Starting phenix.real_space_refine on Sat Sep 12 20:55:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ifu_9657/09_2026/6ifu_9657.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ifu_9657/09_2026/6ifu_9657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6ifu_9657/09_2026/6ifu_9657.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ifu_9657/09_2026/6ifu_9657.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ifu_9657/09_2026/6ifu_9657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ifu_9657/09_2026/6ifu_9657.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ifu_9657/09_2026/6ifu_9657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ifu_9657/09_2026/6ifu_9657.map" } resolution = 3.05 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 ------------------------------------------------------------------------------- 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= 0.026 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: 5 Type Number sf(0) Gaussians P 62 5.49 5 S 39 5.16 5 C 11764 2.51 5 N 3178 2.21 5 O 3707 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 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: 18750 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5561 Classifications: {'peptide': 706} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 8, 'TRANS': 697} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 7, 'ASN:plan1': 4, 'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 975 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 975 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1695 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 210} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1690 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 209} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1626 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2163 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 11, 'TRANS': 260} Chain breaks: 1 Chain: "H" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2744 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 324} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "I" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 715 Classifications: {'RNAv2': 34} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 16, 'rna3p': 17} Chain: "J" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 606 Classifications: {'RNAv2': 28} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 17, 'rna3p_pyr': 8} Link IDs: {'rna2p': 3, 'rna3p': 24} Time building chain proxies: 4.51, per 1000 atoms: 0.24 Number of scatterers: 18750 At special positions: 0 Unit cell: (92.56, 135.2, 170.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 62 15.00 O 3707 8.00 N 3178 7.00 C 11764 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: 1.51 Conformation dependent library (CDL) restraints added in 792.4 milliseconds 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4148 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 21 sheets defined 38.9% alpha, 11.0% beta 22 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 17 through 24 removed outlier: 3.504A pdb=" N ILE A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.553A pdb=" N SER A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 54 " --> pdb=" O ASP A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 removed outlier: 3.797A pdb=" N GLY A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.786A pdb=" N ALA A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 180 removed outlier: 3.728A pdb=" N LEU A 173 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 220 Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 265 through 291 Processing helix chain 'A' and resid 315 through 335 Processing helix chain 'A' and resid 349 through 354 removed outlier: 3.850A pdb=" N ILE A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 349 through 354' Processing helix chain 'A' and resid 359 through 380 removed outlier: 3.901A pdb=" N TYR A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 392 removed outlier: 3.857A pdb=" N MET A 388 " --> pdb=" O TYR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 432 removed outlier: 4.126A pdb=" N LYS A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 530 removed outlier: 3.701A pdb=" N ALA A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 556 removed outlier: 3.630A pdb=" N PHE A 556 " --> pdb=" O MET A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 563 removed outlier: 3.850A pdb=" N GLN A 562 " --> pdb=" O VAL A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 602 removed outlier: 3.511A pdb=" N ALA A 590 " --> pdb=" O GLN A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 606 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 629 through 637 Processing helix chain 'A' and resid 665 through 674 Processing helix chain 'A' and resid 681 through 695 removed outlier: 3.527A pdb=" N ILE A 685 " --> pdb=" O GLY A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 712 removed outlier: 3.637A pdb=" N GLU A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 738 through 755 removed outlier: 4.166A pdb=" N LYS A 742 " --> pdb=" O ASP A 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 19 Processing helix chain 'B' and resid 36 through 57 removed outlier: 3.830A pdb=" N LEU B 46 " --> pdb=" O ASN B 42 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLU B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 80 removed outlier: 3.637A pdb=" N LEU B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASP B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ARG B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 79 " --> pdb=" O TYR B 75 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU B 80 " --> pdb=" O GLN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.568A pdb=" N LYS B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 97 removed outlier: 3.798A pdb=" N LYS B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 122 removed outlier: 3.649A pdb=" N LEU B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.645A pdb=" N ALA C 13 " --> pdb=" O TYR C 9 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 55 removed outlier: 3.622A pdb=" N LEU C 40 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS C 55 " --> pdb=" O PHE C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 62 through 80 removed outlier: 3.924A pdb=" N ARG C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 77 " --> pdb=" O PHE C 73 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU C 80 " --> pdb=" O GLN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 91 through 98 removed outlier: 3.529A pdb=" N LYS C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 122 removed outlier: 3.616A pdb=" N ARG C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 113 " --> pdb=" O CYS C 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 61 Processing helix chain 'D' and resid 79 through 84 Processing helix chain 'D' and resid 107 through 112 removed outlier: 3.710A pdb=" N SER D 111 " --> pdb=" O ASP D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 178 removed outlier: 3.535A pdb=" N VAL D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS D 175 " --> pdb=" O ARG D 171 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 71 through 75 Processing helix chain 'E' and resid 76 through 84 removed outlier: 3.919A pdb=" N LEU E 82 " --> pdb=" O ILE E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.971A pdb=" N LYS E 92 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 112 Processing helix chain 'E' and resid 159 through 162 Processing helix chain 'E' and resid 163 through 178 removed outlier: 4.129A pdb=" N VAL E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 189 removed outlier: 3.829A pdb=" N GLY E 189 " --> pdb=" O GLY E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.673A pdb=" N THR E 211 " --> pdb=" O ASP E 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 60 removed outlier: 3.582A pdb=" N LYS F 55 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU F 60 " --> pdb=" O MET F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 84 removed outlier: 3.507A pdb=" N LEU F 82 " --> pdb=" O ILE F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 113 Processing helix chain 'F' and resid 156 through 162 removed outlier: 4.126A pdb=" N GLN F 162 " --> pdb=" O GLU F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 165 No H-bonds generated for 'chain 'F' and resid 163 through 165' Processing helix chain 'F' and resid 166 through 171 removed outlier: 3.660A pdb=" N ILE F 170 " --> pdb=" O ASP F 166 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG F 171 " --> pdb=" O PHE F 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 166 through 171' Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'G' and resid 29 through 42 removed outlier: 4.042A pdb=" N LYS G 42 " --> pdb=" O LEU G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 54 Processing helix chain 'G' and resid 110 through 115 Processing helix chain 'G' and resid 163 through 177 removed outlier: 3.804A pdb=" N SER G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR G 175 " --> pdb=" O SER G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 230 removed outlier: 4.342A pdb=" N GLU G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 52 removed outlier: 3.646A pdb=" N GLU H 52 " --> pdb=" O ASN H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 64 removed outlier: 3.811A pdb=" N ILE H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 74 removed outlier: 4.240A pdb=" N ARG H 74 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 82 removed outlier: 3.602A pdb=" N LEU H 79 " --> pdb=" O LEU H 75 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN H 82 " --> pdb=" O PHE H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 143 removed outlier: 3.548A pdb=" N ILE H 139 " --> pdb=" O ALA H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 183 Processing helix chain 'H' and resid 236 through 259 removed outlier: 5.325A pdb=" N GLY H 247 " --> pdb=" O ILE H 243 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LYS H 248 " --> pdb=" O GLU H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 295 Processing helix chain 'H' and resid 296 through 301 Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 311 Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 438 removed outlier: 3.701A pdb=" N HIS A 436 " --> pdb=" O VAL A 456 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 569 through 574 removed outlier: 6.815A pdb=" N PHE A 580 " --> pdb=" O ILE A 572 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 519 through 520 removed outlier: 3.538A pdb=" N ASP A 519 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 644 through 645 removed outlier: 3.616A pdb=" N PHE A 653 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 96 through 98 removed outlier: 6.303A pdb=" N LYS D 5 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN D 11 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ASN D 197 " --> pdb=" O GLN D 11 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG D 13 " --> pdb=" O PHE D 195 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N PHE D 195 " --> pdb=" O ARG D 13 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 46 through 47 Processing sheet with id=AA8, first strand: chain 'D' and resid 118 through 122 Processing sheet with id=AA9, first strand: chain 'E' and resid 96 through 98 removed outlier: 6.394A pdb=" N LYS E 5 " --> pdb=" O VAL E 203 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLN E 11 " --> pdb=" O ASN E 197 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASN E 197 " --> pdb=" O GLN E 11 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG E 13 " --> pdb=" O PHE E 195 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE E 195 " --> pdb=" O ARG E 13 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 126 Processing sheet with id=AB2, first strand: chain 'F' and resid 96 through 97 removed outlier: 3.585A pdb=" N LEU F 151 " --> pdb=" O PHE F 8 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS F 5 " --> pdb=" O THR F 202 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N THR F 202 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS F 7 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA F 200 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER F 9 " --> pdb=" O LEU F 198 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU F 198 " --> pdb=" O SER F 9 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 118 through 123 Processing sheet with id=AB4, first strand: chain 'G' and resid 159 through 160 Processing sheet with id=AB5, first strand: chain 'G' and resid 71 through 73 Processing sheet with id=AB6, first strand: chain 'G' and resid 126 through 132 Processing sheet with id=AB7, first strand: chain 'G' and resid 265 through 266 Processing sheet with id=AB8, first strand: chain 'G' and resid 273 through 274 Processing sheet with id=AB9, first strand: chain 'H' and resid 184 through 186 Processing sheet with id=AC1, first strand: chain 'H' and resid 32 through 33 Processing sheet with id=AC2, first strand: chain 'H' and resid 113 through 115 removed outlier: 6.051A pdb=" N GLU H 113 " --> pdb=" O TYR H 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'H' and resid 212 through 214 639 hydrogen bonds defined for protein. 1821 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 3.13 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3316 1.32 - 1.44: 5302 1.44 - 1.57: 10417 1.57 - 1.69: 125 1.69 - 1.81: 70 Bond restraints: 19230 Sorted by residual: bond pdb=" CB ARG E 136 " pdb=" CG ARG E 136 " ideal model delta sigma weight residual 1.520 1.435 0.085 3.00e-02 1.11e+03 8.00e+00 bond pdb=" CB VAL A 516 " pdb=" CG2 VAL A 516 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.70e+00 bond pdb=" CG LEU F 18 " pdb=" CD2 LEU F 18 " ideal model delta sigma weight residual 1.521 1.433 0.088 3.30e-02 9.18e+02 7.18e+00 bond pdb=" CB LEU F 18 " pdb=" CG LEU F 18 " ideal model delta sigma weight residual 1.530 1.477 0.053 2.00e-02 2.50e+03 7.03e+00 bond pdb=" CB ARG C 65 " pdb=" CG ARG C 65 " ideal model delta sigma weight residual 1.520 1.441 0.079 3.00e-02 1.11e+03 7.02e+00 ... (remaining 19225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.33: 25699 4.33 - 8.66: 475 8.66 - 12.99: 55 12.99 - 17.31: 2 17.31 - 21.64: 1 Bond angle restraints: 26232 Sorted by residual: angle pdb=" N LYS H 146 " pdb=" CA LYS H 146 " pdb=" C LYS H 146 " ideal model delta sigma weight residual 114.62 105.55 9.07 1.14e+00 7.69e-01 6.33e+01 angle pdb=" N PRO A 143 " pdb=" CA PRO A 143 " pdb=" CB PRO A 143 " ideal model delta sigma weight residual 103.25 111.40 -8.15 1.05e+00 9.07e-01 6.03e+01 angle pdb=" N PHE A 658 " pdb=" CA PHE A 658 " pdb=" C PHE A 658 " ideal model delta sigma weight residual 110.80 95.79 15.01 2.13e+00 2.20e-01 4.96e+01 angle pdb=" C LEU A 646 " pdb=" N PHE A 647 " pdb=" CA PHE A 647 " ideal model delta sigma weight residual 120.82 130.67 -9.85 1.50e+00 4.44e-01 4.32e+01 angle pdb=" CA LEU H 199 " pdb=" CB LEU H 199 " pdb=" CG LEU H 199 " ideal model delta sigma weight residual 116.30 137.94 -21.64 3.50e+00 8.16e-02 3.82e+01 ... (remaining 26227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.54: 10935 28.54 - 57.08: 413 57.08 - 85.62: 54 85.62 - 114.16: 0 114.16 - 142.69: 2 Dihedral angle restraints: 11404 sinusoidal: 4972 harmonic: 6432 Sorted by residual: dihedral pdb=" C4' A I 26 " pdb=" C3' A I 26 " pdb=" C2' A I 26 " pdb=" C1' A I 26 " ideal model delta sinusoidal sigma weight residual 36.34 -44.79 81.13 1 3.10e+00 1.04e-01 8.45e+02 dihedral pdb=" C4' G I 3 " pdb=" C3' G I 3 " pdb=" C2' G I 3 " pdb=" C1' G I 3 " ideal model delta sinusoidal sigma weight residual 36.34 -42.59 78.94 1 3.10e+00 1.04e-01 8.07e+02 dihedral pdb=" C4' A I 1 " pdb=" C3' A I 1 " pdb=" C2' A I 1 " pdb=" C1' A I 1 " ideal model delta sinusoidal sigma weight residual 36.34 -38.24 74.58 1 3.10e+00 1.04e-01 7.33e+02 ... (remaining 11401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2488 0.106 - 0.211: 383 0.211 - 0.317: 78 0.317 - 0.422: 20 0.422 - 0.528: 3 Chirality restraints: 2972 Sorted by residual: chirality pdb=" CB VAL F 193 " pdb=" CA VAL F 193 " pdb=" CG1 VAL F 193 " pdb=" CG2 VAL F 193 " both_signs ideal model delta sigma weight residual False -2.63 -2.10 -0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" CB ILE A 644 " pdb=" CA ILE A 644 " pdb=" CG1 ILE A 644 " pdb=" CG2 ILE A 644 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" CB ILE F 12 " pdb=" CA ILE F 12 " pdb=" CG1 ILE F 12 " pdb=" CG2 ILE F 12 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.48e+00 ... (remaining 2969 not shown) Planarity restraints: 3141 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A I 27 " 0.070 2.00e-02 2.50e+03 3.22e-02 2.86e+01 pdb=" N9 A I 27 " -0.076 2.00e-02 2.50e+03 pdb=" C8 A I 27 " -0.008 2.00e-02 2.50e+03 pdb=" N7 A I 27 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A I 27 " 0.006 2.00e-02 2.50e+03 pdb=" C6 A I 27 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A I 27 " 0.019 2.00e-02 2.50e+03 pdb=" N1 A I 27 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A I 27 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A I 27 " -0.011 2.00e-02 2.50e+03 pdb=" C4 A I 27 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G I 21 " 0.066 2.00e-02 2.50e+03 2.89e-02 2.50e+01 pdb=" N9 G I 21 " -0.069 2.00e-02 2.50e+03 pdb=" C8 G I 21 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G I 21 " -0.007 2.00e-02 2.50e+03 pdb=" C5 G I 21 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G I 21 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G I 21 " 0.024 2.00e-02 2.50e+03 pdb=" N1 G I 21 " -0.000 2.00e-02 2.50e+03 pdb=" C2 G I 21 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G I 21 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G I 21 " -0.010 2.00e-02 2.50e+03 pdb=" C4 G I 21 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U I 19 " -0.052 2.00e-02 2.50e+03 2.74e-02 1.69e+01 pdb=" N1 U I 19 " 0.059 2.00e-02 2.50e+03 pdb=" C2 U I 19 " 0.003 2.00e-02 2.50e+03 pdb=" O2 U I 19 " 0.005 2.00e-02 2.50e+03 pdb=" N3 U I 19 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U I 19 " -0.012 2.00e-02 2.50e+03 pdb=" O4 U I 19 " -0.015 2.00e-02 2.50e+03 pdb=" C5 U I 19 " 0.004 2.00e-02 2.50e+03 pdb=" C6 U I 19 " 0.008 2.00e-02 2.50e+03 ... (remaining 3138 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2881 2.75 - 3.28: 17610 3.28 - 3.82: 32700 3.82 - 4.36: 40530 4.36 - 4.90: 67785 Nonbonded interactions: 161506 Sorted by model distance: nonbonded pdb=" OG1 THR D 125 " pdb=" O2 U I 25 " model vdw 2.207 3.040 nonbonded pdb=" O PHE G 71 " pdb=" OH TYR G 157 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR D 16 " pdb=" OD2 ASP H 188 " model vdw 2.267 3.040 nonbonded pdb=" OD2 ASP G 62 " pdb=" OG SER G 262 " model vdw 2.282 3.040 nonbonded pdb=" OD2 ASP D 100 " pdb=" NH2 ARG E 140 " model vdw 2.289 3.120 ... (remaining 161501 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 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 66 or resid 76 through 217)) selection = (chain 'E' and (resid 2 through 66 or resid 76 through 217)) selection = (chain 'F' and (resid 2 through 159 or (resid 160 and (name N or name CA or name \ C or name O or name CB )) or resid 161 through 217)) } 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.650 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.012 0.127 19230 Z= 0.538 Angle : 1.441 21.643 26232 Z= 0.739 Chirality : 0.087 0.528 2972 Planarity : 0.008 0.056 3141 Dihedral : 14.807 142.694 7256 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.69 % Allowed : 13.89 % Favored : 85.42 % Rotamer: Outliers : 1.42 % Allowed : 7.01 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.99 % 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: -4.96 (0.14), residues: 2167 helix: -3.23 (0.12), residues: 798 sheet: -2.87 (0.24), residues: 336 loop : -3.47 (0.15), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG E 57 TYR 0.037 0.004 TYR A 470 PHE 0.040 0.005 PHE F 167 TRP 0.068 0.006 TRP A 732 HIS 0.020 0.003 HIS A 695 Details of bonding type rmsd/Z covalent geometry : bond 0.01236 / 0.54 (19230) covalent geometry : angle 1.44079 / 0.74 (26232) hydrogen bonds : bond 0.15048 / 9.80 ( 692) hydrogen bonds : angle 7.74164 / 5.56 ( 1927) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 544 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 VAL cc_start: 0.6863 (t) cc_final: 0.6184 (t) REVERT: A 110 ILE cc_start: 0.6679 (mp) cc_final: 0.6352 (mt) REVERT: A 453 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7704 (tp) REVERT: A 633 GLU cc_start: 0.6931 (pp20) cc_final: 0.6693 (pp20) REVERT: C 102 ARG cc_start: 0.8117 (ppp80) cc_final: 0.7772 (ptp-170) REVERT: E 67 LYS cc_start: 0.8237 (ttpm) cc_final: 0.7977 (ttpp) REVERT: E 105 ASN cc_start: 0.8723 (p0) cc_final: 0.8405 (p0) REVERT: E 117 TYR cc_start: 0.8201 (m-80) cc_final: 0.7239 (m-80) REVERT: E 215 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6487 (tm) REVERT: F 11 GLN cc_start: 0.8268 (mm110) cc_final: 0.8054 (mm110) REVERT: F 89 LYS cc_start: 0.8437 (ptpp) cc_final: 0.8163 (pttt) REVERT: F 168 LYS cc_start: 0.7797 (mtmm) cc_final: 0.7523 (mttm) REVERT: F 185 SER cc_start: 0.8492 (p) cc_final: 0.8228 (t) REVERT: H 65 GLN cc_start: 0.7299 (tp-100) cc_final: 0.7008 (tt0) REVERT: H 351 MET cc_start: 0.6853 (pmt) cc_final: 0.6575 (ppp) outliers start: 26 outliers final: 9 residues processed: 559 average time/residue: 0.1765 time to fit residues: 142.9025 Evaluate side-chains 335 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 324 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 7.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 GLN A 158 ASN A 257 ASN A 297 ASN A 312 ASN A 391 ASN A 536 ASN A 562 GLN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 ASN A 699 ASN A 735 ASN C 76 GLN D 134 ASN D 159 ASN E 137 GLN E 197 ASN E 213 ASN F 11 GLN F 134 ASN F 159 ASN F 161 ASN F 197 ASN G 14 HIS G 144 GLN G 273 GLN G 284 HIS H 80 ASN H 82 ASN H 148 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.166821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.145329 restraints weight = 24742.880| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.50 r_work: 0.3478 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19230 Z= 0.178 Angle : 1.004 15.795 26232 Z= 0.474 Chirality : 0.080 1.112 2972 Planarity : 0.005 0.062 3141 Dihedral : 13.063 144.475 3155 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.91 % Favored : 87.72 % Rotamer: Outliers : 3.62 % Allowed : 12.99 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.52 % 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: -3.77 (0.15), residues: 2167 helix: -1.76 (0.15), residues: 831 sheet: -2.28 (0.26), residues: 335 loop : -3.24 (0.17), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 31 TYR 0.017 0.002 TYR A 307 PHE 0.024 0.002 PHE G 27 TRP 0.026 0.002 TRP A 732 HIS 0.012 0.001 HIS A 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (19230) covalent geometry : angle 1.00351 / 0.47 (26232) hydrogen bonds : bond 0.04619 / 2.97 ( 692) hydrogen bonds : angle 5.45442 / 3.89 ( 1927) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 376 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 110 ILE cc_start: 0.6617 (OUTLIER) cc_final: 0.6255 (mp) REVERT: A 200 ASP cc_start: 0.7131 (m-30) cc_final: 0.6890 (m-30) REVERT: A 208 PHE cc_start: 0.8467 (m-80) cc_final: 0.8191 (m-80) REVERT: A 361 GLU cc_start: 0.6473 (mp0) cc_final: 0.6221 (mt-10) REVERT: A 679 GLU cc_start: 0.8127 (pm20) cc_final: 0.7722 (pm20) REVERT: C 4 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7882 (pp) REVERT: C 101 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7825 (m-30) REVERT: C 102 ARG cc_start: 0.8432 (ppp80) cc_final: 0.7913 (ttm170) REVERT: E 6 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8305 (pt) REVERT: E 65 ASN cc_start: 0.8632 (m-40) cc_final: 0.8430 (m-40) REVERT: E 67 LYS cc_start: 0.8345 (ttpm) cc_final: 0.7985 (ttpp) REVERT: E 127 ASP cc_start: 0.8279 (t0) cc_final: 0.7947 (t0) REVERT: E 215 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6411 (tm) REVERT: F 57 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8481 (ttt90) REVERT: F 89 LYS cc_start: 0.8399 (ptpp) cc_final: 0.8077 (pttt) REVERT: F 103 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8691 (tp) REVERT: F 108 GLU cc_start: 0.7487 (tp30) cc_final: 0.7244 (mp0) REVERT: F 168 LYS cc_start: 0.8068 (mtmm) cc_final: 0.7627 (mttp) REVERT: G 8 MET cc_start: 0.8553 (mtm) cc_final: 0.7824 (mtt) REVERT: G 162 GLU cc_start: 0.6841 (tp30) cc_final: 0.6449 (pm20) REVERT: G 252 TYR cc_start: 0.8347 (m-80) cc_final: 0.8083 (m-80) REVERT: H 45 LYS cc_start: 0.8449 (mtpt) cc_final: 0.8226 (mttt) REVERT: H 65 GLN cc_start: 0.7505 (tp-100) cc_final: 0.6536 (tt0) REVERT: H 141 MET cc_start: 0.8365 (mtp) cc_final: 0.8117 (mtp) REVERT: H 301 ARG cc_start: 0.7806 (ttp80) cc_final: 0.7523 (ttp-110) REVERT: H 351 MET cc_start: 0.7609 (pmt) cc_final: 0.7112 (ppp) outliers start: 66 outliers final: 33 residues processed: 419 average time/residue: 0.1576 time to fit residues: 98.9982 Evaluate side-chains 324 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 284 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 269 THR Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 123 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 204 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 GLN A 78 ASN A 434 HIS ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 HIS E 11 GLN E 33 ASN E 134 ASN E 197 ASN F 159 ASN G 125 HIS G 167 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 300 GLN H 349 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.157652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.135444 restraints weight = 25043.533| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.68 r_work: 0.3294 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 19230 Z= 0.270 Angle : 0.997 14.353 26232 Z= 0.483 Chirality : 0.077 1.139 2972 Planarity : 0.005 0.057 3141 Dihedral : 13.234 175.870 3152 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.37 % Allowed : 12.92 % Favored : 86.71 % Rotamer: Outliers : 4.99 % Allowed : 15.89 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.42 % 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: -3.16 (0.16), residues: 2167 helix: -1.09 (0.17), residues: 837 sheet: -1.99 (0.27), residues: 326 loop : -3.04 (0.17), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 31 TYR 0.021 0.002 TYR A 307 PHE 0.028 0.002 PHE A 246 TRP 0.028 0.003 TRP A 732 HIS 0.012 0.002 HIS A 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.27 (19230) covalent geometry : angle 0.99698 / 0.48 (26232) hydrogen bonds : bond 0.04955 / 3.25 ( 692) hydrogen bonds : angle 5.23299 / 3.74 ( 1927) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 328 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 110 ILE cc_start: 0.6578 (OUTLIER) cc_final: 0.6151 (mp) REVERT: A 277 ASP cc_start: 0.7721 (m-30) cc_final: 0.7466 (m-30) REVERT: A 361 GLU cc_start: 0.6783 (mp0) cc_final: 0.6573 (mt-10) REVERT: A 423 ARG cc_start: 0.7208 (ttp-110) cc_final: 0.6891 (ttp80) REVERT: A 453 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8073 (tp) REVERT: A 470 TYR cc_start: 0.7119 (p90) cc_final: 0.6811 (p90) REVERT: A 471 VAL cc_start: 0.3680 (OUTLIER) cc_final: 0.3464 (m) REVERT: A 679 GLU cc_start: 0.8079 (pm20) cc_final: 0.7850 (pm20) REVERT: B 18 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8368 (mm) REVERT: B 87 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7337 (pp) REVERT: C 4 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7926 (pp) REVERT: C 101 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.8070 (m-30) REVERT: C 102 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7720 (ptp90) REVERT: D 110 ASP cc_start: 0.7401 (m-30) cc_final: 0.7139 (m-30) REVERT: D 180 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7658 (t70) REVERT: E 6 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8713 (pt) REVERT: E 11 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7837 (tp-100) REVERT: E 14 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8411 (mt) REVERT: E 23 SER cc_start: 0.8589 (p) cc_final: 0.8279 (t) REVERT: E 67 LYS cc_start: 0.8341 (ttpm) cc_final: 0.7968 (ttpp) REVERT: E 215 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6683 (tm) REVERT: F 11 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8370 (mm110) REVERT: F 89 LYS cc_start: 0.8577 (ptpp) cc_final: 0.8244 (pttt) REVERT: F 103 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8784 (tp) REVERT: F 108 GLU cc_start: 0.7493 (tp30) cc_final: 0.7202 (mp0) REVERT: F 163 VAL cc_start: 0.8298 (t) cc_final: 0.8036 (t) REVERT: F 168 LYS cc_start: 0.8141 (mtmm) cc_final: 0.7821 (mttm) REVERT: G 104 GLN cc_start: 0.6387 (OUTLIER) cc_final: 0.6032 (tm130) REVERT: G 162 GLU cc_start: 0.7141 (tp30) cc_final: 0.6894 (pm20) REVERT: G 267 SER cc_start: 0.8322 (OUTLIER) cc_final: 0.8053 (m) REVERT: H 45 LYS cc_start: 0.8504 (mtpt) cc_final: 0.8222 (mttt) REVERT: H 65 GLN cc_start: 0.7751 (tp-100) cc_final: 0.6650 (tt0) REVERT: H 301 ARG cc_start: 0.7977 (ttp80) cc_final: 0.7742 (ttp-110) REVERT: H 351 MET cc_start: 0.7631 (pmt) cc_final: 0.7126 (ppp) outliers start: 91 outliers final: 50 residues processed: 395 average time/residue: 0.1650 time to fit residues: 96.2158 Evaluate side-chains 356 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 290 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 269 THR Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 210 optimal weight: 8.9990 chunk 178 optimal weight: 0.8980 chunk 169 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 203 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN A 334 ASN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN E 11 GLN E 144 ASN F 159 ASN G 55 GLN G 104 GLN H 148 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.167244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.146224 restraints weight = 25067.179| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.48 r_work: 0.3500 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19230 Z= 0.135 Angle : 0.806 12.867 26232 Z= 0.390 Chirality : 0.062 0.694 2972 Planarity : 0.004 0.037 3141 Dihedral : 12.767 179.319 3148 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.77 % Favored : 88.05 % Rotamer: Outliers : 3.73 % Allowed : 17.86 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.60 (0.17), residues: 2167 helix: -0.43 (0.18), residues: 833 sheet: -1.72 (0.27), residues: 317 loop : -2.90 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 278 TYR 0.019 0.001 TYR B 68 PHE 0.023 0.001 PHE G 27 TRP 0.019 0.002 TRP A 732 HIS 0.005 0.001 HIS G 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (19230) covalent geometry : angle 0.80581 / 0.39 (26232) hydrogen bonds : bond 0.04036 / 2.57 ( 692) hydrogen bonds : angle 4.76096 / 3.39 ( 1927) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 349 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7412 (mptt) cc_final: 0.6699 (ptmt) REVERT: A 277 ASP cc_start: 0.7719 (m-30) cc_final: 0.7380 (m-30) REVERT: A 398 GLU cc_start: 0.7741 (tt0) cc_final: 0.7480 (pm20) REVERT: A 423 ARG cc_start: 0.6961 (ttp-110) cc_final: 0.6644 (ttp80) REVERT: A 445 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8042 (tp) REVERT: A 625 MET cc_start: 0.8556 (mtp) cc_final: 0.8277 (mtm) REVERT: A 679 GLU cc_start: 0.8043 (pm20) cc_final: 0.7658 (pm20) REVERT: B 53 GLU cc_start: 0.8249 (mp0) cc_final: 0.7809 (mp0) REVERT: B 65 ARG cc_start: 0.7773 (ttp80) cc_final: 0.7544 (mtp180) REVERT: C 4 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7557 (pp) REVERT: C 89 LYS cc_start: 0.8294 (mmtp) cc_final: 0.8054 (mttp) REVERT: C 102 ARG cc_start: 0.8476 (ppp80) cc_final: 0.7938 (ttm170) REVERT: D 132 GLU cc_start: 0.8037 (tp30) cc_final: 0.7794 (tp30) REVERT: E 6 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8048 (pt) REVERT: E 215 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6444 (tm) REVERT: F 11 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8334 (mm110) REVERT: F 103 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8692 (tp) REVERT: F 107 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7398 (m-30) REVERT: F 108 GLU cc_start: 0.7543 (tp30) cc_final: 0.7227 (mp0) REVERT: F 168 LYS cc_start: 0.8109 (mtmm) cc_final: 0.7801 (mttm) REVERT: G 8 MET cc_start: 0.8740 (mtm) cc_final: 0.8294 (mtm) REVERT: G 130 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7901 (m) REVERT: G 162 GLU cc_start: 0.6946 (tp30) cc_final: 0.6599 (pm20) REVERT: G 192 ASP cc_start: 0.7958 (t0) cc_final: 0.7650 (t0) REVERT: G 267 SER cc_start: 0.8149 (OUTLIER) cc_final: 0.7888 (m) REVERT: H 45 LYS cc_start: 0.8425 (mtpt) cc_final: 0.8074 (mttt) REVERT: H 65 GLN cc_start: 0.7638 (tp-100) cc_final: 0.6755 (tt0) REVERT: H 178 ASP cc_start: 0.5480 (p0) cc_final: 0.4940 (t70) REVERT: H 243 ILE cc_start: 0.8661 (mm) cc_final: 0.8291 (mm) REVERT: H 251 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7327 (mt0) REVERT: H 345 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8071 (mmm) REVERT: H 351 MET cc_start: 0.7590 (pmt) cc_final: 0.7335 (ttm) outliers start: 68 outliers final: 33 residues processed: 398 average time/residue: 0.1672 time to fit residues: 98.3509 Evaluate side-chains 335 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 293 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 269 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 345 MET Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 93 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 GLN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 ASN B 106 GLN E 134 ASN E 197 ASN F 159 ASN G 55 GLN ** G 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 ASN ** H 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.156167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.133891 restraints weight = 24804.005| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.66 r_work: 0.3276 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 19230 Z= 0.290 Angle : 0.953 13.141 26232 Z= 0.463 Chirality : 0.072 0.834 2972 Planarity : 0.005 0.049 3141 Dihedral : 13.000 172.960 3146 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.37 % Allowed : 12.78 % Favored : 86.85 % Rotamer: Outliers : 5.10 % Allowed : 17.32 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.38 % 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: -2.57 (0.17), residues: 2167 helix: -0.40 (0.17), residues: 842 sheet: -1.71 (0.26), residues: 328 loop : -2.91 (0.18), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 741 TYR 0.021 0.002 TYR D 181 PHE 0.025 0.002 PHE A 246 TRP 0.022 0.002 TRP A 732 HIS 0.009 0.002 HIS A 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.29 (19230) covalent geometry : angle 0.95281 / 0.46 (26232) hydrogen bonds : bond 0.04808 / 3.19 ( 692) hydrogen bonds : angle 5.01643 / 3.57 ( 1927) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 295 time to evaluate : 0.617 Fit side-chains REVERT: A 178 GLU cc_start: 0.7791 (tt0) cc_final: 0.7496 (tt0) REVERT: A 277 ASP cc_start: 0.7805 (m-30) cc_final: 0.7450 (m-30) REVERT: A 413 TYR cc_start: 0.6760 (t80) cc_final: 0.6486 (t80) REVERT: A 414 HIS cc_start: 0.6022 (OUTLIER) cc_final: 0.5386 (m-70) REVERT: A 471 VAL cc_start: 0.3649 (OUTLIER) cc_final: 0.3431 (p) REVERT: A 677 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8102 (tm-30) REVERT: B 65 ARG cc_start: 0.7942 (ttp80) cc_final: 0.7579 (mtp180) REVERT: C 4 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7990 (pp) REVERT: C 102 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7657 (ptp90) REVERT: D 112 LEU cc_start: 0.7711 (mp) cc_final: 0.7320 (mt) REVERT: E 6 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8804 (pt) REVERT: E 20 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8149 (mt) REVERT: E 215 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6698 (tm) REVERT: F 103 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8784 (tp) REVERT: F 108 GLU cc_start: 0.7529 (tp30) cc_final: 0.7183 (mp0) REVERT: F 168 LYS cc_start: 0.8236 (mtmm) cc_final: 0.7860 (mttm) REVERT: G 8 MET cc_start: 0.8879 (mtm) cc_final: 0.8428 (mtm) REVERT: G 162 GLU cc_start: 0.7252 (tp30) cc_final: 0.6905 (pm20) REVERT: H 45 LYS cc_start: 0.8466 (mtpt) cc_final: 0.8114 (mttt) REVERT: H 65 GLN cc_start: 0.7718 (tp-100) cc_final: 0.6765 (tt0) REVERT: H 251 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8079 (mm-40) REVERT: H 345 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8324 (mmm) outliers start: 93 outliers final: 59 residues processed: 359 average time/residue: 0.1566 time to fit residues: 83.8617 Evaluate side-chains 344 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 276 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 213 MET Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 269 THR Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 345 MET Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 chunk 184 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 211 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 GLN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 ASN G 55 GLN ** H 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.156099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.134204 restraints weight = 24836.041| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.69 r_work: 0.3297 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 19230 Z= 0.233 Angle : 0.891 13.611 26232 Z= 0.433 Chirality : 0.069 0.801 2972 Planarity : 0.005 0.060 3141 Dihedral : 12.916 172.981 3146 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.37 % Favored : 87.31 % Rotamer: Outliers : 4.44 % Allowed : 18.90 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.38 % 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: -2.39 (0.17), residues: 2167 helix: -0.21 (0.18), residues: 835 sheet: -1.56 (0.26), residues: 318 loop : -2.84 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 171 TYR 0.023 0.002 TYR G 289 PHE 0.019 0.002 PHE A 246 TRP 0.020 0.002 TRP A 732 HIS 0.008 0.001 HIS A 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 (19230) covalent geometry : angle 0.89125 / 0.43 (26232) hydrogen bonds : bond 0.04476 / 2.94 ( 692) hydrogen bonds : angle 4.90924 / 3.49 ( 1927) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 294 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.7532 (m-40) cc_final: 0.7256 (m110) REVERT: A 277 ASP cc_start: 0.7734 (m-30) cc_final: 0.7347 (m-30) REVERT: A 414 HIS cc_start: 0.5805 (OUTLIER) cc_final: 0.5435 (m-70) REVERT: A 423 ARG cc_start: 0.7190 (ttm110) cc_final: 0.6804 (ttp80) REVERT: B 65 ARG cc_start: 0.7910 (ttp80) cc_final: 0.7596 (mtp180) REVERT: C 4 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7896 (pp) REVERT: D 18 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8553 (pt) REVERT: D 112 LEU cc_start: 0.7667 (mp) cc_final: 0.7304 (mt) REVERT: D 132 GLU cc_start: 0.8192 (tp30) cc_final: 0.7950 (tp30) REVERT: E 6 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8564 (pt) REVERT: E 215 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6603 (tm) REVERT: F 103 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8753 (tp) REVERT: F 108 GLU cc_start: 0.7525 (tp30) cc_final: 0.7165 (mp0) REVERT: F 136 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8251 (mtm180) REVERT: F 163 VAL cc_start: 0.8347 (t) cc_final: 0.8091 (t) REVERT: F 168 LYS cc_start: 0.8239 (mtmm) cc_final: 0.7863 (mttm) REVERT: G 8 MET cc_start: 0.8911 (mtm) cc_final: 0.8450 (mtm) REVERT: H 45 LYS cc_start: 0.8486 (mtpt) cc_final: 0.8092 (mttt) REVERT: H 58 LYS cc_start: 0.6878 (OUTLIER) cc_final: 0.6567 (mtpp) REVERT: H 65 GLN cc_start: 0.7784 (tp-100) cc_final: 0.6907 (tt0) REVERT: H 251 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8050 (mm-40) REVERT: H 345 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8214 (mmm) outliers start: 81 outliers final: 59 residues processed: 347 average time/residue: 0.1603 time to fit residues: 83.3714 Evaluate side-chains 342 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 274 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 213 MET Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 269 THR Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 345 MET Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 61 optimal weight: 7.9990 chunk 180 optimal weight: 0.0040 chunk 117 optimal weight: 8.9990 chunk 216 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 188 optimal weight: 8.9990 overall best weight: 2.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 GLN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 ASN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 ASN C 26 ASN F 144 ASN G 55 GLN ** H 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 338 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.157599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.136039 restraints weight = 24686.252| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.61 r_work: 0.3328 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19230 Z= 0.201 Angle : 0.857 13.308 26232 Z= 0.416 Chirality : 0.066 0.777 2972 Planarity : 0.004 0.046 3141 Dihedral : 12.798 174.038 3146 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.37 % Allowed : 12.46 % Favored : 87.17 % Rotamer: Outliers : 4.88 % Allowed : 18.79 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.23 (0.17), residues: 2167 helix: -0.05 (0.18), residues: 834 sheet: -1.45 (0.27), residues: 308 loop : -2.78 (0.18), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 171 TYR 0.021 0.002 TYR G 289 PHE 0.018 0.002 PHE G 27 TRP 0.019 0.002 TRP A 732 HIS 0.007 0.001 HIS A 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (19230) covalent geometry : angle 0.85695 / 0.42 (26232) hydrogen bonds : bond 0.04300 / 2.80 ( 692) hydrogen bonds : angle 4.83128 / 3.43 ( 1927) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 297 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 71 TYR cc_start: 0.6196 (m-80) cc_final: 0.5917 (m-10) REVERT: A 78 ASN cc_start: 0.7589 (m-40) cc_final: 0.7252 (m110) REVERT: A 277 ASP cc_start: 0.7809 (m-30) cc_final: 0.7471 (m-30) REVERT: A 398 GLU cc_start: 0.7957 (tt0) cc_final: 0.7288 (pm20) REVERT: A 414 HIS cc_start: 0.5755 (OUTLIER) cc_final: 0.5385 (m-70) REVERT: A 423 ARG cc_start: 0.7213 (ttm110) cc_final: 0.6851 (ttp80) REVERT: B 65 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7612 (mtp180) REVERT: C 4 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7929 (pp) REVERT: D 18 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8563 (pt) REVERT: E 6 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8559 (pt) REVERT: E 215 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6607 (tm) REVERT: F 103 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8761 (tp) REVERT: F 108 GLU cc_start: 0.7577 (tp30) cc_final: 0.7208 (mp0) REVERT: F 136 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8244 (mtm180) REVERT: F 163 VAL cc_start: 0.8238 (t) cc_final: 0.7972 (t) REVERT: F 168 LYS cc_start: 0.8242 (mtmm) cc_final: 0.7934 (mttm) REVERT: G 8 MET cc_start: 0.8910 (mtm) cc_final: 0.8441 (mtm) REVERT: G 267 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.7954 (m) REVERT: H 45 LYS cc_start: 0.8485 (mtpt) cc_final: 0.8110 (mttt) REVERT: H 58 LYS cc_start: 0.6815 (OUTLIER) cc_final: 0.6594 (mtpp) REVERT: H 65 GLN cc_start: 0.7859 (tp-100) cc_final: 0.6980 (tt0) REVERT: H 149 ASN cc_start: 0.7392 (OUTLIER) cc_final: 0.7078 (p0) REVERT: H 178 ASP cc_start: 0.5673 (p0) cc_final: 0.5013 (t70) REVERT: H 251 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8053 (mm-40) REVERT: H 345 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8210 (mmm) outliers start: 89 outliers final: 62 residues processed: 360 average time/residue: 0.1579 time to fit residues: 85.3662 Evaluate side-chains 350 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 277 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 213 MET Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 269 THR Chi-restraints excluded: chain G residue 281 ASP Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 345 MET Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 147 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 12 optimal weight: 0.3980 chunk 9 optimal weight: 7.9990 chunk 30 optimal weight: 0.0770 overall best weight: 1.2944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 GLN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 ASN C 26 ASN D 124 ASN G 55 GLN H 22 ASN H 148 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.163841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.142955 restraints weight = 24658.288| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.44 r_work: 0.3447 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19230 Z= 0.142 Angle : 0.788 12.500 26232 Z= 0.383 Chirality : 0.061 0.703 2972 Planarity : 0.004 0.042 3141 Dihedral : 12.531 176.575 3146 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.91 % Favored : 87.91 % Rotamer: Outliers : 4.11 % Allowed : 19.51 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.02 (0.17), residues: 2167 helix: 0.24 (0.18), residues: 834 sheet: -1.39 (0.27), residues: 302 loop : -2.76 (0.18), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 171 TYR 0.022 0.002 TYR G 289 PHE 0.019 0.001 PHE G 27 TRP 0.017 0.001 TRP A 732 HIS 0.003 0.001 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (19230) covalent geometry : angle 0.78848 / 0.38 (26232) hydrogen bonds : bond 0.03921 / 2.53 ( 692) hydrogen bonds : angle 4.63604 / 3.28 ( 1927) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 312 time to evaluate : 0.700 Fit side-chains REVERT: A 51 GLN cc_start: 0.6161 (OUTLIER) cc_final: 0.5904 (mp10) REVERT: A 71 TYR cc_start: 0.6089 (m-80) cc_final: 0.5817 (m-10) REVERT: A 78 ASN cc_start: 0.7503 (m-40) cc_final: 0.7181 (m110) REVERT: A 177 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7230 (t80) REVERT: A 241 PHE cc_start: 0.7703 (m-80) cc_final: 0.7384 (m-10) REVERT: A 277 ASP cc_start: 0.7841 (m-30) cc_final: 0.7566 (m-30) REVERT: A 414 HIS cc_start: 0.5601 (OUTLIER) cc_final: 0.5323 (m-70) REVERT: B 65 ARG cc_start: 0.7824 (ttp80) cc_final: 0.7496 (mtp180) REVERT: C 4 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7731 (pp) REVERT: C 102 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7656 (ptp90) REVERT: D 7 LYS cc_start: 0.8587 (ttpp) cc_final: 0.8309 (ttmm) REVERT: D 180 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7448 (t70) REVERT: E 6 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8253 (pt) REVERT: E 215 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6414 (tm) REVERT: F 103 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8728 (tp) REVERT: F 108 GLU cc_start: 0.7502 (tp30) cc_final: 0.7222 (mp0) REVERT: F 136 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8086 (mtm180) REVERT: F 163 VAL cc_start: 0.8136 (t) cc_final: 0.7846 (t) REVERT: F 168 LYS cc_start: 0.8181 (mtmm) cc_final: 0.7890 (mttm) REVERT: G 41 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7601 (tm) REVERT: G 130 THR cc_start: 0.8241 (OUTLIER) cc_final: 0.7987 (m) REVERT: G 192 ASP cc_start: 0.7868 (t0) cc_final: 0.7594 (t0) REVERT: G 267 SER cc_start: 0.8125 (OUTLIER) cc_final: 0.7816 (m) REVERT: H 45 LYS cc_start: 0.8417 (mtpt) cc_final: 0.7986 (mttt) REVERT: H 65 GLN cc_start: 0.7708 (tp-100) cc_final: 0.6838 (tt0) REVERT: H 149 ASN cc_start: 0.7123 (OUTLIER) cc_final: 0.6886 (p0) REVERT: H 162 GLU cc_start: 0.6750 (tt0) cc_final: 0.6504 (mt-10) REVERT: H 178 ASP cc_start: 0.5476 (p0) cc_final: 0.5009 (t70) REVERT: H 243 ILE cc_start: 0.8538 (mm) cc_final: 0.8184 (mm) REVERT: H 251 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7808 (mm-40) REVERT: H 255 LYS cc_start: 0.8783 (mmtm) cc_final: 0.8542 (mmtm) REVERT: H 264 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7059 (pt0) REVERT: H 345 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8089 (mmm) outliers start: 75 outliers final: 50 residues processed: 360 average time/residue: 0.1570 time to fit residues: 84.5348 Evaluate side-chains 348 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 282 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 213 MET Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 269 THR Chi-restraints excluded: chain G residue 281 ASP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 264 GLU Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 345 MET Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 5 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 193 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 GLN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN C 26 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.163396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.142668 restraints weight = 24600.127| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.50 r_work: 0.3419 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19230 Z= 0.161 Angle : 0.805 12.559 26232 Z= 0.391 Chirality : 0.062 0.704 2972 Planarity : 0.004 0.042 3141 Dihedral : 12.489 175.422 3144 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.09 % Favored : 87.68 % Rotamer: Outliers : 4.66 % Allowed : 19.34 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -1.95 (0.18), residues: 2167 helix: 0.33 (0.18), residues: 833 sheet: -1.39 (0.27), residues: 315 loop : -2.74 (0.18), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 171 TYR 0.021 0.002 TYR G 289 PHE 0.019 0.001 PHE G 27 TRP 0.018 0.001 TRP A 732 HIS 0.007 0.001 HIS A 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (19230) covalent geometry : angle 0.80537 / 0.39 (26232) hydrogen bonds : bond 0.04098 / 2.64 ( 692) hydrogen bonds : angle 4.65866 / 3.30 ( 1927) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 297 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 71 TYR cc_start: 0.6108 (m-80) cc_final: 0.5832 (m-10) REVERT: A 78 ASN cc_start: 0.7456 (m-40) cc_final: 0.7141 (m110) REVERT: A 177 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7212 (t80) REVERT: A 219 LYS cc_start: 0.6561 (mtmt) cc_final: 0.4731 (tttm) REVERT: A 277 ASP cc_start: 0.7864 (m-30) cc_final: 0.7579 (m-30) REVERT: A 414 HIS cc_start: 0.5705 (OUTLIER) cc_final: 0.5328 (m-70) REVERT: A 423 ARG cc_start: 0.7077 (ttm110) cc_final: 0.6547 (ttp80) REVERT: A 651 TYR cc_start: 0.8728 (m-80) cc_final: 0.8429 (m-10) REVERT: B 65 ARG cc_start: 0.7857 (ttp80) cc_final: 0.7538 (mtp180) REVERT: C 4 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7722 (pp) REVERT: C 102 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7636 (ptp90) REVERT: D 180 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7544 (t70) REVERT: E 6 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8349 (pt) REVERT: E 215 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6440 (tm) REVERT: F 103 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8758 (tp) REVERT: F 108 GLU cc_start: 0.7669 (tp30) cc_final: 0.7286 (mp0) REVERT: F 136 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8136 (mtm180) REVERT: F 163 VAL cc_start: 0.8111 (t) cc_final: 0.7896 (t) REVERT: F 168 LYS cc_start: 0.8226 (mtmm) cc_final: 0.7902 (mttm) REVERT: G 130 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.7989 (m) REVERT: H 45 LYS cc_start: 0.8428 (mtpt) cc_final: 0.7994 (mttt) REVERT: H 65 GLN cc_start: 0.7818 (tp-100) cc_final: 0.7000 (tt0) REVERT: H 149 ASN cc_start: 0.7096 (OUTLIER) cc_final: 0.6853 (p0) REVERT: H 162 GLU cc_start: 0.6773 (tt0) cc_final: 0.6474 (mt-10) REVERT: H 178 ASP cc_start: 0.5498 (p0) cc_final: 0.5081 (t70) REVERT: H 243 ILE cc_start: 0.8549 (mm) cc_final: 0.8195 (mm) REVERT: H 251 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8022 (mm-40) REVERT: H 264 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7037 (pt0) REVERT: H 300 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7605 (mp10) REVERT: H 345 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8190 (mmm) outliers start: 85 outliers final: 56 residues processed: 351 average time/residue: 0.1442 time to fit residues: 76.4741 Evaluate side-chains 355 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 285 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 213 MET Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 252 TYR Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 269 THR Chi-restraints excluded: chain G residue 281 ASP Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 264 GLU Chi-restraints excluded: chain H residue 300 GLN Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 345 MET Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 5 optimal weight: 20.0000 chunk 177 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 213 optimal weight: 0.0370 chunk 202 optimal weight: 8.9990 chunk 60 optimal weight: 0.0770 chunk 154 optimal weight: 0.0870 chunk 6 optimal weight: 5.9990 chunk 190 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 72 optimal weight: 0.0000 overall best weight: 0.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN A 604 ASN B 106 GLN D 144 ASN F 19 HIS F 159 ASN G 273 GLN H 148 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.175387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.155290 restraints weight = 24677.276| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.38 r_work: 0.3640 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19230 Z= 0.122 Angle : 0.742 11.304 26232 Z= 0.359 Chirality : 0.055 0.579 2972 Planarity : 0.004 0.040 3141 Dihedral : 12.168 178.376 3144 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.17 % Favored : 88.69 % Rotamer: Outliers : 3.18 % Allowed : 20.71 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.75 (0.18), residues: 2167 helix: 0.63 (0.18), residues: 833 sheet: -1.41 (0.27), residues: 322 loop : -2.70 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 278 TYR 0.024 0.001 TYR G 289 PHE 0.024 0.001 PHE G 27 TRP 0.011 0.001 TRP H 203 HIS 0.004 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (19230) covalent geometry : angle 0.74225 / 0.36 (26232) hydrogen bonds : bond 0.03752 / 2.37 ( 692) hydrogen bonds : angle 4.44903 / 3.12 ( 1927) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 347 time to evaluate : 0.745 Fit side-chains REVERT: A 71 TYR cc_start: 0.5929 (m-80) cc_final: 0.5708 (m-10) REVERT: A 78 ASN cc_start: 0.7504 (m-40) cc_final: 0.7179 (m110) REVERT: A 114 PHE cc_start: 0.6010 (m-80) cc_final: 0.5779 (m-80) REVERT: A 177 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.7047 (t80) REVERT: A 213 TYR cc_start: 0.7508 (t80) cc_final: 0.7291 (t80) REVERT: A 219 LYS cc_start: 0.6575 (mtmt) cc_final: 0.4856 (tttm) REVERT: A 277 ASP cc_start: 0.7688 (m-30) cc_final: 0.7392 (m-30) REVERT: A 414 HIS cc_start: 0.5183 (OUTLIER) cc_final: 0.4974 (m-70) REVERT: A 679 GLU cc_start: 0.7451 (pm20) cc_final: 0.7158 (mt-10) REVERT: A 741 ARG cc_start: 0.8056 (ttm110) cc_final: 0.7607 (mtm180) REVERT: C 88 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7219 (mt-10) REVERT: E 6 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7874 (pt) REVERT: E 14 LEU cc_start: 0.8275 (mt) cc_final: 0.8014 (mt) REVERT: E 77 ASP cc_start: 0.7970 (m-30) cc_final: 0.7737 (t0) REVERT: E 127 ASP cc_start: 0.7765 (t0) cc_final: 0.7461 (t70) REVERT: F 103 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8725 (tp) REVERT: F 108 GLU cc_start: 0.7375 (tp30) cc_final: 0.7171 (mp0) REVERT: F 168 LYS cc_start: 0.8167 (mtmm) cc_final: 0.7898 (mttm) REVERT: F 171 ARG cc_start: 0.6875 (ptm160) cc_final: 0.6665 (ptm160) REVERT: G 8 MET cc_start: 0.8715 (mtm) cc_final: 0.8455 (mtm) REVERT: H 22 ASN cc_start: 0.7523 (t0) cc_final: 0.7259 (t0) REVERT: H 65 GLN cc_start: 0.7811 (tp-100) cc_final: 0.7014 (tt0) REVERT: H 178 ASP cc_start: 0.4637 (p0) cc_final: 0.4417 (t0) REVERT: H 243 ILE cc_start: 0.8336 (mm) cc_final: 0.7956 (mm) REVERT: H 251 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7262 (mt0) REVERT: H 264 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6714 (pt0) outliers start: 58 outliers final: 33 residues processed: 386 average time/residue: 0.1628 time to fit residues: 93.2840 Evaluate side-chains 339 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 301 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 269 THR Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 264 GLU Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 125 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 167 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 203 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN A 414 HIS C 26 ASN D 124 ASN F 19 HIS H 148 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.162814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141388 restraints weight = 24747.019| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.57 r_work: 0.3403 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19230 Z= 0.200 Angle : 0.842 12.483 26232 Z= 0.408 Chirality : 0.063 0.745 2972 Planarity : 0.004 0.042 3141 Dihedral : 12.458 175.501 3142 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.35 % Favored : 88.42 % Rotamer: Outliers : 3.07 % Allowed : 20.55 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.18), residues: 2167 helix: 0.57 (0.18), residues: 838 sheet: -1.36 (0.27), residues: 323 loop : -2.75 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 81 TYR 0.019 0.002 TYR A 104 PHE 0.019 0.002 PHE G 27 TRP 0.026 0.002 TRP A 732 HIS 0.010 0.001 HIS A 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (19230) covalent geometry : angle 0.84226 / 0.41 (26232) hydrogen bonds : bond 0.04230 / 2.76 ( 692) hydrogen bonds : angle 4.62182 / 3.27 ( 1927) =============================================================================== Job complete usr+sys time: 5542.61 seconds wall clock time: 95 minutes 43.69 seconds (5743.69 seconds total)