Starting phenix.real_space_refine on Thu Sep 18 16:37:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ifu_9657/09_2025/6ifu_9657.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ifu_9657/09_2025/6ifu_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 { model { file = "/net/cci-nas-00/data/ceres_data/6ifu_9657/09_2025/6ifu_9657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ifu_9657/09_2025/6ifu_9657.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ifu_9657/09_2025/6ifu_9657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ifu_9657/09_2025/6ifu_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: {'RNA': 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: {'RNA': 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: 3.79, per 1000 atoms: 0.20 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: 1.68 Conformation dependent library (CDL) restraints added in 671.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.99 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: 3.25 Time building geometry restraints manager: 2.18 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: 25758 4.33 - 8.66: 420 8.66 - 12.99: 51 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 - 29.39: 11175 29.39 - 58.78: 352 58.78 - 88.16: 58 88.16 - 117.55: 5 117.55 - 146.94: 4 Dihedral angle restraints: 11594 sinusoidal: 5162 harmonic: 6432 Sorted by residual: dihedral pdb=" CA ASP E 157 " pdb=" C ASP E 157 " pdb=" N GLU E 158 " pdb=" CA GLU E 158 " ideal model delta harmonic sigma weight residual 180.00 -122.67 -57.33 0 5.00e+00 4.00e-02 1.31e+02 dihedral pdb=" CA SER E 185 " pdb=" C SER E 185 " pdb=" N GLY E 186 " pdb=" CA GLY E 186 " ideal model delta harmonic sigma weight residual 180.00 128.80 51.20 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" CA VAL F 203 " pdb=" C VAL F 203 " pdb=" N PHE F 204 " pdb=" CA PHE F 204 " ideal model delta harmonic sigma weight residual -180.00 -135.05 -44.95 0 5.00e+00 4.00e-02 8.08e+01 ... (remaining 11591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2575 0.106 - 0.211: 353 0.211 - 0.317: 30 0.317 - 0.422: 11 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: 0.510 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: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.220 Find NCS groups from input model: 0.170 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: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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= 0.542 Angle : 1.401 21.643 26232 Z= 0.738 Chirality : 0.076 0.528 2972 Planarity : 0.008 0.056 3141 Dihedral : 14.855 146.940 7446 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 aren 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 covalent geometry : bond 0.01233 (19230) covalent geometry : angle 1.40125 (26232) hydrogen bonds : bond 0.15048 ( 692) hydrogen bonds : angle 7.74164 ( 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 : 0.694 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: 0.8406 (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: 0.1628 time to fit residues: 130.7100 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 : 0.462 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 B 76 GLN 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: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.164580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.143274 restraints weight = 24766.286| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.68 r_work: 0.3434 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2739 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= 0.164 Angle : 0.784 14.283 26232 Z= 0.416 Chirality : 0.047 0.357 2972 Planarity : 0.005 0.045 3141 Dihedral : 15.664 152.757 3345 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.72 % Favored : 87.91 % Rotamer: Outliers : 3.56 % Allowed : 12.99 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.47 % 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 aren not related in a simple way. whole: -3.75 (0.15), residues: 2167 helix: -1.75 (0.15), residues: 827 sheet: -2.26 (0.26), residues: 335 loop : -3.21 (0.17), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 136 TYR 0.017 0.002 TYR A 307 PHE 0.019 0.002 PHE A 466 TRP 0.025 0.002 TRP A 732 HIS 0.012 0.001 HIS A 695 Details of bonding type rmsd covalent geometry : bond 0.00347 (19230) covalent geometry : angle 0.78398 (26232) hydrogen bonds : bond 0.04486 ( 692) hydrogen bonds : angle 5.39046 ( 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 444 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 379 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 ASP cc_start: 0.7011 (m-30) cc_final: 0.6785 (m-30) REVERT: A 208 PHE cc_start: 0.8446 (m-80) cc_final: 0.8161 (m-80) REVERT: A 361 GLU cc_start: 0.6364 (mp0) cc_final: 0.6150 (mt-10) REVERT: A 679 GLU cc_start: 0.8099 (pm20) cc_final: 0.7688 (pm20) REVERT: C 4 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7794 (pp) REVERT: C 101 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7823 (m-30) REVERT: C 102 ARG cc_start: 0.8449 (ppp80) cc_final: 0.7867 (ttm170) REVERT: E 6 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8264 (pt) REVERT: E 67 LYS cc_start: 0.8296 (ttpm) cc_final: 0.7940 (ttpp) REVERT: E 127 ASP cc_start: 0.8304 (t0) cc_final: 0.7909 (t0) REVERT: E 175 LYS cc_start: 0.8018 (ttmt) cc_final: 0.7811 (ttmt) REVERT: E 215 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6311 (tm) REVERT: F 89 LYS cc_start: 0.8435 (ptpp) cc_final: 0.8176 (pttt) REVERT: F 103 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8692 (tp) REVERT: F 108 GLU cc_start: 0.7433 (tp30) cc_final: 0.7227 (mp0) REVERT: F 168 LYS cc_start: 0.8077 (mtmm) cc_final: 0.7617 (mttp) REVERT: G 8 MET cc_start: 0.8650 (mtm) cc_final: 0.7940 (mtt) REVERT: G 162 GLU cc_start: 0.6851 (tp30) cc_final: 0.6426 (pm20) REVERT: G 252 TYR cc_start: 0.8347 (m-80) cc_final: 0.7986 (m-80) REVERT: H 45 LYS cc_start: 0.8458 (mtpt) cc_final: 0.8183 (mttt) REVERT: H 65 GLN cc_start: 0.7498 (tp-100) cc_final: 0.6553 (tt0) REVERT: H 141 MET cc_start: 0.8411 (mtp) cc_final: 0.8169 (mtp) REVERT: H 178 ASP cc_start: 0.5672 (p0) cc_final: 0.4829 (t70) REVERT: H 301 ARG cc_start: 0.7785 (ttp80) cc_final: 0.7488 (ttp-110) REVERT: H 351 MET cc_start: 0.7646 (pmt) cc_final: 0.7112 (ppp) outliers start: 65 outliers final: 33 residues processed: 423 average time/residue: 0.1535 time to fit residues: 95.5386 Evaluate side-chains 327 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 289 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN 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 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: 4.9990 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN F 159 ASN G 110 ASN G 125 HIS G 167 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.154659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.131128 restraints weight = 25089.816| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.89 r_work: 0.3215 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3296 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= 0.296 Angle : 0.857 14.305 26232 Z= 0.454 Chirality : 0.051 0.340 2972 Planarity : 0.005 0.054 3141 Dihedral : 15.557 150.526 3342 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.83 % Favored : 86.76 % Rotamer: Outliers : 4.93 % Allowed : 16.33 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.47 % 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 aren not related in a simple way. whole: -3.20 (0.16), residues: 2167 helix: -1.17 (0.16), residues: 836 sheet: -1.96 (0.27), residues: 326 loop : -3.04 (0.17), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 136 TYR 0.022 0.002 TYR D 181 PHE 0.029 0.002 PHE A 246 TRP 0.028 0.003 TRP A 732 HIS 0.013 0.002 HIS A 695 Details of bonding type rmsd covalent geometry : bond 0.00667 (19230) covalent geometry : angle 0.85697 (26232) hydrogen bonds : bond 0.05018 ( 692) hydrogen bonds : angle 5.28231 ( 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 417 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 327 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 277 ASP cc_start: 0.7481 (m-30) cc_final: 0.7195 (m-30) REVERT: A 423 ARG cc_start: 0.7026 (ttp-110) cc_final: 0.6705 (ttp80) REVERT: A 453 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8110 (tp) REVERT: B 18 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8304 (mm) REVERT: B 55 LYS cc_start: 0.8201 (mttm) cc_final: 0.7965 (mttt) REVERT: B 87 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7256 (pp) REVERT: C 4 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7889 (pp) REVERT: C 101 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7852 (m-30) REVERT: C 102 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7569 (ptp90) REVERT: D 110 ASP cc_start: 0.7258 (m-30) cc_final: 0.7014 (m-30) REVERT: D 132 GLU cc_start: 0.7980 (tp30) cc_final: 0.7770 (tp30) REVERT: D 180 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7654 (t70) REVERT: E 11 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7685 (tp-100) REVERT: E 14 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8305 (mt) REVERT: E 23 SER cc_start: 0.8396 (p) cc_final: 0.7992 (t) REVERT: E 67 LYS cc_start: 0.8294 (ttpm) cc_final: 0.7924 (ttpp) REVERT: E 215 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6629 (tm) REVERT: F 11 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8274 (mm110) REVERT: F 89 LYS cc_start: 0.8584 (ptpp) cc_final: 0.8321 (pttt) REVERT: F 103 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8780 (tp) REVERT: F 163 VAL cc_start: 0.8220 (t) cc_final: 0.7969 (t) REVERT: F 168 LYS cc_start: 0.8115 (mtmm) cc_final: 0.7780 (mttm) REVERT: F 171 ARG cc_start: 0.7703 (ptm160) cc_final: 0.7436 (ptm160) REVERT: G 104 GLN cc_start: 0.6359 (OUTLIER) cc_final: 0.6036 (tm130) REVERT: G 250 GLU cc_start: 0.7579 (tp30) cc_final: 0.7347 (mt-10) REVERT: H 45 LYS cc_start: 0.8461 (mtpt) cc_final: 0.8144 (mttt) REVERT: H 65 GLN cc_start: 0.7721 (tp-100) cc_final: 0.6685 (tt0) REVERT: H 141 MET cc_start: 0.8403 (mtp) cc_final: 0.8145 (mtp) REVERT: H 301 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7682 (ttp-110) REVERT: H 351 MET cc_start: 0.7572 (pmt) cc_final: 0.7059 (ppp) outliers start: 90 outliers final: 50 residues processed: 393 average time/residue: 0.1539 time to fit residues: 89.1801 Evaluate side-chains 351 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 289 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 251 ILE 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 541 THR Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 703 LEU 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 101 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 180 ASP Chi-restraints excluded: chain D residue 202 THR 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 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 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 46 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 108 LEU 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: 0.8980 chunk 178 optimal weight: 0.5980 chunk 169 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 0.2980 chunk 203 optimal weight: 20.0000 chunk 65 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** E 33 ASN E 137 GLN E 144 ASN F 159 ASN G 104 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 = 0.3873 r_free = 0.3873 target = 0.165161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.143175 restraints weight = 25099.711| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.70 r_work: 0.3426 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19230 Z= 0.125 Angle : 0.675 12.791 26232 Z= 0.360 Chirality : 0.044 0.358 2972 Planarity : 0.004 0.036 3141 Dihedral : 15.255 153.950 3340 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.86 % Favored : 87.91 % Rotamer: Outliers : 3.62 % Allowed : 18.03 % Favored : 78.36 % 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 aren not related in a simple way. whole: -2.59 (0.17), residues: 2167 helix: -0.46 (0.17), residues: 834 sheet: -1.64 (0.28), residues: 314 loop : -2.89 (0.18), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 136 TYR 0.018 0.001 TYR B 68 PHE 0.019 0.001 PHE G 27 TRP 0.019 0.002 TRP A 732 HIS 0.003 0.001 HIS E 19 Details of bonding type rmsd covalent geometry : bond 0.00256 (19230) covalent geometry : angle 0.67541 (26232) hydrogen bonds : bond 0.03783 ( 692) hydrogen bonds : angle 4.73017 ( 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 411 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 345 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7406 (mptt) cc_final: 0.6754 (ptmt) REVERT: A 135 ASN cc_start: 0.8040 (t0) cc_final: 0.7489 (t0) REVERT: A 277 ASP cc_start: 0.7468 (m-30) cc_final: 0.7098 (m-30) REVERT: A 414 HIS cc_start: 0.5645 (OUTLIER) cc_final: 0.5343 (m-70) REVERT: A 423 ARG cc_start: 0.6797 (ttp-110) cc_final: 0.6481 (ttp80) REVERT: A 445 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7998 (tp) REVERT: A 625 MET cc_start: 0.8508 (mtp) cc_final: 0.8268 (mtm) REVERT: A 679 GLU cc_start: 0.7760 (pm20) cc_final: 0.7477 (pm20) REVERT: B 55 LYS cc_start: 0.8057 (mttm) cc_final: 0.7748 (mtpt) REVERT: B 68 TYR cc_start: 0.8990 (t80) cc_final: 0.8754 (t80) REVERT: B 103 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7374 (mm-30) REVERT: C 4 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7497 (pp) REVERT: C 102 ARG cc_start: 0.8337 (ppp80) cc_final: 0.7789 (ttm170) REVERT: E 6 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.7921 (pt) REVERT: E 215 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6493 (tm) REVERT: F 11 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8239 (mm110) REVERT: F 89 LYS cc_start: 0.8584 (ptpp) cc_final: 0.8276 (pttt) REVERT: F 103 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8673 (tp) REVERT: F 168 LYS cc_start: 0.8110 (mtmm) cc_final: 0.7808 (mttm) REVERT: G 8 MET cc_start: 0.8664 (mtm) cc_final: 0.8191 (mtm) REVERT: G 130 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7836 (m) REVERT: G 162 GLU cc_start: 0.6064 (pm20) cc_final: 0.5810 (pm20) REVERT: G 198 LEU cc_start: 0.6659 (mm) cc_final: 0.6457 (tp) REVERT: G 267 SER cc_start: 0.8094 (OUTLIER) cc_final: 0.7831 (m) REVERT: H 45 LYS cc_start: 0.8354 (mtpt) cc_final: 0.8101 (mttt) REVERT: H 65 GLN cc_start: 0.7594 (tp-100) cc_final: 0.6738 (tt0) REVERT: H 178 ASP cc_start: 0.5461 (p0) cc_final: 0.5054 (t70) REVERT: H 243 ILE cc_start: 0.8606 (mm) cc_final: 0.8235 (mm) REVERT: H 251 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7262 (mt0) REVERT: H 345 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8174 (mmm) REVERT: H 351 MET cc_start: 0.7522 (pmt) cc_final: 0.7305 (ttm) outliers start: 66 outliers final: 34 residues processed: 389 average time/residue: 0.1524 time to fit residues: 86.9768 Evaluate side-chains 335 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 292 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 414 HIS 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 659 ILE 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 20 LEU Chi-restraints excluded: chain C residue 85 ASP 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 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 29 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 G residue 34 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 76 ILE 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 148 ASN 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: 6.9990 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 211 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 297 ASN A 604 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 ASN F 159 ASN G 55 GLN G 161 ASN G 255 GLN ** 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 = 0.3792 r_free = 0.3792 target = 0.158264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.134804 restraints weight = 24804.505| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.91 r_work: 0.3294 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19230 Z= 0.188 Angle : 0.716 12.301 26232 Z= 0.380 Chirality : 0.046 0.337 2972 Planarity : 0.004 0.037 3141 Dihedral : 15.162 152.488 3336 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.23 % Favored : 87.45 % Rotamer: Outliers : 4.44 % Allowed : 17.70 % Favored : 77.86 % 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 aren not related in a simple way. whole: -2.41 (0.17), residues: 2167 helix: -0.21 (0.18), residues: 837 sheet: -1.59 (0.27), residues: 322 loop : -2.88 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 136 TYR 0.020 0.002 TYR B 68 PHE 0.020 0.002 PHE A 246 TRP 0.022 0.002 TRP A 732 HIS 0.006 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00417 (19230) covalent geometry : angle 0.71604 (26232) hydrogen bonds : bond 0.04176 ( 692) hydrogen bonds : angle 4.78005 ( 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: 81 poor density : 307 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 135 ASN cc_start: 0.8152 (t0) cc_final: 0.7596 (t0) REVERT: A 277 ASP cc_start: 0.7468 (m-30) cc_final: 0.7057 (m-30) REVERT: A 297 ASN cc_start: 0.8354 (OUTLIER) cc_final: 0.8145 (m-40) REVERT: A 414 HIS cc_start: 0.5905 (OUTLIER) cc_final: 0.5412 (m-70) REVERT: A 423 ARG cc_start: 0.6916 (ttp-110) cc_final: 0.6544 (ttp80) REVERT: A 445 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8266 (tp) REVERT: A 677 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7896 (tm-30) REVERT: A 679 GLU cc_start: 0.7770 (pm20) cc_final: 0.7538 (pm20) REVERT: B 55 LYS cc_start: 0.8098 (mttm) cc_final: 0.7870 (mtpt) REVERT: B 65 ARG cc_start: 0.7713 (ttp80) cc_final: 0.7393 (mtp180) REVERT: C 4 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7779 (pp) REVERT: E 6 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8294 (pt) REVERT: E 215 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6399 (tm) REVERT: F 89 LYS cc_start: 0.8653 (ptpp) cc_final: 0.8350 (pttt) REVERT: F 103 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8735 (tp) REVERT: F 123 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7768 (mt-10) REVERT: F 168 LYS cc_start: 0.8127 (mtmm) cc_final: 0.7761 (mttm) REVERT: G 8 MET cc_start: 0.8725 (mtm) cc_final: 0.8288 (mtm) REVERT: G 130 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.7914 (m) REVERT: G 192 ASP cc_start: 0.7958 (t0) cc_final: 0.7598 (t0) REVERT: G 252 TYR cc_start: 0.8613 (m-80) cc_final: 0.8379 (m-80) REVERT: H 45 LYS cc_start: 0.8376 (mtpt) cc_final: 0.8049 (mttt) REVERT: H 57 GLU cc_start: 0.6331 (tp30) cc_final: 0.6089 (tt0) REVERT: H 65 GLN cc_start: 0.7664 (tp-100) cc_final: 0.6735 (tt0) REVERT: H 178 ASP cc_start: 0.5625 (p0) cc_final: 0.5048 (t70) REVERT: H 345 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8282 (mmm) outliers start: 81 outliers final: 52 residues processed: 356 average time/residue: 0.1527 time to fit residues: 80.2952 Evaluate side-chains 346 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 284 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 297 ASN Chi-restraints excluded: chain A residue 414 HIS 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 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 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 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 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 119 GLU Chi-restraints excluded: chain F residue 123 GLU 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 41 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 76 ILE 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 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 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: 3.9990 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 ASN E 11 GLN G 55 GLN ** H 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 251 GLN H 349 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.158896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.136624 restraints weight = 24703.326| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.79 r_work: 0.3300 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19230 Z= 0.185 Angle : 0.707 13.079 26232 Z= 0.375 Chirality : 0.046 0.342 2972 Planarity : 0.004 0.058 3141 Dihedral : 15.171 152.214 3336 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.37 % Allowed : 12.32 % Favored : 87.31 % Rotamer: Outliers : 4.60 % Allowed : 18.14 % Favored : 77.26 % 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 aren not related in a simple way. whole: -2.26 (0.17), residues: 2167 helix: -0.05 (0.18), residues: 838 sheet: -1.49 (0.26), residues: 320 loop : -2.83 (0.18), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 171 TYR 0.025 0.002 TYR G 289 PHE 0.018 0.002 PHE A 246 TRP 0.021 0.002 TRP A 732 HIS 0.006 0.001 HIS A 695 Details of bonding type rmsd covalent geometry : bond 0.00409 (19230) covalent geometry : angle 0.70717 (26232) hydrogen bonds : bond 0.04123 ( 692) hydrogen bonds : angle 4.75021 ( 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 379 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 295 time to evaluate : 0.730 Fit side-chains REVERT: A 78 ASN cc_start: 0.7503 (m-40) cc_final: 0.7237 (m110) REVERT: A 277 ASP cc_start: 0.7433 (m-30) cc_final: 0.7133 (m-30) REVERT: A 414 HIS cc_start: 0.5651 (OUTLIER) cc_final: 0.5201 (m-70) REVERT: A 445 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8244 (tp) REVERT: A 679 GLU cc_start: 0.7686 (pm20) cc_final: 0.7170 (mt-10) REVERT: B 55 LYS cc_start: 0.8101 (mttm) cc_final: 0.7884 (mtpt) REVERT: B 65 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7516 (mtp180) REVERT: C 4 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7753 (pp) REVERT: C 102 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7439 (ptp90) REVERT: E 6 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8349 (pt) REVERT: E 11 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7489 (tp-100) REVERT: E 215 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6427 (tm) REVERT: F 103 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8736 (tp) REVERT: F 154 GLU cc_start: 0.7664 (tt0) cc_final: 0.7454 (tt0) REVERT: F 163 VAL cc_start: 0.8122 (t) cc_final: 0.7917 (t) REVERT: F 168 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7868 (mttm) REVERT: G 8 MET cc_start: 0.8726 (mtm) cc_final: 0.8285 (mtm) REVERT: G 41 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7914 (tm) REVERT: G 192 ASP cc_start: 0.7918 (t0) cc_final: 0.7548 (t0) REVERT: H 45 LYS cc_start: 0.8411 (mtpt) cc_final: 0.8106 (mttt) REVERT: H 65 GLN cc_start: 0.7762 (tp-100) cc_final: 0.6892 (tt0) REVERT: H 178 ASP cc_start: 0.5593 (p0) cc_final: 0.5070 (t70) REVERT: H 345 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8224 (mmm) outliers start: 84 outliers final: 59 residues processed: 350 average time/residue: 0.1597 time to fit residues: 82.2093 Evaluate side-chains 343 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 274 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 320 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 414 HIS 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 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 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 11 GLN 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 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 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 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 41 LEU 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 280 LEU 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 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: 5.9990 chunk 180 optimal weight: 0.9990 chunk 117 optimal weight: 0.0980 chunk 216 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 188 optimal weight: 8.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 297 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN F 144 ASN G 55 GLN ** H 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.163283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.141412 restraints weight = 24678.852| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.73 r_work: 0.3388 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19230 Z= 0.130 Angle : 0.655 12.550 26232 Z= 0.348 Chirality : 0.043 0.346 2972 Planarity : 0.004 0.035 3141 Dihedral : 15.048 152.999 3336 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.91 % Favored : 87.91 % Rotamer: Outliers : 4.05 % Allowed : 19.07 % Favored : 76.88 % 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 aren not related in a simple way. whole: -2.03 (0.18), residues: 2167 helix: 0.23 (0.18), residues: 834 sheet: -1.39 (0.27), residues: 320 loop : -2.78 (0.18), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 136 TYR 0.024 0.002 TYR G 289 PHE 0.017 0.001 PHE G 27 TRP 0.018 0.002 TRP A 732 HIS 0.005 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00273 (19230) covalent geometry : angle 0.65490 (26232) hydrogen bonds : bond 0.03721 ( 692) hydrogen bonds : angle 4.60134 ( 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 389 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 315 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 71 TYR cc_start: 0.6163 (m-80) cc_final: 0.5795 (m-10) REVERT: A 78 ASN cc_start: 0.7526 (m-40) cc_final: 0.7243 (m110) REVERT: A 177 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.7181 (t80) REVERT: A 241 PHE cc_start: 0.7697 (m-80) cc_final: 0.7474 (m-80) REVERT: A 277 ASP cc_start: 0.7551 (m-30) cc_final: 0.7219 (m-30) REVERT: A 414 HIS cc_start: 0.5639 (OUTLIER) cc_final: 0.5260 (m-70) REVERT: A 445 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8158 (tp) REVERT: A 651 TYR cc_start: 0.8526 (m-80) cc_final: 0.8166 (m-10) REVERT: A 679 GLU cc_start: 0.7591 (pm20) cc_final: 0.7285 (mt-10) REVERT: B 65 ARG cc_start: 0.7692 (ttp80) cc_final: 0.7462 (mtp180) REVERT: C 4 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7522 (pp) REVERT: E 6 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8130 (pt) REVERT: E 215 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6376 (tm) REVERT: F 103 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8741 (tp) REVERT: F 123 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: F 163 VAL cc_start: 0.8028 (t) cc_final: 0.7807 (t) REVERT: F 168 LYS cc_start: 0.8109 (mtmm) cc_final: 0.7811 (mttm) REVERT: G 8 MET cc_start: 0.8731 (mtm) cc_final: 0.8343 (mtm) REVERT: G 130 THR cc_start: 0.8004 (OUTLIER) cc_final: 0.7768 (m) REVERT: G 192 ASP cc_start: 0.7867 (t0) cc_final: 0.7532 (t0) REVERT: H 45 LYS cc_start: 0.8379 (mtpt) cc_final: 0.8080 (mttt) REVERT: H 65 GLN cc_start: 0.7611 (tp-100) cc_final: 0.6749 (tt0) REVERT: H 178 ASP cc_start: 0.5387 (p0) cc_final: 0.4668 (t70) REVERT: H 243 ILE cc_start: 0.8540 (mm) cc_final: 0.8125 (mm) REVERT: H 300 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7534 (mp10) REVERT: H 345 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8100 (mmm) outliers start: 74 outliers final: 53 residues processed: 359 average time/residue: 0.1713 time to fit residues: 89.5313 Evaluate side-chains 354 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 290 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE 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 402 GLU Chi-restraints excluded: chain A residue 414 HIS 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 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 87 ILE 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 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 119 GLU Chi-restraints excluded: chain F residue 123 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 46 LEU Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 134 ASN Chi-restraints excluded: chain G residue 174 GLN 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 280 LEU Chi-restraints excluded: chain G residue 281 ASP Chi-restraints excluded: chain H residue 28 SER 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 153 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 147 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 172 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.0570 chunk 30 optimal weight: 0.0370 overall best weight: 2.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.159445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.138295 restraints weight = 24711.584| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.75 r_work: 0.3342 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19230 Z= 0.176 Angle : 0.695 12.784 26232 Z= 0.367 Chirality : 0.045 0.341 2972 Planarity : 0.004 0.037 3141 Dihedral : 15.025 152.232 3334 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.46 % Favored : 87.22 % Rotamer: Outliers : 4.44 % Allowed : 19.23 % 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 aren not related in a simple way. whole: -2.00 (0.18), residues: 2167 helix: 0.26 (0.18), residues: 835 sheet: -1.44 (0.27), residues: 323 loop : -2.75 (0.18), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 171 TYR 0.024 0.002 TYR B 68 PHE 0.018 0.002 PHE A 246 TRP 0.019 0.002 TRP A 732 HIS 0.008 0.001 HIS A 695 Details of bonding type rmsd covalent geometry : bond 0.00388 (19230) covalent geometry : angle 0.69476 (26232) hydrogen bonds : bond 0.04019 ( 692) hydrogen bonds : angle 4.66675 ( 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 381 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 300 time to evaluate : 0.738 Fit side-chains REVERT: A 51 GLN cc_start: 0.7276 (pt0) cc_final: 0.6993 (mp10) REVERT: A 71 TYR cc_start: 0.6238 (m-80) cc_final: 0.6019 (m-10) REVERT: A 78 ASN cc_start: 0.7515 (m-40) cc_final: 0.7146 (m110) REVERT: A 177 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.7134 (t80) REVERT: A 219 LYS cc_start: 0.6642 (mtmt) cc_final: 0.4792 (tttm) REVERT: A 277 ASP cc_start: 0.7499 (m-30) cc_final: 0.7243 (m-30) REVERT: A 414 HIS cc_start: 0.5560 (OUTLIER) cc_final: 0.5103 (m-70) REVERT: A 679 GLU cc_start: 0.7483 (pm20) cc_final: 0.7264 (mt-10) REVERT: A 715 ARG cc_start: 0.8001 (ttm110) cc_final: 0.7521 (mtm-85) REVERT: B 65 ARG cc_start: 0.7812 (ttp80) cc_final: 0.7496 (mtp180) REVERT: C 4 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7741 (pp) REVERT: D 180 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7569 (t70) REVERT: E 6 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8359 (pt) REVERT: E 215 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6397 (tm) REVERT: F 103 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8734 (tp) REVERT: F 123 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: F 136 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7952 (mtm180) REVERT: F 168 LYS cc_start: 0.8199 (mtmm) cc_final: 0.7860 (mttm) REVERT: G 130 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7902 (m) REVERT: G 192 ASP cc_start: 0.7888 (t0) cc_final: 0.7527 (t0) REVERT: H 45 LYS cc_start: 0.8418 (mtpt) cc_final: 0.8108 (mttt) REVERT: H 65 GLN cc_start: 0.7757 (tp-100) cc_final: 0.6880 (tt0) REVERT: H 178 ASP cc_start: 0.5500 (p0) cc_final: 0.5022 (t70) REVERT: H 300 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7541 (mp10) REVERT: H 345 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8186 (mmm) outliers start: 81 outliers final: 58 residues processed: 355 average time/residue: 0.1594 time to fit residues: 84.4075 Evaluate side-chains 360 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 290 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE 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 339 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 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 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 87 ILE 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 180 ASP 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 123 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 G residue 46 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 134 ASN Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 174 GLN 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 280 LEU Chi-restraints excluded: chain G residue 281 ASP Chi-restraints excluded: chain H residue 7 THR 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 153 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 5 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 193 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 96 optimal weight: 20.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 ASN ** H 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.160089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.137933 restraints weight = 24672.079| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.76 r_work: 0.3325 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19230 Z= 0.173 Angle : 0.695 12.789 26232 Z= 0.369 Chirality : 0.045 0.342 2972 Planarity : 0.004 0.036 3141 Dihedral : 15.012 152.184 3334 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.14 % Favored : 87.59 % Rotamer: Outliers : 4.60 % Allowed : 19.01 % Favored : 76.38 % 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 aren not related in a simple way. whole: -1.94 (0.18), residues: 2167 helix: 0.31 (0.18), residues: 832 sheet: -1.39 (0.26), residues: 323 loop : -2.71 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 136 TYR 0.022 0.002 TYR G 289 PHE 0.017 0.002 PHE A 246 TRP 0.018 0.002 TRP A 732 HIS 0.008 0.001 HIS A 695 Details of bonding type rmsd covalent geometry : bond 0.00380 (19230) covalent geometry : angle 0.69497 (26232) hydrogen bonds : bond 0.03975 ( 692) hydrogen bonds : angle 4.68596 ( 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 381 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 297 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 51 GLN cc_start: 0.7234 (pt0) cc_final: 0.6912 (mp10) REVERT: A 71 TYR cc_start: 0.6277 (m-80) cc_final: 0.6051 (m-10) REVERT: A 78 ASN cc_start: 0.7454 (m-40) cc_final: 0.7137 (m110) REVERT: A 177 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7111 (t80) REVERT: A 219 LYS cc_start: 0.6537 (mtmt) cc_final: 0.4717 (tttm) REVERT: A 241 PHE cc_start: 0.7594 (m-10) cc_final: 0.7387 (m-10) REVERT: A 277 ASP cc_start: 0.7499 (m-30) cc_final: 0.7224 (m-30) REVERT: A 414 HIS cc_start: 0.5552 (OUTLIER) cc_final: 0.5134 (m-70) REVERT: A 664 ASP cc_start: 0.6803 (m-30) cc_final: 0.6465 (m-30) REVERT: A 679 GLU cc_start: 0.7540 (pm20) cc_final: 0.7308 (mt-10) REVERT: A 715 ARG cc_start: 0.7952 (ttm110) cc_final: 0.7488 (mtm-85) REVERT: B 65 ARG cc_start: 0.7825 (ttp80) cc_final: 0.7503 (mtp180) REVERT: C 4 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7768 (pp) REVERT: C 102 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7420 (ptp90) REVERT: D 180 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7531 (t70) REVERT: E 6 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8331 (pt) REVERT: E 215 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.6443 (tm) REVERT: F 103 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8759 (tp) REVERT: F 123 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: F 136 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7963 (mtm180) REVERT: F 168 LYS cc_start: 0.8203 (mtmm) cc_final: 0.7878 (mttm) REVERT: G 41 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7737 (tm) REVERT: G 130 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7903 (m) REVERT: G 192 ASP cc_start: 0.7872 (t0) cc_final: 0.7528 (t0) REVERT: H 45 LYS cc_start: 0.8465 (mtpt) cc_final: 0.8137 (mttt) REVERT: H 65 GLN cc_start: 0.7772 (tp-100) cc_final: 0.6948 (tt0) REVERT: H 178 ASP cc_start: 0.5422 (p0) cc_final: 0.4697 (t70) REVERT: H 264 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7114 (pt0) REVERT: H 300 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7527 (mp10) REVERT: H 345 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8095 (mmm) outliers start: 84 outliers final: 61 residues processed: 352 average time/residue: 0.1489 time to fit residues: 78.2860 Evaluate side-chains 363 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 287 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE 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 248 LEU Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 339 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 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 87 ILE 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 180 ASP 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 123 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 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 134 ASN Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 174 GLN 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 280 LEU 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 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 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: 4.9990 chunk 213 optimal weight: 20.0000 chunk 202 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 190 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN A 598 ASN ** A 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 ASN E 137 GLN F 159 ASN G 249 ASN ** H 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.152735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.131492 restraints weight = 24797.374| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.77 r_work: 0.3238 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 19230 Z= 0.279 Angle : 0.801 13.423 26232 Z= 0.423 Chirality : 0.049 0.340 2972 Planarity : 0.005 0.044 3141 Dihedral : 15.159 150.297 3334 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.37 % Allowed : 12.83 % Favored : 86.80 % Rotamer: Outliers : 4.33 % Allowed : 19.18 % Favored : 76.49 % 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 aren not related in a simple way. whole: -2.07 (0.17), residues: 2167 helix: 0.12 (0.18), residues: 831 sheet: -1.31 (0.28), residues: 308 loop : -2.75 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 171 TYR 0.032 0.002 TYR B 68 PHE 0.022 0.002 PHE A 246 TRP 0.019 0.002 TRP A 732 HIS 0.011 0.002 HIS A 695 Details of bonding type rmsd covalent geometry : bond 0.00628 (19230) covalent geometry : angle 0.80143 (26232) hydrogen bonds : bond 0.04678 ( 692) hydrogen bonds : angle 4.91529 ( 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 369 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 290 time to evaluate : 0.727 Fit side-chains REVERT: A 51 GLN cc_start: 0.7166 (pt0) cc_final: 0.6894 (mp10) REVERT: A 71 TYR cc_start: 0.6319 (m-80) cc_final: 0.5996 (m-10) REVERT: A 78 ASN cc_start: 0.7453 (m-40) cc_final: 0.7136 (m110) REVERT: A 157 LYS cc_start: 0.7864 (tmmm) cc_final: 0.7374 (tppt) REVERT: A 219 LYS cc_start: 0.6556 (mtmt) cc_final: 0.4704 (tttm) REVERT: A 277 ASP cc_start: 0.7417 (m-30) cc_final: 0.7132 (m-30) REVERT: A 414 HIS cc_start: 0.5935 (OUTLIER) cc_final: 0.5345 (m-70) REVERT: A 423 ARG cc_start: 0.7208 (ttm110) cc_final: 0.6845 (ttp80) REVERT: A 679 GLU cc_start: 0.7618 (pm20) cc_final: 0.7369 (mt-10) REVERT: A 715 ARG cc_start: 0.8092 (ttm110) cc_final: 0.7525 (mtm-85) REVERT: B 65 ARG cc_start: 0.7832 (ttp80) cc_final: 0.7513 (mtp180) REVERT: C 4 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7878 (pp) REVERT: C 102 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7524 (ptp90) REVERT: D 180 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7741 (t70) REVERT: E 6 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8580 (pt) REVERT: E 215 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6679 (tm) REVERT: F 103 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8771 (tp) REVERT: F 123 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7616 (mt-10) REVERT: F 136 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8238 (mtm180) REVERT: F 163 VAL cc_start: 0.8129 (t) cc_final: 0.7904 (t) REVERT: F 168 LYS cc_start: 0.8275 (mtmm) cc_final: 0.7947 (mttm) REVERT: G 192 ASP cc_start: 0.7906 (t0) cc_final: 0.7566 (t0) REVERT: H 45 LYS cc_start: 0.8475 (mtpt) cc_final: 0.8129 (mttt) REVERT: H 65 GLN cc_start: 0.7829 (tp-100) cc_final: 0.6964 (tt0) REVERT: H 178 ASP cc_start: 0.5630 (p0) cc_final: 0.5048 (t70) REVERT: H 264 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7235 (pt0) REVERT: H 345 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8288 (mmm) outliers start: 79 outliers final: 62 residues processed: 344 average time/residue: 0.1574 time to fit residues: 80.4985 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 : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 402 GLU Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 469 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 87 ILE 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 180 ASP 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 119 GLU Chi-restraints excluded: chain F residue 123 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 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 134 ASN Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 174 GLN 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 280 LEU 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 125 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 203 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN ** H 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.159321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.137222 restraints weight = 24861.155| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.74 r_work: 0.3332 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19230 Z= 0.170 Angle : 0.705 12.858 26232 Z= 0.373 Chirality : 0.045 0.350 2972 Planarity : 0.004 0.052 3141 Dihedral : 15.058 151.910 3334 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.00 % Favored : 87.68 % Rotamer: Outliers : 4.11 % Allowed : 19.62 % Favored : 76.27 % 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 aren not related in a simple way. whole: -1.93 (0.18), residues: 2167 helix: 0.30 (0.18), residues: 832 sheet: -1.23 (0.28), residues: 308 loop : -2.73 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 121 TYR 0.034 0.002 TYR B 68 PHE 0.017 0.002 PHE A 246 TRP 0.018 0.002 TRP A 732 HIS 0.007 0.001 HIS A 695 Details of bonding type rmsd covalent geometry : bond 0.00371 (19230) covalent geometry : angle 0.70514 (26232) hydrogen bonds : bond 0.03976 ( 692) hydrogen bonds : angle 4.71715 ( 1927) =============================================================================== Job complete usr+sys time: 4381.92 seconds wall clock time: 76 minutes 2.89 seconds (4562.89 seconds total)