residues: 752 sheet: -1.29 (0.30), residues: 275 loop : -1.64 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 319 TYR 0.015 0.001 TYR E 90 PHE 0.013 0.001 PHE E 159 TRP 0.013 0.001 TRP A 131 HIS 0.004 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00248 (18070) covalent geometry : angle 0.51200 (24653) hydrogen bonds : bond 0.03326 ( 551) hydrogen bonds : angle 4.34038 ( 1558) metal coordination : bond 0.00466 ( 12) metal coordination : angle 1.99917 ( 12) link_TRANS : bond 0.00018 ( 1) link_TRANS : angle 0.09912 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8404 (tm130) cc_final: 0.8009 (tm-30) REVERT: A 26 TYR cc_start: 0.7654 (m-80) cc_final: 0.7386 (m-80) REVERT: A 438 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.7450 (p0) REVERT: A 545 MET cc_start: 0.8593 (tpp) cc_final: 0.8325 (tpp) REVERT: A 572 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6336 (ppp80) REVERT: B 152 MET cc_start: 0.7216 (mtm) cc_final: 0.6349 (ttm) REVERT: B 178 TYR cc_start: 0.6948 (m-80) cc_final: 0.6580 (m-80) REVERT: C 66 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8671 (tt) REVERT: C 84 TYR cc_start: 0.9228 (m-80) cc_final: 0.8887 (m-80) REVERT: D 1 MET cc_start: 0.6887 (ttp) cc_final: 0.6596 (ttt) REVERT: D 21 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8402 (tp) REVERT: D 70 ARG cc_start: 0.6818 (mtt-85) cc_final: 0.6585 (mtt90) REVERT: E 145 PHE cc_start: 0.9110 (m-80) cc_final: 0.8801 (m-80) REVERT: E 148 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7132 (mt-10) REVERT: Y 101 LYS cc_start: 0.4076 (mtpp) cc_final: 0.3708 (mtpt) REVERT: Y 105 LYS cc_start: 0.7145 (mtmm) cc_final: 0.6857 (mtmm) REVERT: Y 221 HIS cc_start: 0.6417 (m-70) cc_final: 0.6039 (m170) REVERT: Y 319 ARG cc_start: 0.5724 (mmm160) cc_final: 0.4511 (mmt-90) outliers start: 36 outliers final: 24 residues processed: 219 average time/residue: 0.1555 time to fit residues: 50.1738 Evaluate side-chains 211 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain Y residue 106 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 34 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 143 optimal weight: 0.6980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 ASN E 38 GLN E 200 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.186805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.139599 restraints weight = 22932.056| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.64 r_work: 0.3183 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18083 Z= 0.115 Angle : 0.519 8.650 24668 Z= 0.265 Chirality : 0.041 0.183 2714 Planarity : 0.004 0.063 3006 Dihedral : 15.706 175.002 3145 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.22 % Allowed : 13.03 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.18), residues: 2018 helix: 0.18 (0.20), residues: 755 sheet: -1.16 (0.30), residues: 275 loop : -1.61 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 160 TYR 0.015 0.001 TYR E 90 PHE 0.014 0.001 PHE E 159 TRP 0.016 0.001 TRP A 131 HIS 0.004 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00266 (18070) covalent geometry : angle 0.51730 (24653) hydrogen bonds : bond 0.03273 ( 551) hydrogen bonds : angle 4.24050 ( 1558) metal coordination : bond 0.00580 ( 12) metal coordination : angle 1.85594 ( 12) link_TRANS : bond 0.00017 ( 1) link_TRANS : angle 0.10127 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8425 (tm130) cc_final: 0.8032 (tm-30) REVERT: A 26 TYR cc_start: 0.7636 (m-80) cc_final: 0.7311 (m-80) REVERT: A 156 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7834 (tp30) REVERT: A 545 MET cc_start: 0.8639 (tpp) cc_final: 0.8353 (tpp) REVERT: A 572 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6441 (ppp80) REVERT: A 673 GLU cc_start: 0.7667 (tt0) cc_final: 0.7454 (tp30) REVERT: A 775 VAL cc_start: 0.5466 (OUTLIER) cc_final: 0.5232 (m) REVERT: B 152 MET cc_start: 0.7287 (mtm) cc_final: 0.6394 (ttm) REVERT: B 178 TYR cc_start: 0.6925 (m-80) cc_final: 0.6564 (m-80) REVERT: C 66 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8706 (tt) REVERT: C 84 TYR cc_start: 0.9227 (m-80) cc_final: 0.8887 (m-80) REVERT: C 117 GLU cc_start: 0.8276 (pm20) cc_final: 0.8053 (mp0) REVERT: C 195 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7468 (tp30) REVERT: D 1 MET cc_start: 0.6824 (ttp) cc_final: 0.6518 (ttt) REVERT: D 21 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8357 (tp) REVERT: D 70 ARG cc_start: 0.6817 (mtt-85) cc_final: 0.6615 (mtt90) REVERT: E 145 PHE cc_start: 0.9119 (m-80) cc_final: 0.8848 (m-80) REVERT: E 148 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7206 (mt-10) REVERT: Y 101 LYS cc_start: 0.3766 (mtpp) cc_final: 0.3473 (mtpt) REVERT: Y 221 HIS cc_start: 0.6601 (m-70) cc_final: 0.6221 (m170) REVERT: Y 390 PRO cc_start: 0.2346 (Cg_exo) cc_final: 0.2013 (Cg_endo) outliers start: 37 outliers final: 25 residues processed: 211 average time/residue: 0.1479 time to fit residues: 46.4496 Evaluate side-chains 199 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 268 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 53 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 122 optimal weight: 0.3980 chunk 70 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 163 optimal weight: 0.0970 chunk 116 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 ASN E 38 GLN E 200 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.184535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.138438 restraints weight = 22714.056| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.51 r_work: 0.3178 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18083 Z= 0.125 Angle : 0.527 8.719 24668 Z= 0.270 Chirality : 0.042 0.178 2714 Planarity : 0.004 0.074 3006 Dihedral : 15.681 174.808 3145 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.04 % Allowed : 13.45 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.19 (0.19), residues: 2018 helix: 0.31 (0.20), residues: 757 sheet: -1.08 (0.31), residues: 275 loop : -1.59 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 114 TYR 0.015 0.001 TYR E 90 PHE 0.022 0.001 PHE D 276 TRP 0.018 0.001 TRP A 131 HIS 0.009 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00292 (18070) covalent geometry : angle 0.52554 (24653) hydrogen bonds : bond 0.03372 ( 551) hydrogen bonds : angle 4.26406 ( 1558) metal coordination : bond 0.00672 ( 12) metal coordination : angle 1.89977 ( 12) link_TRANS : bond 0.00018 ( 1) link_TRANS : angle 0.09856 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8383 (tm130) cc_final: 0.8014 (tm-30) REVERT: A 26 TYR cc_start: 0.7614 (m-80) cc_final: 0.7363 (m-80) REVERT: A 545 MET cc_start: 0.8652 (tpp) cc_final: 0.8360 (tpp) REVERT: A 572 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6462 (ppp80) REVERT: A 775 VAL cc_start: 0.5562 (OUTLIER) cc_final: 0.5327 (m) REVERT: B 152 MET cc_start: 0.7278 (mtm) cc_final: 0.6367 (ttm) REVERT: B 178 TYR cc_start: 0.6939 (m-80) cc_final: 0.6595 (m-80) REVERT: C 66 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8719 (tt) REVERT: C 84 TYR cc_start: 0.9215 (m-80) cc_final: 0.8925 (m-80) REVERT: C 117 GLU cc_start: 0.8319 (pm20) cc_final: 0.8110 (mp0) REVERT: C 195 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7495 (tp30) REVERT: D 1 MET cc_start: 0.6847 (ttp) cc_final: 0.6528 (ttt) REVERT: D 21 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8349 (tp) REVERT: D 253 THR cc_start: 0.9122 (t) cc_final: 0.8519 (p) REVERT: E 148 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7195 (mt-10) REVERT: Y 101 LYS cc_start: 0.4035 (mtpp) cc_final: 0.3774 (mtpt) REVERT: Y 105 LYS cc_start: 0.7361 (mtmm) cc_final: 0.7040 (mtmm) REVERT: Y 221 HIS cc_start: 0.6589 (m-70) cc_final: 0.6174 (m170) outliers start: 34 outliers final: 27 residues processed: 212 average time/residue: 0.1477 time to fit residues: 46.6255 Evaluate side-chains 208 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 268 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 103 optimal weight: 0.0670 chunk 14 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 GLN E 38 GLN E 200 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.186106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.139126 restraints weight = 22756.676| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.73 r_work: 0.3177 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18083 Z= 0.118 Angle : 0.523 8.863 24668 Z= 0.268 Chirality : 0.041 0.175 2714 Planarity : 0.004 0.065 3006 Dihedral : 15.673 174.734 3145 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.04 % Allowed : 14.05 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.19), residues: 2018 helix: 0.50 (0.20), residues: 752 sheet: -1.03 (0.31), residues: 277 loop : -1.54 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 114 TYR 0.016 0.001 TYR E 90 PHE 0.021 0.001 PHE D 276 TRP 0.021 0.001 TRP A 131 HIS 0.011 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00273 (18070) covalent geometry : angle 0.52177 (24653) hydrogen bonds : bond 0.03259 ( 551) hydrogen bonds : angle 4.21224 ( 1558) metal coordination : bond 0.00590 ( 12) metal coordination : angle 1.81400 ( 12) link_TRANS : bond 0.00021 ( 1) link_TRANS : angle 0.09297 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8404 (tm130) cc_final: 0.8037 (tm-30) REVERT: A 26 TYR cc_start: 0.7568 (m-80) cc_final: 0.7322 (m-80) REVERT: A 160 ARG cc_start: 0.7356 (ttm170) cc_final: 0.7156 (mtm-85) REVERT: A 545 MET cc_start: 0.8664 (tpp) cc_final: 0.8375 (tpp) REVERT: A 572 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6445 (ppp80) REVERT: A 673 GLU cc_start: 0.7694 (tt0) cc_final: 0.7448 (tp30) REVERT: B 178 TYR cc_start: 0.6883 (m-80) cc_final: 0.6527 (m-80) REVERT: C 66 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8675 (tt) REVERT: C 84 TYR cc_start: 0.9247 (m-80) cc_final: 0.8988 (m-80) REVERT: C 115 ASP cc_start: 0.7547 (t70) cc_final: 0.7283 (t0) REVERT: C 195 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7556 (tp30) REVERT: D 1 MET cc_start: 0.6723 (ttp) cc_final: 0.6397 (ttt) REVERT: D 21 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8303 (tp) REVERT: E 148 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7207 (mt-10) REVERT: Y 101 LYS cc_start: 0.3804 (mtpp) cc_final: 0.3515 (mtpt) REVERT: Y 221 HIS cc_start: 0.6590 (m-70) cc_final: 0.6203 (m170) outliers start: 34 outliers final: 27 residues processed: 213 average time/residue: 0.1508 time to fit residues: 47.7298 Evaluate side-chains 208 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 268 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 122 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 95 optimal weight: 0.0980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.185155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138595 restraints weight = 22657.660| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.60 r_work: 0.3170 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18083 Z= 0.135 Angle : 0.545 9.971 24668 Z= 0.279 Chirality : 0.042 0.193 2714 Planarity : 0.004 0.078 3006 Dihedral : 15.678 174.821 3145 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.04 % Allowed : 13.81 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.19), residues: 2018 helix: 0.56 (0.20), residues: 752 sheet: -1.00 (0.31), residues: 277 loop : -1.52 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 114 TYR 0.016 0.001 TYR E 90 PHE 0.022 0.001 PHE D 276 TRP 0.022 0.001 TRP A 131 HIS 0.012 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00317 (18070) covalent geometry : angle 0.54311 (24653) hydrogen bonds : bond 0.03304 ( 551) hydrogen bonds : angle 4.23570 ( 1558) metal coordination : bond 0.00771 ( 12) metal coordination : angle 1.93975 ( 12) link_TRANS : bond 0.00022 ( 1) link_TRANS : angle 0.08980 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8396 (tm130) cc_final: 0.8027 (tm-30) REVERT: A 26 TYR cc_start: 0.7608 (m-80) cc_final: 0.7357 (m-80) REVERT: A 545 MET cc_start: 0.8661 (tpp) cc_final: 0.8343 (tpp) REVERT: A 572 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6485 (ppp80) REVERT: A 673 GLU cc_start: 0.7754 (tt0) cc_final: 0.7488 (tp30) REVERT: B 178 TYR cc_start: 0.6896 (m-80) cc_final: 0.6541 (m-80) REVERT: C 66 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8684 (tt) REVERT: C 84 TYR cc_start: 0.9243 (m-80) cc_final: 0.8979 (m-80) REVERT: C 115 ASP cc_start: 0.7532 (t70) cc_final: 0.7276 (t0) REVERT: C 195 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7537 (tp30) REVERT: D 1 MET cc_start: 0.6786 (ttp) cc_final: 0.6448 (ttt) REVERT: D 21 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8331 (tp) REVERT: E 261 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: Y 101 LYS cc_start: 0.3811 (mtpp) cc_final: 0.3524 (mtpt) REVERT: Y 105 LYS cc_start: 0.7358 (mtmm) cc_final: 0.7037 (mtmm) REVERT: Y 221 HIS cc_start: 0.6604 (m-70) cc_final: 0.6220 (m170) REVERT: Y 390 PRO cc_start: 0.2972 (Cg_exo) cc_final: 0.2571 (Cg_endo) outliers start: 34 outliers final: 28 residues processed: 202 average time/residue: 0.1388 time to fit residues: 41.7714 Evaluate side-chains 200 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 268 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 177 optimal weight: 20.0000 chunk 139 optimal weight: 0.7980 chunk 166 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 chunk 45 optimal weight: 7.9990 chunk 162 optimal weight: 0.5980 chunk 136 optimal weight: 0.0670 chunk 99 optimal weight: 0.0670 chunk 84 optimal weight: 4.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.185947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.139372 restraints weight = 23254.102| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.56 r_work: 0.3219 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18083 Z= 0.095 Angle : 0.509 9.453 24668 Z= 0.260 Chirality : 0.040 0.166 2714 Planarity : 0.004 0.057 3006 Dihedral : 15.608 174.764 3145 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.74 % Allowed : 14.23 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.19), residues: 2018 helix: 0.62 (0.20), residues: 775 sheet: -0.93 (0.31), residues: 277 loop : -1.49 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 114 TYR 0.016 0.001 TYR E 90 PHE 0.023 0.001 PHE D 276 TRP 0.023 0.001 TRP A 131 HIS 0.011 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00214 (18070) covalent geometry : angle 0.50768 (24653) hydrogen bonds : bond 0.03027 ( 551) hydrogen bonds : angle 4.08507 ( 1558) metal coordination : bond 0.00277 ( 12) metal coordination : angle 1.58650 ( 12) link_TRANS : bond 0.00022 ( 1) link_TRANS : angle 0.08909 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4255.92 seconds wall clock time: 73 minutes 33.50 seconds (4413.50 seconds total)