Starting phenix.real_space_refine on Sun Sep 13 14:11:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ven_21157/09_2026/6ven_21157.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ven_21157/09_2026/6ven_21157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6ven_21157/09_2026/6ven_21157.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ven_21157/09_2026/6ven_21157.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ven_21157/09_2026/6ven_21157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ven_21157/09_2026/6ven_21157.map" model { file = "/net/cci-nas-00/data/ceres_data/6ven_21157/09_2026/6ven_21157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ven_21157/09_2026/6ven_21157.cif" } resolution = 3.37 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= 0.002 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 292 5.49 5 S 73 5.16 5 C 14264 2.51 5 N 4291 2.21 5 O 5107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24028 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 871 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'NLE:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 727 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'NLE:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "F" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 732 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 597 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "L" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2367 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 11, 'TRANS': 296} Chain breaks: 2 Chain: "M" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3183 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 377} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1710 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 3 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "O" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2595 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 12, 'TRANS': 302} Chain breaks: 8 Chain: "P" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 336 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "Q" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 26} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 966 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 7, 'TYR:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19473 SG CYS N1019 84.930 78.071 29.381 1.00134.18 S ATOM 19794 SG CYS N1068 84.039 81.697 29.593 1.00129.18 S ATOM 19808 SG CYS N1070 87.089 80.901 27.747 1.00138.24 S Time building chain proxies: 5.01, per 1000 atoms: 0.21 Number of scatterers: 24028 At special positions: 0 Unit cell: (172.8, 143.64, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 73 16.00 P 292 15.00 O 5107 8.00 N 4291 7.00 C 14264 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 Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN N1101 " pdb="ZN ZN N1101 " - pdb=" SG CYS N1019 " pdb="ZN ZN N1101 " - pdb=" SG CYS N1068 " pdb="ZN ZN N1101 " - pdb=" SG CYS N1070 " 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4278 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 27 sheets defined 36.8% alpha, 15.9% beta 142 base pairs and 244 stacking pairs defined. Time for finding SS restraints: 3.36 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.741A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.643A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.806A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N NLE A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.605A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.796A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.829A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.518A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.642A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.816A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.549A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 122 removed outlier: 3.806A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 4.144A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 removed outlier: 3.515A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA E 75 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.670A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N NLE E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 4.188A pdb=" N ILE E 124 " --> pdb=" O NLE E 120 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.528A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.711A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.713A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.767A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.817A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.694A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 removed outlier: 3.546A pdb=" N LEU G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.688A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 84 removed outlier: 3.733A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 102 Processing helix chain 'H' and resid 103 through 123 removed outlier: 4.244A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 35 Processing helix chain 'K' and resid 56 through 60 Processing helix chain 'L' and resid 180 through 184 removed outlier: 3.927A pdb=" N LYS L 184 " --> pdb=" O LYS L 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 189 Processing helix chain 'M' and resid 347 through 352 removed outlier: 4.211A pdb=" N ALA M 352 " --> pdb=" O SER M 349 " (cutoff:3.500A) Processing helix chain 'N' and resid 804 through 825 Processing helix chain 'N' and resid 899 through 918 removed outlier: 3.615A pdb=" N ASN N 903 " --> pdb=" O SER N 899 " (cutoff:3.500A) Processing helix chain 'N' and resid 919 through 921 No H-bonds generated for 'chain 'N' and resid 919 through 921' Processing helix chain 'N' and resid 973 through 987 Processing helix chain 'N' and resid 1011 through 1015 removed outlier: 3.997A pdb=" N ILE N1015 " --> pdb=" O ALA N1012 " (cutoff:3.500A) Processing helix chain 'O' and resid 243 through 261 removed outlier: 4.318A pdb=" N PHE O 260 " --> pdb=" O LYS O 256 " (cutoff:3.500A) Processing helix chain 'O' and resid 293 through 299 Processing helix chain 'O' and resid 384 through 392 removed outlier: 3.585A pdb=" N TYR O 388 " --> pdb=" O ASN O 384 " (cutoff:3.500A) Processing helix chain 'O' and resid 453 through 457 Processing helix chain 'O' and resid 477 through 497 removed outlier: 3.769A pdb=" N LEU O 481 " --> pdb=" O THR O 477 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU O 497 " --> pdb=" O ASP O 493 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 129 Processing helix chain 'P' and resid 130 through 144 removed outlier: 3.564A pdb=" N GLN P 144 " --> pdb=" O LEU P 140 " (cutoff:3.500A) Processing helix chain 'P' and resid 148 through 161 Processing helix chain 'Q' and resid 130 through 141 Processing helix chain 'Q' and resid 149 through 161 removed outlier: 4.217A pdb=" N LEU Q 153 " --> pdb=" O PRO Q 149 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER Q 161 " --> pdb=" O LEU Q 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 241 removed outlier: 4.290A pdb=" N LEU R 209 " --> pdb=" O LYS R 205 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU R 210 " --> pdb=" O LYS R 206 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU R 211 " --> pdb=" O LEU R 207 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU R 217 " --> pdb=" O TYR R 213 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASP R 218 " --> pdb=" O LEU R 214 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP R 228 " --> pdb=" O MET R 224 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP R 229 " --> pdb=" O ARG R 225 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP R 230 " --> pdb=" O LYS R 226 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL R 235 " --> pdb=" O ALA R 231 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP R 241 " --> pdb=" O CYS R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 283 Processing helix chain 'R' and resid 310 through 349 removed outlier: 4.258A pdb=" N GLN R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR R 315 " --> pdb=" O ASN R 311 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE R 342 " --> pdb=" O LYS R 338 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU R 349 " --> pdb=" O TYR R 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.502A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.304A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.817A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'K' and resid 12 through 16 removed outlier: 9.140A pdb=" N LEU K 67 " --> pdb=" O GLN K 2 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE K 4 " --> pdb=" O LEU K 67 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU K 69 " --> pdb=" O PHE K 4 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LYS K 6 " --> pdb=" O LEU K 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 19 through 21 removed outlier: 3.558A pdb=" N LYS L 20 " --> pdb=" O ALA L 29 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA L 29 " --> pdb=" O LYS L 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 58 through 62 removed outlier: 6.885A pdb=" N ALA L 73 " --> pdb=" O SER L 59 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU L 61 " --> pdb=" O ALA L 71 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA L 71 " --> pdb=" O LEU L 61 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N HIS L 83 " --> pdb=" O LEU L 88 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU L 88 " --> pdb=" O HIS L 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 102 through 104 removed outlier: 6.499A pdb=" N ILE L 120 " --> pdb=" O THR L 133 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR L 133 " --> pdb=" O ILE L 120 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE L 122 " --> pdb=" O MET L 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 141 through 145 removed outlier: 6.848A pdb=" N ILE L 163 " --> pdb=" O THR L 176 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N THR L 176 " --> pdb=" O ILE L 163 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE L 165 " --> pdb=" O LEU L 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 192 through 197 removed outlier: 3.637A pdb=" N ARG L 225 " --> pdb=" O ILE L 215 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASP L 217 " --> pdb=" O VAL L 223 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL L 223 " --> pdb=" O ASP L 217 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 243 through 246 removed outlier: 3.695A pdb=" N SER L 258 " --> pdb=" O TYR L 266 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE L 265 " --> pdb=" O LEU L 278 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU L 278 " --> pdb=" O ILE L 265 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS L 267 " --> pdb=" O LEU L 276 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 290 through 296 removed outlier: 3.929A pdb=" N MET L 300 " --> pdb=" O TRP L 312 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 18 through 23 removed outlier: 4.242A pdb=" N LYS M 18 " --> pdb=" O SER M 341 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL M 339 " --> pdb=" O THR M 20 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR M 22 " --> pdb=" O VAL M 337 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N VAL M 337 " --> pdb=" O THR M 22 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 40 through 44 removed outlier: 6.851A pdb=" N ILE M 52 " --> pdb=" O ILE M 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 75 through 80 removed outlier: 6.444A pdb=" N SER M 90 " --> pdb=" O THR M 76 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE M 78 " --> pdb=" O LEU M 88 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU M 88 " --> pdb=" O ILE M 78 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TRP M 80 " --> pdb=" O LEU M 86 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU M 86 " --> pdb=" O TRP M 80 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER M 91 " --> pdb=" O SER M 95 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N SER M 95 " --> pdb=" O SER M 91 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 117 through 123 removed outlier: 6.856A pdb=" N THR M 133 " --> pdb=" O TRP M 118 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N CYS M 120 " --> pdb=" O VAL M 131 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL M 131 " --> pdb=" O CYS M 120 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N TRP M 122 " --> pdb=" O LEU M 129 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU M 129 " --> pdb=" O TRP M 122 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 173 through 176 removed outlier: 3.821A pdb=" N VAL M 173 " --> pdb=" O GLY M 187 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS M 208 " --> pdb=" O PHE M 195 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LYS M 197 " --> pdb=" O CYS M 206 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N CYS M 206 " --> pdb=" O LYS M 197 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 217 through 222 removed outlier: 6.481A pdb=" N ASN M 232 " --> pdb=" O LYS M 218 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU M 220 " --> pdb=" O ALA M 230 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA M 230 " --> pdb=" O LEU M 220 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 244 through 246 removed outlier: 3.730A pdb=" N SER M 244 " --> pdb=" O GLU M 253 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU M 253 " --> pdb=" O SER M 244 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 269 through 274 removed outlier: 6.669A pdb=" N SER M 285 " --> pdb=" O ASN M 270 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE M 272 " --> pdb=" O VAL M 283 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL M 283 " --> pdb=" O ILE M 272 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 940 through 944 Processing sheet with id=AC5, first strand: chain 'N' and resid 963 through 966 removed outlier: 6.727A pdb=" N ILE N1038 " --> pdb=" O ILE N 964 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU N 966 " --> pdb=" O ILE N1036 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE N1036 " --> pdb=" O GLU N 966 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 969 through 972 removed outlier: 6.980A pdb=" N THR N1001 " --> pdb=" O VAL N 997 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 80 through 82 removed outlier: 4.078A pdb=" N CYS O 69 " --> pdb=" O LEU O 321 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU O 321 " --> pdb=" O CYS O 69 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 92 through 97 removed outlier: 4.277A pdb=" N SER O 93 " --> pdb=" O ARG O 123 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ARG O 123 " --> pdb=" O SER O 93 " (cutoff:3.500A) removed outlier: 9.697A pdb=" N MET O 95 " --> pdb=" O THR O 121 " (cutoff:3.500A) removed outlier: 11.286A pdb=" N THR O 121 " --> pdb=" O MET O 95 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 362 through 368 removed outlier: 6.437A pdb=" N ILE O 357 " --> pdb=" O LEU O 364 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS O 366 " --> pdb=" O LEU O 355 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU O 355 " --> pdb=" O LYS O 366 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU O 136 " --> pdb=" O ILE O 451 " (cutoff:3.500A) 752 hydrogen bonds defined for protein. 2130 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 366 hydrogen bonds 732 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 244 stacking parallelities Total time for adding SS restraints: 5.97 Time building geometry restraints manager: 2.79 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: 6118 1.33 - 1.45: 6197 1.45 - 1.57: 12070 1.57 - 1.70: 582 1.70 - 1.82: 103 Bond restraints: 25070 Sorted by residual: bond pdb=" C THR K 14 " pdb=" N LEU K 15 " ideal model delta sigma weight residual 1.330 1.373 -0.043 1.31e-02 5.83e+03 1.06e+01 bond pdb=" C3' DA I 7 " pdb=" C2' DA I 7 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DT J 7 " pdb=" C2' DT J 7 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.68e+00 bond pdb=" C3' DT J 50 " pdb=" C2' DT J 50 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.57e+00 bond pdb=" C3' DC I 45 " pdb=" C2' DC I 45 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.37e+00 ... (remaining 25065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 33551 1.79 - 3.58: 1483 3.58 - 5.37: 97 5.37 - 7.15: 15 7.15 - 8.94: 3 Bond angle restraints: 35149 Sorted by residual: angle pdb=" O4' DG I 25 " pdb=" C4' DG I 25 " pdb=" C3' DG I 25 " ideal model delta sigma weight residual 106.00 103.09 2.91 6.00e-01 2.78e+00 2.35e+01 angle pdb=" O4' DC I 56 " pdb=" C4' DC I 56 " pdb=" C3' DC I 56 " ideal model delta sigma weight residual 106.00 103.14 2.86 6.00e-01 2.78e+00 2.28e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT I 77 " pdb=" C4 DT I 77 " pdb=" O4 DT I 77 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT I 112 " pdb=" C4 DT I 112 " pdb=" O4 DT I 112 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 ... (remaining 35144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.94: 12385 30.94 - 61.89: 1821 61.89 - 92.83: 70 92.83 - 123.78: 1 123.78 - 154.72: 2 Dihedral angle restraints: 14279 sinusoidal: 7674 harmonic: 6605 Sorted by residual: dihedral pdb=" CA ARG R 271 " pdb=" C ARG R 271 " pdb=" N ILE R 272 " pdb=" CA ILE R 272 " ideal model delta harmonic sigma weight residual 180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA LEU R 207 " pdb=" C LEU R 207 " pdb=" N GLU R 208 " pdb=" CA GLU R 208 " ideal model delta harmonic sigma weight residual 180.00 155.78 24.22 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA PHE M 145 " pdb=" C PHE M 145 " pdb=" N SER M 146 " pdb=" CA SER M 146 " ideal model delta harmonic sigma weight residual 180.00 155.79 24.21 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 14276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3094 0.054 - 0.108: 750 0.108 - 0.162: 130 0.162 - 0.216: 3 0.216 - 0.270: 4 Chirality restraints: 3981 Sorted by residual: chirality pdb=" CB ILE H 89 " pdb=" CA ILE H 89 " pdb=" CG1 ILE H 89 " pdb=" CG2 ILE H 89 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA LEU Q 153 " pdb=" N LEU Q 153 " pdb=" C LEU Q 153 " pdb=" CB LEU Q 153 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB VAL Q 152 " pdb=" CA VAL Q 152 " pdb=" CG1 VAL Q 152 " pdb=" CG2 VAL Q 152 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 3978 not shown) Planarity restraints: 3455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN R 339 " -0.021 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C GLN R 339 " 0.071 2.00e-02 2.50e+03 pdb=" O GLN R 339 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU R 340 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 322 " -0.020 2.00e-02 2.50e+03 4.07e-02 1.65e+01 pdb=" C LEU R 322 " 0.070 2.00e-02 2.50e+03 pdb=" O LEU R 322 " -0.026 2.00e-02 2.50e+03 pdb=" N GLU R 323 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 341 " 0.019 2.00e-02 2.50e+03 3.75e-02 1.40e+01 pdb=" C ASN R 341 " -0.065 2.00e-02 2.50e+03 pdb=" O ASN R 341 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE R 342 " 0.022 2.00e-02 2.50e+03 ... (remaining 3452 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1782 2.73 - 3.27: 23161 3.27 - 3.81: 41452 3.81 - 4.36: 50879 4.36 - 4.90: 78842 Nonbonded interactions: 196116 Sorted by model distance: nonbonded pdb=" O LYS N1076 " pdb="ZN ZN N1101 " model vdw 2.184 2.230 nonbonded pdb=" OG SER L 114 " pdb=" O VAL L 141 " model vdw 2.216 3.040 nonbonded pdb=" OE1 GLN M 240 " pdb=" OH TYR M 260 " model vdw 2.234 3.040 nonbonded pdb=" OE1 GLU M 298 " pdb=" OG SER M 301 " model vdw 2.259 3.040 nonbonded pdb=" O PHE O 260 " pdb=" OG SER O 264 " model vdw 2.265 3.040 ... (remaining 196111 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 22 through 100) selection = (chain 'F' and resid 22 through 100) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 15 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 31 through 123) } 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: 6.330 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: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 28.860 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 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 : 0.005 0.043 25073 Z= 0.411 Angle : 0.780 8.942 35149 Z= 0.596 Chirality : 0.047 0.270 3981 Planarity : 0.005 0.085 3455 Dihedral : 23.361 154.722 10001 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.05 % Allowed : 8.49 % Favored : 91.46 % 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: -3.46 (0.15), residues: 2186 helix: -1.45 (0.16), residues: 767 sheet: -2.10 (0.25), residues: 369 loop : -3.05 (0.15), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 69 TYR 0.016 0.001 TYR O 482 PHE 0.030 0.002 PHE M 274 TRP 0.016 0.001 TRP M 297 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.41 (25070) covalent geometry : angle 0.78032 / 0.60 (35149) hydrogen bonds : bond 0.11356 / 7.50 ( 1118) hydrogen bonds : angle 5.64421 / 3.99 ( 2862) metal coordination : bond 0.02399 / 1.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8137 (tt0) REVERT: D 68 ASP cc_start: 0.8198 (t0) cc_final: 0.7696 (t0) REVERT: K 39 ASP cc_start: 0.7554 (p0) cc_final: 0.7302 (p0) REVERT: K 42 ARG cc_start: 0.7393 (ttm170) cc_final: 0.6825 (ttp-170) REVERT: K 72 ARG cc_start: 0.6334 (ttp-110) cc_final: 0.5897 (ttp-170) REVERT: K 73 LEU cc_start: 0.5907 (tp) cc_final: 0.5385 (tt) REVERT: M 1 MET cc_start: 0.7776 (tpp) cc_final: 0.7304 (tpt) REVERT: M 94 TRP cc_start: 0.6718 (m-10) cc_final: 0.6290 (m-90) REVERT: N 815 ASP cc_start: 0.7848 (t0) cc_final: 0.7614 (p0) REVERT: N 974 GLN cc_start: 0.8246 (tp40) cc_final: 0.7968 (tp40) REVERT: N 979 MET cc_start: 0.7410 (tpt) cc_final: 0.7112 (tpp) REVERT: N 1000 ASN cc_start: 0.8602 (m110) cc_final: 0.8158 (m110) REVERT: O 135 TRP cc_start: 0.6220 (p90) cc_final: 0.5959 (p90) REVERT: O 224 GLU cc_start: 0.6616 (mp0) cc_final: 0.5242 (pm20) REVERT: R 214 LEU cc_start: 0.7961 (tt) cc_final: 0.7575 (pp) REVERT: R 327 GLU cc_start: 0.8127 (pp20) cc_final: 0.7869 (pp20) outliers start: 1 outliers final: 0 residues processed: 293 average time/residue: 0.2068 time to fit residues: 89.4247 Evaluate side-chains 205 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN F 64 ASN H 84 ASN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN L 48 GLN L 83 HIS L 172 HIS L 228 GLN M 15 HIS M 71 HIS M 199 HIS M 216 ASN M 268 GLN M 319 ASN M 361 ASN N 821 ASN N 912 GLN N1080 ASN O 181 HIS P 127 ASN R 304 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.123381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.080111 restraints weight = 56419.844| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.76 r_work: 0.2895 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25073 Z= 0.205 Angle : 0.715 11.320 35149 Z= 0.391 Chirality : 0.049 0.237 3981 Planarity : 0.005 0.080 3455 Dihedral : 26.857 158.335 5667 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.01 % Allowed : 13.63 % Favored : 84.36 % 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: -2.32 (0.16), residues: 2186 helix: -0.22 (0.18), residues: 779 sheet: -1.76 (0.25), residues: 378 loop : -2.52 (0.17), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 44 TYR 0.045 0.002 TYR Q 156 PHE 0.020 0.002 PHE M 145 TRP 0.015 0.001 TRP M 297 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (25070) covalent geometry : angle 0.71541 / 0.39 (35149) hydrogen bonds : bond 0.05315 / 3.45 ( 1118) hydrogen bonds : angle 4.44076 / 3.14 ( 2862) metal coordination : bond 0.00422 / 0.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9230 (tm-30) cc_final: 0.8671 (tt0) REVERT: D 68 ASP cc_start: 0.8789 (t0) cc_final: 0.8276 (t0) REVERT: K 43 LEU cc_start: 0.8791 (tp) cc_final: 0.8329 (tt) REVERT: K 72 ARG cc_start: 0.6376 (ttp-110) cc_final: 0.5924 (ttp-170) REVERT: K 73 LEU cc_start: 0.5997 (tp) cc_final: 0.5435 (tt) REVERT: L 169 GLU cc_start: 0.8416 (mp0) cc_final: 0.8158 (mp0) REVERT: M 67 MET cc_start: 0.7903 (tpp) cc_final: 0.7674 (tpp) REVERT: N 979 MET cc_start: 0.7960 (tpt) cc_final: 0.7491 (tpp) REVERT: O 224 GLU cc_start: 0.7026 (mp0) cc_final: 0.5606 (pm20) REVERT: O 381 LEU cc_start: 0.8394 (pt) cc_final: 0.8178 (pp) REVERT: Q 156 TYR cc_start: 0.6204 (p90) cc_final: 0.5890 (p90) REVERT: R 214 LEU cc_start: 0.7936 (tt) cc_final: 0.7693 (pp) REVERT: R 327 GLU cc_start: 0.7665 (pp20) cc_final: 0.7420 (pp20) outliers start: 39 outliers final: 22 residues processed: 236 average time/residue: 0.1702 time to fit residues: 62.4790 Evaluate side-chains 210 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain L residue 291 MET Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 199 HIS Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 319 ASN Chi-restraints excluded: chain N residue 821 ASN Chi-restraints excluded: chain N residue 963 MET Chi-restraints excluded: chain N residue 1030 VAL Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 197 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 81 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 237 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 176 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** N 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 974 GLN O 359 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.123650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.080466 restraints weight = 56707.647| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.78 r_work: 0.2901 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25073 Z= 0.182 Angle : 0.671 10.786 35149 Z= 0.369 Chirality : 0.047 0.230 3981 Planarity : 0.004 0.074 3455 Dihedral : 26.831 159.413 5667 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.67 % Allowed : 14.97 % Favored : 82.36 % 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: -1.70 (0.17), residues: 2186 helix: 0.43 (0.18), residues: 767 sheet: -1.51 (0.25), residues: 379 loop : -2.22 (0.17), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 35 TYR 0.033 0.001 TYR Q 156 PHE 0.023 0.002 PHE N 910 TRP 0.015 0.001 TRP M 297 HIS 0.006 0.001 HIS M 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (25070) covalent geometry : angle 0.67094 / 0.37 (35149) hydrogen bonds : bond 0.04848 / 3.11 ( 1118) hydrogen bonds : angle 4.20082 / 2.96 ( 2862) metal coordination : bond 0.00345 / 0.17 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 219 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8717 (tt0) REVERT: D 80 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9289 (tp) REVERT: K 6 LYS cc_start: 0.7685 (ttmm) cc_final: 0.7110 (tptp) REVERT: K 43 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8320 (tt) REVERT: K 72 ARG cc_start: 0.6627 (ttp-110) cc_final: 0.6323 (ttp-110) REVERT: K 73 LEU cc_start: 0.6114 (tp) cc_final: 0.5539 (tt) REVERT: L 164 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.6322 (mmt180) REVERT: L 169 GLU cc_start: 0.8393 (mp0) cc_final: 0.8137 (mp0) REVERT: M 1 MET cc_start: 0.8069 (tpt) cc_final: 0.7726 (tpt) REVERT: M 67 MET cc_start: 0.8067 (tpp) cc_final: 0.7802 (tpp) REVERT: M 199 HIS cc_start: 0.7741 (t-170) cc_final: 0.7482 (m170) REVERT: N 963 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8581 (ttp) REVERT: N 979 MET cc_start: 0.7902 (tpt) cc_final: 0.7395 (tpp) REVERT: O 135 TRP cc_start: 0.5962 (p90) cc_final: 0.5645 (p90) REVERT: O 224 GLU cc_start: 0.7136 (mp0) cc_final: 0.5873 (pm20) REVERT: O 327 ASP cc_start: 0.6302 (OUTLIER) cc_final: 0.5564 (m-30) REVERT: O 381 LEU cc_start: 0.8490 (pt) cc_final: 0.8254 (pp) REVERT: Q 156 TYR cc_start: 0.6169 (OUTLIER) cc_final: 0.5903 (p90) outliers start: 52 outliers final: 25 residues processed: 259 average time/residue: 0.1654 time to fit residues: 67.0376 Evaluate side-chains 223 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 164 ARG Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 245 PHE Chi-restraints excluded: chain L residue 291 MET Chi-restraints excluded: chain L residue 306 ASN Chi-restraints excluded: chain M residue 180 HIS Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain N residue 847 LEU Chi-restraints excluded: chain N residue 963 MET Chi-restraints excluded: chain N residue 1011 ILE Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 327 ASP Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 440 ILE Chi-restraints excluded: chain Q residue 156 TYR Chi-restraints excluded: chain R residue 329 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 134 optimal weight: 10.0000 chunk 202 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 48 optimal weight: 0.0570 chunk 111 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 86 optimal weight: 20.0000 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 149 ASN L 228 GLN ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 224 GLN M 319 ASN ** N 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.124760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.081713 restraints weight = 56315.759| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.62 r_work: 0.2941 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25073 Z= 0.136 Angle : 0.635 11.083 35149 Z= 0.352 Chirality : 0.046 0.284 3981 Planarity : 0.004 0.069 3455 Dihedral : 26.702 159.823 5667 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.42 % Allowed : 16.31 % Favored : 81.28 % 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: -1.22 (0.17), residues: 2186 helix: 0.88 (0.19), residues: 770 sheet: -1.24 (0.26), residues: 373 loop : -1.99 (0.17), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 185 TYR 0.034 0.001 TYR Q 156 PHE 0.022 0.001 PHE L 58 TRP 0.013 0.001 TRP M 297 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (25070) covalent geometry : angle 0.63497 / 0.35 (35149) hydrogen bonds : bond 0.04326 / 2.78 ( 1118) hydrogen bonds : angle 3.99595 / 2.82 ( 2862) metal coordination : bond 0.00211 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 222 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9159 (tm-30) cc_final: 0.8747 (tt0) REVERT: K 6 LYS cc_start: 0.7781 (ttmm) cc_final: 0.7218 (tptp) REVERT: K 43 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8374 (tt) REVERT: K 72 ARG cc_start: 0.6879 (ttp-110) cc_final: 0.6596 (ttp-110) REVERT: K 73 LEU cc_start: 0.6071 (tp) cc_final: 0.5489 (tt) REVERT: L 169 GLU cc_start: 0.8365 (mp0) cc_final: 0.8107 (mp0) REVERT: L 237 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8025 (pp) REVERT: N 963 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8604 (ttp) REVERT: N 979 MET cc_start: 0.7908 (tpt) cc_final: 0.7407 (tpp) REVERT: O 53 ARG cc_start: 0.4268 (mpt180) cc_final: 0.3820 (mpp-170) REVERT: O 135 TRP cc_start: 0.5939 (p90) cc_final: 0.5735 (p90) REVERT: O 327 ASP cc_start: 0.6298 (OUTLIER) cc_final: 0.5541 (m-30) REVERT: O 381 LEU cc_start: 0.8502 (pt) cc_final: 0.8292 (pp) REVERT: Q 156 TYR cc_start: 0.6045 (OUTLIER) cc_final: 0.5802 (p90) outliers start: 47 outliers final: 27 residues processed: 259 average time/residue: 0.1656 time to fit residues: 66.9119 Evaluate side-chains 224 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 237 LEU Chi-restraints excluded: chain L residue 245 PHE Chi-restraints excluded: chain L residue 256 VAL Chi-restraints excluded: chain L residue 291 MET Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 319 ASN Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain N residue 847 LEU Chi-restraints excluded: chain N residue 963 MET Chi-restraints excluded: chain N residue 968 VAL Chi-restraints excluded: chain N residue 1002 VAL Chi-restraints excluded: chain N residue 1011 ILE Chi-restraints excluded: chain O residue 125 ASP Chi-restraints excluded: chain O residue 327 ASP Chi-restraints excluded: chain O residue 440 ILE Chi-restraints excluded: chain Q residue 156 TYR Chi-restraints excluded: chain R residue 333 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 44 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 64 optimal weight: 0.0980 chunk 118 optimal weight: 0.7980 chunk 196 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 237 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.124406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.081440 restraints weight = 56198.230| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.75 r_work: 0.2919 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25073 Z= 0.157 Angle : 0.634 9.873 35149 Z= 0.349 Chirality : 0.046 0.243 3981 Planarity : 0.004 0.067 3455 Dihedral : 26.710 160.075 5667 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.24 % Allowed : 16.26 % Favored : 80.50 % 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: -1.03 (0.17), residues: 2186 helix: 1.04 (0.19), residues: 768 sheet: -1.14 (0.25), residues: 378 loop : -1.86 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 44 TYR 0.034 0.001 TYR Q 156 PHE 0.017 0.001 PHE M 145 TRP 0.013 0.001 TRP M 297 HIS 0.004 0.001 HIS M 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (25070) covalent geometry : angle 0.63425 / 0.35 (35149) hydrogen bonds : bond 0.04393 / 2.82 ( 1118) hydrogen bonds : angle 3.92232 / 2.77 ( 2862) metal coordination : bond 0.00801 / 0.40 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 197 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8776 (tt0) REVERT: K 6 LYS cc_start: 0.7790 (ttmm) cc_final: 0.7160 (tptp) REVERT: K 43 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8250 (tt) REVERT: K 72 ARG cc_start: 0.6863 (ttp-110) cc_final: 0.6592 (ttp-110) REVERT: K 73 LEU cc_start: 0.6018 (tp) cc_final: 0.5383 (tt) REVERT: L 169 GLU cc_start: 0.8386 (mp0) cc_final: 0.8132 (mp0) REVERT: L 237 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7988 (pp) REVERT: L 305 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7564 (tt) REVERT: N 963 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8688 (ttp) REVERT: N 979 MET cc_start: 0.7862 (tpt) cc_final: 0.7331 (tpp) REVERT: O 53 ARG cc_start: 0.4274 (mpt180) cc_final: 0.3675 (mpp-170) REVERT: O 135 TRP cc_start: 0.5939 (p90) cc_final: 0.5732 (p90) REVERT: O 224 GLU cc_start: 0.7386 (mp0) cc_final: 0.5726 (pm20) REVERT: O 327 ASP cc_start: 0.6379 (OUTLIER) cc_final: 0.5270 (m-30) REVERT: O 381 LEU cc_start: 0.8500 (pt) cc_final: 0.7750 (tt) REVERT: O 391 TYR cc_start: 0.3698 (OUTLIER) cc_final: 0.3243 (m-10) REVERT: Q 156 TYR cc_start: 0.6040 (OUTLIER) cc_final: 0.5793 (p90) REVERT: R 325 MET cc_start: 0.7311 (tpt) cc_final: 0.6904 (tpp) outliers start: 63 outliers final: 36 residues processed: 246 average time/residue: 0.1653 time to fit residues: 64.3461 Evaluate side-chains 230 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 237 LEU Chi-restraints excluded: chain L residue 245 PHE Chi-restraints excluded: chain L residue 256 VAL Chi-restraints excluded: chain L residue 291 MET Chi-restraints excluded: chain L residue 300 MET Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain N residue 847 LEU Chi-restraints excluded: chain N residue 963 MET Chi-restraints excluded: chain N residue 968 VAL Chi-restraints excluded: chain N residue 1002 VAL Chi-restraints excluded: chain N residue 1011 ILE Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 327 ASP Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 391 TYR Chi-restraints excluded: chain O residue 440 ILE Chi-restraints excluded: chain Q residue 156 TYR Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain R residue 333 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 71 optimal weight: 0.0060 chunk 133 optimal weight: 0.7980 chunk 192 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 224 GLN M 319 ASN ** N 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.124529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.081604 restraints weight = 56396.296| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.77 r_work: 0.2919 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25073 Z= 0.153 Angle : 0.625 9.522 35149 Z= 0.345 Chirality : 0.046 0.316 3981 Planarity : 0.004 0.064 3455 Dihedral : 26.671 160.537 5667 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.29 % Allowed : 16.67 % Favored : 80.04 % 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: -0.86 (0.18), residues: 2186 helix: 1.16 (0.19), residues: 767 sheet: -1.04 (0.26), residues: 376 loop : -1.76 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 44 TYR 0.033 0.001 TYR Q 156 PHE 0.016 0.001 PHE L 104 TRP 0.013 0.001 TRP M 297 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (25070) covalent geometry : angle 0.62537 / 0.34 (35149) hydrogen bonds : bond 0.04300 / 2.76 ( 1118) hydrogen bonds : angle 3.85153 / 2.72 ( 2862) metal coordination : bond 0.00273 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 194 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9158 (tm-30) cc_final: 0.8794 (tt0) REVERT: K 6 LYS cc_start: 0.7816 (ttmm) cc_final: 0.7173 (tptp) REVERT: K 34 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6471 (pp20) REVERT: K 41 GLN cc_start: 0.6685 (pp30) cc_final: 0.6452 (pp30) REVERT: K 43 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8277 (tt) REVERT: K 48 LYS cc_start: 0.8884 (ptpp) cc_final: 0.8682 (mmmm) REVERT: K 72 ARG cc_start: 0.6890 (ttp-110) cc_final: 0.6586 (ttp-110) REVERT: L 169 GLU cc_start: 0.8402 (mp0) cc_final: 0.8139 (mp0) REVERT: L 237 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8065 (pp) REVERT: M 67 MET cc_start: 0.7692 (tpp) cc_final: 0.7449 (tpp) REVERT: M 145 PHE cc_start: 0.6517 (OUTLIER) cc_final: 0.5850 (p90) REVERT: N 963 MET cc_start: 0.9315 (OUTLIER) cc_final: 0.8704 (ttp) REVERT: N 979 MET cc_start: 0.7943 (tpt) cc_final: 0.7395 (tpp) REVERT: O 53 ARG cc_start: 0.3811 (mpt180) cc_final: 0.3419 (mpp-170) REVERT: O 135 TRP cc_start: 0.5943 (p90) cc_final: 0.5740 (p90) REVERT: O 224 GLU cc_start: 0.7358 (mp0) cc_final: 0.5732 (pm20) REVERT: O 322 PHE cc_start: 0.6635 (m-80) cc_final: 0.6425 (m-80) REVERT: O 381 LEU cc_start: 0.8490 (pt) cc_final: 0.7751 (tt) REVERT: O 391 TYR cc_start: 0.3717 (OUTLIER) cc_final: 0.3264 (m-10) REVERT: Q 156 TYR cc_start: 0.6006 (OUTLIER) cc_final: 0.5759 (p90) REVERT: R 325 MET cc_start: 0.7233 (tpt) cc_final: 0.7004 (tpt) outliers start: 64 outliers final: 39 residues processed: 246 average time/residue: 0.1710 time to fit residues: 66.2035 Evaluate side-chains 228 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 183 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 237 LEU Chi-restraints excluded: chain L residue 245 PHE Chi-restraints excluded: chain L residue 256 VAL Chi-restraints excluded: chain L residue 300 MET Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 145 PHE Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain N residue 847 LEU Chi-restraints excluded: chain N residue 897 VAL Chi-restraints excluded: chain N residue 963 MET Chi-restraints excluded: chain N residue 968 VAL Chi-restraints excluded: chain N residue 1002 VAL Chi-restraints excluded: chain N residue 1011 ILE Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 125 ASP Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 391 TYR Chi-restraints excluded: chain O residue 440 ILE Chi-restraints excluded: chain Q residue 156 TYR Chi-restraints excluded: chain R residue 227 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 83 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 48 optimal weight: 0.0970 chunk 134 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 182 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 154 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.123548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.079933 restraints weight = 56045.599| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.71 r_work: 0.2878 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25073 Z= 0.229 Angle : 0.679 9.077 35149 Z= 0.367 Chirality : 0.048 0.254 3981 Planarity : 0.004 0.062 3455 Dihedral : 26.775 161.301 5667 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.24 % Allowed : 17.59 % Favored : 79.17 % 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: -0.95 (0.17), residues: 2186 helix: 0.98 (0.19), residues: 767 sheet: -0.97 (0.26), residues: 368 loop : -1.77 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 131 TYR 0.032 0.002 TYR Q 156 PHE 0.034 0.002 PHE L 104 TRP 0.014 0.001 TRP M 297 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.23 (25070) covalent geometry : angle 0.67903 / 0.37 (35149) hydrogen bonds : bond 0.04946 / 3.16 ( 1118) hydrogen bonds : angle 3.93772 / 2.78 ( 2862) metal coordination : bond 0.00500 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 189 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8561 (pt0) REVERT: D 51 ASP cc_start: 0.8906 (p0) cc_final: 0.8631 (p0) REVERT: K 6 LYS cc_start: 0.7722 (ttmm) cc_final: 0.7155 (tptp) REVERT: K 34 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6695 (tp30) REVERT: K 41 GLN cc_start: 0.7015 (pp30) cc_final: 0.6745 (pp30) REVERT: K 43 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8333 (tt) REVERT: K 72 ARG cc_start: 0.6910 (ttp-110) cc_final: 0.6641 (ttp-110) REVERT: L 237 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8093 (pp) REVERT: M 1 MET cc_start: 0.8107 (tpt) cc_final: 0.7853 (tpt) REVERT: M 67 MET cc_start: 0.7840 (tpp) cc_final: 0.7517 (tpp) REVERT: M 145 PHE cc_start: 0.6659 (OUTLIER) cc_final: 0.5873 (p90) REVERT: N 912 GLN cc_start: 0.6962 (pt0) cc_final: 0.6720 (pt0) REVERT: N 979 MET cc_start: 0.7915 (tpt) cc_final: 0.7372 (tpp) REVERT: O 53 ARG cc_start: 0.3401 (mpt180) cc_final: 0.3022 (mpp-170) REVERT: O 224 GLU cc_start: 0.7487 (mp0) cc_final: 0.5832 (pm20) REVERT: O 381 LEU cc_start: 0.8407 (pt) cc_final: 0.7650 (tt) REVERT: O 391 TYR cc_start: 0.3715 (OUTLIER) cc_final: 0.3250 (m-10) REVERT: Q 156 TYR cc_start: 0.6013 (OUTLIER) cc_final: 0.5760 (p90) outliers start: 63 outliers final: 44 residues processed: 242 average time/residue: 0.1720 time to fit residues: 65.6684 Evaluate side-chains 233 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 183 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 237 LEU Chi-restraints excluded: chain L residue 245 PHE Chi-restraints excluded: chain L residue 256 VAL Chi-restraints excluded: chain L residue 300 MET Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 145 PHE Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 180 HIS Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain N residue 847 LEU Chi-restraints excluded: chain N residue 897 VAL Chi-restraints excluded: chain N residue 968 VAL Chi-restraints excluded: chain N residue 1002 VAL Chi-restraints excluded: chain N residue 1011 ILE Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 125 ASP Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 264 SER Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 391 TYR Chi-restraints excluded: chain O residue 440 ILE Chi-restraints excluded: chain Q residue 156 TYR Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 329 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 199 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 206 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 chunk 100 optimal weight: 20.0000 chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 319 ASN N 821 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.125072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.081653 restraints weight = 55959.234| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.52 r_work: 0.2933 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25073 Z= 0.142 Angle : 0.626 10.261 35149 Z= 0.344 Chirality : 0.045 0.258 3981 Planarity : 0.004 0.060 3455 Dihedral : 26.630 161.798 5667 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.78 % Allowed : 18.67 % Favored : 78.55 % 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: -0.75 (0.18), residues: 2186 helix: 1.22 (0.19), residues: 774 sheet: -0.96 (0.26), residues: 376 loop : -1.69 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 185 TYR 0.032 0.001 TYR Q 156 PHE 0.024 0.001 PHE L 104 TRP 0.018 0.001 TRP O 135 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (25070) covalent geometry : angle 0.62576 / 0.34 (35149) hydrogen bonds : bond 0.04232 / 2.70 ( 1118) hydrogen bonds : angle 3.80562 / 2.68 ( 2862) metal coordination : bond 0.00215 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 197 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8528 (pt0) REVERT: A 73 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8782 (tt0) REVERT: D 51 ASP cc_start: 0.8782 (p0) cc_final: 0.8487 (p0) REVERT: K 6 LYS cc_start: 0.7817 (ttmm) cc_final: 0.7280 (tptp) REVERT: K 34 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6769 (tp30) REVERT: K 43 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8383 (tt) REVERT: L 169 GLU cc_start: 0.8365 (mp0) cc_final: 0.8136 (mp0) REVERT: L 174 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9105 (mt) REVERT: L 237 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8091 (pp) REVERT: M 1 MET cc_start: 0.8069 (tpt) cc_final: 0.7852 (tpt) REVERT: M 67 MET cc_start: 0.7899 (tpp) cc_final: 0.7637 (tpp) REVERT: N 912 GLN cc_start: 0.6972 (pt0) cc_final: 0.6731 (pt0) REVERT: N 979 MET cc_start: 0.7951 (tpt) cc_final: 0.7420 (tpp) REVERT: O 224 GLU cc_start: 0.7413 (mp0) cc_final: 0.5674 (pm20) REVERT: O 381 LEU cc_start: 0.8395 (pt) cc_final: 0.7630 (tt) REVERT: O 391 TYR cc_start: 0.3965 (OUTLIER) cc_final: 0.3504 (m-10) REVERT: Q 156 TYR cc_start: 0.6049 (OUTLIER) cc_final: 0.5817 (p90) outliers start: 54 outliers final: 38 residues processed: 242 average time/residue: 0.1691 time to fit residues: 65.2184 Evaluate side-chains 231 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 104 PHE Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 174 LEU Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 237 LEU Chi-restraints excluded: chain L residue 245 PHE Chi-restraints excluded: chain L residue 256 VAL Chi-restraints excluded: chain L residue 300 MET Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain N residue 821 ASN Chi-restraints excluded: chain N residue 847 LEU Chi-restraints excluded: chain N residue 968 VAL Chi-restraints excluded: chain N residue 1002 VAL Chi-restraints excluded: chain N residue 1011 ILE Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 125 ASP Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 391 TYR Chi-restraints excluded: chain O residue 440 ILE Chi-restraints excluded: chain Q residue 156 TYR Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 329 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 182 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 245 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 246 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.124692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.080811 restraints weight = 55939.861| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.70 r_work: 0.2919 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25073 Z= 0.166 Angle : 0.642 9.272 35149 Z= 0.350 Chirality : 0.046 0.331 3981 Planarity : 0.004 0.057 3455 Dihedral : 26.617 161.966 5667 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.62 % Allowed : 19.24 % Favored : 78.14 % 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: -0.72 (0.18), residues: 2186 helix: 1.23 (0.19), residues: 773 sheet: -0.98 (0.26), residues: 376 loop : -1.64 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 185 TYR 0.032 0.001 TYR Q 156 PHE 0.023 0.001 PHE L 104 TRP 0.014 0.001 TRP M 297 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (25070) covalent geometry : angle 0.64200 / 0.35 (35149) hydrogen bonds : bond 0.04371 / 2.79 ( 1118) hydrogen bonds : angle 3.79730 / 2.67 ( 2862) metal coordination : bond 0.00298 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 192 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8530 (pt0) REVERT: D 51 ASP cc_start: 0.8788 (p0) cc_final: 0.8502 (p0) REVERT: K 6 LYS cc_start: 0.7808 (ttmm) cc_final: 0.7274 (tptp) REVERT: K 34 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6792 (tp30) REVERT: K 43 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8332 (tt) REVERT: K 73 LEU cc_start: 0.5879 (OUTLIER) cc_final: 0.5448 (tp) REVERT: L 169 GLU cc_start: 0.8392 (mp0) cc_final: 0.8162 (mp0) REVERT: L 174 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9112 (mt) REVERT: L 237 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8025 (pp) REVERT: M 1 MET cc_start: 0.8033 (tpt) cc_final: 0.7812 (tpt) REVERT: M 67 MET cc_start: 0.7928 (tpp) cc_final: 0.7655 (tpp) REVERT: N 912 GLN cc_start: 0.6957 (pt0) cc_final: 0.6703 (pt0) REVERT: N 979 MET cc_start: 0.7939 (tpt) cc_final: 0.7405 (tpp) REVERT: O 224 GLU cc_start: 0.7461 (mp0) cc_final: 0.5731 (pm20) REVERT: O 381 LEU cc_start: 0.8443 (pt) cc_final: 0.7664 (tt) REVERT: O 391 TYR cc_start: 0.3932 (OUTLIER) cc_final: 0.3473 (m-10) REVERT: Q 156 TYR cc_start: 0.6022 (OUTLIER) cc_final: 0.5812 (p90) outliers start: 51 outliers final: 41 residues processed: 234 average time/residue: 0.1685 time to fit residues: 62.4821 Evaluate side-chains 235 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 187 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 104 PHE Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 174 LEU Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 237 LEU Chi-restraints excluded: chain L residue 245 PHE Chi-restraints excluded: chain L residue 256 VAL Chi-restraints excluded: chain L residue 291 MET Chi-restraints excluded: chain L residue 300 MET Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain N residue 847 LEU Chi-restraints excluded: chain N residue 968 VAL Chi-restraints excluded: chain N residue 1002 VAL Chi-restraints excluded: chain N residue 1011 ILE Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 125 ASP Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 391 TYR Chi-restraints excluded: chain O residue 440 ILE Chi-restraints excluded: chain Q residue 156 TYR Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 123 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 171 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 192 optimal weight: 0.8980 chunk 222 optimal weight: 20.0000 chunk 182 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.124935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.081178 restraints weight = 56110.498| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.69 r_work: 0.2924 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25073 Z= 0.155 Angle : 0.635 9.061 35149 Z= 0.347 Chirality : 0.045 0.322 3981 Planarity : 0.004 0.056 3455 Dihedral : 26.565 162.282 5667 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.57 % Allowed : 19.03 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.18), residues: 2186 helix: 1.31 (0.19), residues: 774 sheet: -0.92 (0.26), residues: 376 loop : -1.61 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 23 TYR 0.032 0.001 TYR Q 156 PHE 0.022 0.001 PHE L 104 TRP 0.014 0.001 TRP M 297 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (25070) covalent geometry : angle 0.63512 / 0.35 (35149) hydrogen bonds : bond 0.04261 / 2.72 ( 1118) hydrogen bonds : angle 3.75444 / 2.63 ( 2862) metal coordination : bond 0.00278 / 0.11 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 189 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8478 (pt0) REVERT: D 51 ASP cc_start: 0.8790 (p0) cc_final: 0.8503 (p0) REVERT: K 6 LYS cc_start: 0.7940 (ttmm) cc_final: 0.7409 (tptp) REVERT: K 34 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6888 (tp30) REVERT: K 43 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8379 (tt) REVERT: K 73 LEU cc_start: 0.5698 (OUTLIER) cc_final: 0.5287 (tp) REVERT: L 68 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8492 (mm-40) REVERT: L 169 GLU cc_start: 0.8382 (mp0) cc_final: 0.8143 (mp0) REVERT: L 174 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9105 (mt) REVERT: L 237 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8090 (pp) REVERT: M 67 MET cc_start: 0.7937 (tpp) cc_final: 0.7664 (tpp) REVERT: M 262 ASP cc_start: 0.7541 (t0) cc_final: 0.7200 (t0) REVERT: N 912 GLN cc_start: 0.6969 (pt0) cc_final: 0.6720 (pt0) REVERT: N 979 MET cc_start: 0.7935 (tpt) cc_final: 0.7413 (tpp) REVERT: O 224 GLU cc_start: 0.7384 (mp0) cc_final: 0.5571 (pm20) REVERT: O 381 LEU cc_start: 0.8456 (pt) cc_final: 0.7648 (tt) REVERT: O 391 TYR cc_start: 0.3982 (OUTLIER) cc_final: 0.3517 (m-10) REVERT: Q 156 TYR cc_start: 0.6020 (OUTLIER) cc_final: 0.5786 (p90) outliers start: 50 outliers final: 41 residues processed: 231 average time/residue: 0.1714 time to fit residues: 62.4472 Evaluate side-chains 233 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 185 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 104 PHE Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 174 LEU Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 237 LEU Chi-restraints excluded: chain L residue 245 PHE Chi-restraints excluded: chain L residue 256 VAL Chi-restraints excluded: chain L residue 300 MET Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain N residue 847 LEU Chi-restraints excluded: chain N residue 968 VAL Chi-restraints excluded: chain N residue 1002 VAL Chi-restraints excluded: chain N residue 1011 ILE Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 125 ASP Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 391 TYR Chi-restraints excluded: chain O residue 440 ILE Chi-restraints excluded: chain Q residue 156 TYR Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 230 ASP Chi-restraints excluded: chain R residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 162 optimal weight: 1.9990 chunk 148 optimal weight: 0.4980 chunk 94 optimal weight: 10.0000 chunk 212 optimal weight: 7.9990 chunk 46 optimal weight: 0.4980 chunk 228 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 202 optimal weight: 0.5980 chunk 76 optimal weight: 9.9990 chunk 184 optimal weight: 6.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.123660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.079605 restraints weight = 56015.142| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.58 r_work: 0.2888 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25073 Z= 0.225 Angle : 0.682 8.791 35149 Z= 0.367 Chirality : 0.047 0.326 3981 Planarity : 0.004 0.055 3455 Dihedral : 26.684 162.788 5667 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.67 % Allowed : 19.14 % Favored : 78.19 % 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: -0.79 (0.17), residues: 2186 helix: 1.09 (0.19), residues: 777 sheet: -0.94 (0.26), residues: 375 loop : -1.64 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 17 TYR 0.031 0.001 TYR Q 156 PHE 0.028 0.002 PHE L 104 TRP 0.014 0.001 TRP M 297 HIS 0.005 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.23 (25070) covalent geometry : angle 0.68174 / 0.37 (35149) hydrogen bonds : bond 0.04899 / 3.12 ( 1118) hydrogen bonds : angle 3.83609 / 2.69 ( 2862) metal coordination : bond 0.00501 / 0.20 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6312.84 seconds wall clock time: 108 minutes 48.28 seconds (6528.28 seconds total)