Starting phenix.real_space_refine on Sat Sep 12 20:15:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rwn_10043/09_2026/6rwn_10043.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rwn_10043/09_2026/6rwn_10043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6rwn_10043/09_2026/6rwn_10043.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rwn_10043/09_2026/6rwn_10043.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rwn_10043/09_2026/6rwn_10043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rwn_10043/09_2026/6rwn_10043.map" model { file = "/net/cci-nas-00/data/ceres_data/6rwn_10043/09_2026/6rwn_10043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rwn_10043/09_2026/6rwn_10043.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.186 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: 9 Type Number sf(0) Gaussians Zn 8 6.06 5 P 84 5.49 5 Mg 4 5.21 5 S 74 5.16 5 Cl 2 4.86 5 C 11352 2.51 5 N 3278 2.21 5 O 3540 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18346 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2137 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 9, 'TRANS': 260} Chain: "Q" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 470 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "W" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 408 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "E" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 378 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 566 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "L" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1641 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 1 Chain: "K" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1518 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain breaks: 2 Chain: "J" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2014 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 7, 'TRANS': 244} Chain breaks: 2 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 34 Unusual residues: {' CL': 1, ' MG': 2, ' ZN': 1, 'DLU': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 335 SG CYS A 40 80.008 61.992 31.717 1.00 9.39 S ATOM 357 SG CYS A 43 76.922 63.959 33.090 1.00 10.07 S ATOM 3350 SG CYS E 40 92.377 40.886 54.089 1.00 26.92 S ATOM 3372 SG CYS E 43 94.483 42.719 56.858 1.00 33.31 S ATOM 5904 SG CYS K 40 23.599 48.297 22.341 1.00 46.00 S ATOM 5926 SG CYS K 43 25.607 45.727 24.538 1.00 40.43 S ATOM 7449 SG CYS J 40 58.498 30.261 59.675 1.00 35.26 S ATOM 7471 SG CYS J 43 56.734 31.887 56.596 1.00 40.77 S Restraints were copied for chains: I, S, T, M, F, D, C, B Time building chain proxies: 3.72, per 1000 atoms: 0.20 Number of scatterers: 18346 At special positions: 0 Unit cell: (131.1, 175.26, 100.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 8 29.99 Cl 2 17.00 S 74 16.00 P 84 15.00 Mg 4 11.99 F 4 9.00 O 3540 8.00 N 3278 7.00 C 11352 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: 1.36 Conformation dependent library (CDL) restraints added in 792.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 40 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 43 " pdb=" ZN B 500 " pdb="ZN ZN B 500 " - pdb=" NE2 HIS B 12 " pdb="ZN ZN B 500 " - pdb=" ND1 HIS B 16 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 43 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 40 " pdb=" ZN C 500 " pdb="ZN ZN C 500 " - pdb=" NE2 HIS C 12 " pdb="ZN ZN C 500 " - pdb=" ND1 HIS C 16 " pdb="ZN ZN C 500 " - pdb=" SG CYS C 40 " pdb="ZN ZN C 500 " - pdb=" SG CYS C 43 " pdb=" ZN E 500 " pdb="ZN ZN E 500 " - pdb=" ND1 HIS E 16 " pdb="ZN ZN E 500 " - pdb=" NE2 HIS E 12 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 43 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 40 " pdb=" ZN I 301 " pdb="ZN ZN I 301 " - pdb=" NE2 HIS I 12 " pdb="ZN ZN I 301 " - pdb=" ND1 HIS I 16 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 40 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 43 " pdb=" ZN J 500 " pdb="ZN ZN J 500 " - pdb=" NE2 HIS J 12 " pdb="ZN ZN J 500 " - pdb=" ND1 HIS J 16 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 43 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 40 " pdb=" ZN K 500 " pdb="ZN ZN K 500 " - pdb=" NE2 HIS K 12 " pdb="ZN ZN K 500 " - pdb=" ND1 HIS K 16 " pdb="ZN ZN K 500 " - pdb=" SG CYS K 40 " pdb="ZN ZN K 500 " - pdb=" SG CYS K 43 " pdb=" ZN M 500 " pdb="ZN ZN M 500 " - pdb=" ND1 HIS M 16 " pdb="ZN ZN M 500 " - pdb=" NE2 HIS M 12 " pdb="ZN ZN M 500 " - pdb=" SG CYS M 43 " pdb="ZN ZN M 500 " - pdb=" SG CYS M 40 " Number of angles added : 10 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3864 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 20 sheets defined 50.0% alpha, 18.6% beta 32 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 1 through 16 Processing helix chain 'A' and resid 18 through 26 removed outlier: 3.582A pdb=" N MET A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 39 Processing helix chain 'A' and resid 93 through 108 removed outlier: 3.930A pdb=" N THR A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 148 through 165 removed outlier: 3.684A pdb=" N GLU A 152 " --> pdb=" O GLN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 169 removed outlier: 3.531A pdb=" N ALA A 169 " --> pdb=" O ARG A 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 166 through 169' Processing helix chain 'A' and resid 171 through 186 removed outlier: 3.789A pdb=" N ALA A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 219 Processing helix chain 'E' and resid 1 through 16 Processing helix chain 'E' and resid 18 through 26 removed outlier: 3.517A pdb=" N MET E 22 " --> pdb=" O ASN E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 39 Processing helix chain 'N' and resid 204 through 219 Processing helix chain 'L' and resid 93 through 108 removed outlier: 3.628A pdb=" N THR L 97 " --> pdb=" O THR L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 134 Processing helix chain 'L' and resid 151 through 165 Processing helix chain 'L' and resid 166 through 169 removed outlier: 3.514A pdb=" N ALA L 169 " --> pdb=" O ARG L 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 166 through 169' Processing helix chain 'L' and resid 171 through 186 removed outlier: 3.671A pdb=" N ALA L 175 " --> pdb=" O LYS L 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 221 removed outlier: 3.528A pdb=" N ARG L 199 " --> pdb=" O SER L 195 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER L 218 " --> pdb=" O GLN L 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 16 Processing helix chain 'K' and resid 18 through 27 removed outlier: 3.531A pdb=" N MET K 22 " --> pdb=" O ASN K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 39 removed outlier: 3.677A pdb=" N ALA K 33 " --> pdb=" O PRO K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 108 removed outlier: 3.929A pdb=" N THR K 97 " --> pdb=" O THR K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 134 Processing helix chain 'K' and resid 150 through 165 Processing helix chain 'K' and resid 166 through 169 removed outlier: 3.572A pdb=" N ALA K 169 " --> pdb=" O ARG K 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 166 through 169' Processing helix chain 'K' and resid 171 through 186 removed outlier: 3.738A pdb=" N ALA K 175 " --> pdb=" O LYS K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 217 Processing helix chain 'J' and resid 2 through 16 Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 29 through 39 Processing helix chain 'J' and resid 40 through 44 removed outlier: 3.579A pdb=" N CYS J 43 " --> pdb=" O CYS J 40 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN J 44 " --> pdb=" O PRO J 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 40 through 44' Processing helix chain 'J' and resid 93 through 108 removed outlier: 3.796A pdb=" N THR J 97 " --> pdb=" O THR J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 134 Processing helix chain 'J' and resid 151 through 165 Processing helix chain 'J' and resid 166 through 169 Processing helix chain 'J' and resid 171 through 186 removed outlier: 3.856A pdb=" N ALA J 175 " --> pdb=" O LYS J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 221 removed outlier: 3.651A pdb=" N ARG J 199 " --> pdb=" O SER J 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 16 Processing helix chain 'I' and resid 18 through 26 removed outlier: 3.582A pdb=" N MET I 22 " --> pdb=" O ASN I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 39 Processing helix chain 'I' and resid 93 through 108 removed outlier: 3.930A pdb=" N THR I 97 " --> pdb=" O THR I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 134 Processing helix chain 'I' and resid 148 through 165 removed outlier: 3.684A pdb=" N GLU I 152 " --> pdb=" O GLN I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 169 removed outlier: 3.531A pdb=" N ALA I 169 " --> pdb=" O ARG I 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 166 through 169' Processing helix chain 'I' and resid 171 through 186 removed outlier: 3.789A pdb=" N ALA I 175 " --> pdb=" O LYS I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 219 Processing helix chain 'M' and resid 1 through 16 Processing helix chain 'M' and resid 18 through 26 removed outlier: 3.518A pdb=" N MET M 22 " --> pdb=" O ASN M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 39 Processing helix chain 'F' and resid 204 through 219 Processing helix chain 'D' and resid 93 through 108 removed outlier: 3.628A pdb=" N THR D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 134 Processing helix chain 'D' and resid 151 through 165 Processing helix chain 'D' and resid 166 through 169 removed outlier: 3.515A pdb=" N ALA D 169 " --> pdb=" O ARG D 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 166 through 169' Processing helix chain 'D' and resid 171 through 186 removed outlier: 3.670A pdb=" N ALA D 175 " --> pdb=" O LYS D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 221 removed outlier: 3.529A pdb=" N ARG D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 16 Processing helix chain 'C' and resid 18 through 27 removed outlier: 3.531A pdb=" N MET C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 39 removed outlier: 3.677A pdb=" N ALA C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 108 removed outlier: 3.929A pdb=" N THR C 97 " --> pdb=" O THR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 150 through 165 Processing helix chain 'C' and resid 166 through 169 removed outlier: 3.572A pdb=" N ALA C 169 " --> pdb=" O ARG C 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 166 through 169' Processing helix chain 'C' and resid 171 through 186 removed outlier: 3.738A pdb=" N ALA C 175 " --> pdb=" O LYS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 217 Processing helix chain 'B' and resid 2 through 16 Processing helix chain 'B' and resid 18 through 26 Processing helix chain 'B' and resid 29 through 39 Processing helix chain 'B' and resid 40 through 44 removed outlier: 3.579A pdb=" N CYS B 43 " --> pdb=" O CYS B 40 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN B 44 " --> pdb=" O PRO B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 44' Processing helix chain 'B' and resid 93 through 108 removed outlier: 3.796A pdb=" N THR B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 151 through 165 Processing helix chain 'B' and resid 166 through 169 Processing helix chain 'B' and resid 171 through 186 removed outlier: 3.855A pdb=" N ALA B 175 " --> pdb=" O LYS B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 221 removed outlier: 3.652A pdb=" N ARG B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 89 removed outlier: 4.244A pdb=" N VAL A 72 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 256 through 261 removed outlier: 7.434A pdb=" N ALA A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LYS A 244 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL A 250 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 234 through 235 removed outlier: 3.933A pdb=" N GLN N 234 " --> pdb=" O GLU N 229 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU N 229 " --> pdb=" O GLN N 234 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 240 through 244 removed outlier: 6.738A pdb=" N VAL N 250 " --> pdb=" O ILE N 242 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LYS N 244 " --> pdb=" O ALA N 248 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ALA N 248 " --> pdb=" O LYS N 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 83 through 89 removed outlier: 4.027A pdb=" N VAL L 72 " --> pdb=" O LEU L 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 257 through 261 removed outlier: 7.004A pdb=" N ALA L 248 " --> pdb=" O LYS L 244 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS L 244 " --> pdb=" O ALA L 248 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL L 250 " --> pdb=" O ILE L 242 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 83 through 89 removed outlier: 4.057A pdb=" N VAL K 72 " --> pdb=" O LEU K 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 83 through 89 removed outlier: 4.308A pdb=" N VAL J 72 " --> pdb=" O LEU J 89 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 223 through 227 Processing sheet with id=AB1, first strand: chain 'J' and resid 240 through 244 removed outlier: 6.788A pdb=" N VAL J 250 " --> pdb=" O ILE J 242 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LYS J 244 " --> pdb=" O ALA J 248 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ALA J 248 " --> pdb=" O LYS J 244 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 83 through 89 removed outlier: 4.244A pdb=" N VAL I 72 " --> pdb=" O LEU I 89 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 256 through 261 removed outlier: 7.434A pdb=" N ALA I 248 " --> pdb=" O LYS I 244 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LYS I 244 " --> pdb=" O ALA I 248 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL I 250 " --> pdb=" O ILE I 242 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 234 through 235 removed outlier: 3.933A pdb=" N GLN F 234 " --> pdb=" O GLU F 229 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU F 229 " --> pdb=" O GLN F 234 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 240 through 244 removed outlier: 6.738A pdb=" N VAL F 250 " --> pdb=" O ILE F 242 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LYS F 244 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ALA F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 83 through 89 removed outlier: 4.027A pdb=" N VAL D 72 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 257 through 261 removed outlier: 7.004A pdb=" N ALA D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS D 244 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL D 250 " --> pdb=" O ILE D 242 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 83 through 89 removed outlier: 4.058A pdb=" N VAL C 72 " --> pdb=" O LEU C 89 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 83 through 89 removed outlier: 4.307A pdb=" N VAL B 72 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 223 through 227 Processing sheet with id=AC2, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.788A pdb=" N VAL B 250 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LYS B 244 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA B 248 " --> pdb=" O LYS B 244 " (cutoff:3.500A) 978 hydrogen bonds defined for protein. 2820 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4443 1.33 - 1.45: 4073 1.45 - 1.57: 10086 1.57 - 1.69: 166 1.69 - 1.81: 108 Bond restraints: 18876 Sorted by residual: bond pdb=" CAN DLU I 303 " pdb=" CAV DLU I 303 " ideal model delta sigma weight residual 1.505 1.383 0.122 2.00e-02 2.50e+03 3.75e+01 bond pdb=" CAN DLU A 303 " pdb=" CAV DLU A 303 " ideal model delta sigma weight residual 1.505 1.383 0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" CAR DLU A 303 " pdb=" CAX DLU A 303 " ideal model delta sigma weight residual 1.491 1.388 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" CAR DLU I 303 " pdb=" CAX DLU I 303 " ideal model delta sigma weight residual 1.491 1.389 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" CAS DLU I 303 " pdb=" CAY DLU I 303 " ideal model delta sigma weight residual 1.491 1.391 0.100 2.00e-02 2.50e+03 2.48e+01 ... (remaining 18871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 24949 1.59 - 3.18: 861 3.18 - 4.77: 56 4.77 - 6.36: 6 6.36 - 7.95: 2 Bond angle restraints: 25874 Sorted by residual: angle pdb=" N3 DT W 17 " pdb=" C4 DT W 17 " pdb=" O4 DT W 17 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.09e+01 angle pdb=" N3 DT T 17 " pdb=" C4 DT T 17 " pdb=" O4 DT T 17 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT S 7 " pdb=" C4 DT S 7 " pdb=" O4 DT S 7 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT S 13 " pdb=" C4 DT S 13 " pdb=" O4 DT S 13 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT S 4 " pdb=" C4 DT S 4 " pdb=" O4 DT S 4 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 ... (remaining 25869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.12: 10319 26.12 - 52.25: 681 52.25 - 78.37: 104 78.37 - 104.49: 16 104.49 - 130.62: 2 Dihedral angle restraints: 11122 sinusoidal: 5164 harmonic: 5958 Sorted by residual: dihedral pdb=" CAM DLU A 303 " pdb=" CAL DLU A 303 " pdb=" OAQ DLU A 303 " pdb=" CBB DLU A 303 " ideal model delta sinusoidal sigma weight residual -69.82 60.80 -130.62 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" CAM DLU I 303 " pdb=" CAL DLU I 303 " pdb=" OAQ DLU I 303 " pdb=" CBB DLU I 303 " ideal model delta sinusoidal sigma weight residual -69.82 60.74 -130.56 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" CA TYR I 194 " pdb=" C TYR I 194 " pdb=" N SER I 195 " pdb=" CA SER I 195 " ideal model delta harmonic sigma weight residual 180.00 160.87 19.13 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 11119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1608 0.034 - 0.069: 862 0.069 - 0.103: 256 0.103 - 0.137: 102 0.137 - 0.172: 22 Chirality restraints: 2850 Sorted by residual: chirality pdb=" CBA DLU I 303 " pdb=" CAA DLU I 303 " pdb=" CAM DLU I 303 " pdb=" NBC DLU I 303 " both_signs ideal model delta sigma weight residual False 2.49 2.66 -0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CBA DLU A 303 " pdb=" CAA DLU A 303 " pdb=" CAM DLU A 303 " pdb=" NBC DLU A 303 " both_signs ideal model delta sigma weight residual False 2.49 2.66 -0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA ILE K 28 " pdb=" N ILE K 28 " pdb=" C ILE K 28 " pdb=" CB ILE K 28 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 2847 not shown) Planarity restraints: 3014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAS DLU I 303 " -0.009 2.00e-02 2.50e+03 3.15e-02 1.49e+01 pdb=" CAY DLU I 303 " 0.011 2.00e-02 2.50e+03 pdb=" CBA DLU I 303 " 0.024 2.00e-02 2.50e+03 pdb=" CBB DLU I 303 " 0.025 2.00e-02 2.50e+03 pdb=" NBC DLU I 303 " -0.066 2.00e-02 2.50e+03 pdb=" OAC DLU I 303 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAS DLU A 303 " -0.007 2.00e-02 2.50e+03 3.09e-02 1.43e+01 pdb=" CAY DLU A 303 " 0.011 2.00e-02 2.50e+03 pdb=" CBA DLU A 303 " 0.023 2.00e-02 2.50e+03 pdb=" CBB DLU A 303 " 0.025 2.00e-02 2.50e+03 pdb=" NBC DLU A 303 " -0.065 2.00e-02 2.50e+03 pdb=" OAC DLU A 303 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 260 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO D 261 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 261 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 261 " 0.029 5.00e-02 4.00e+02 ... (remaining 3011 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 118 2.60 - 3.17: 13056 3.17 - 3.75: 26058 3.75 - 4.32: 37165 4.32 - 4.90: 62015 Nonbonded interactions: 138412 Sorted by model distance: nonbonded pdb=" OAD DLU A 303 " pdb="MG MG A 305 " model vdw 2.021 2.170 nonbonded pdb=" OE2 GLU I 152 " pdb="MG MG I 305 " model vdw 2.022 2.170 nonbonded pdb="MG MG A 305 " pdb=" O HOH A 403 " model vdw 2.023 2.170 nonbonded pdb="MG MG I 305 " pdb=" O HOH I 402 " model vdw 2.025 2.170 nonbonded pdb=" OAD DLU I 303 " pdb="MG MG I 305 " model vdw 2.028 2.170 ... (remaining 138407 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'W' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'N' selection = chain 'F' } ncs_group { reference = chain 'L' selection = chain 'D' } ncs_group { reference = chain 'K' selection = chain 'C' } ncs_group { reference = chain 'J' selection = chain 'B' } 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: 4.170 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.810 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.007 0.176 18908 Z= 0.353 Angle : 0.655 7.946 25884 Z= 0.452 Chirality : 0.048 0.172 2850 Planarity : 0.005 0.052 3014 Dihedral : 16.964 130.617 7258 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.66 % Allowed : 3.78 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.15), residues: 2032 helix: -1.84 (0.12), residues: 944 sheet: 0.02 (0.22), residues: 440 loop : -3.41 (0.18), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 199 TYR 0.012 0.001 TYR A 83 PHE 0.012 0.001 PHE M 1 TRP 0.012 0.001 TRP I 19 HIS 0.004 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.33 (18876) covalent geometry : angle 0.64338 / 0.45 (25874) hydrogen bonds : bond 0.13609 / 9.13 ( 1056) hydrogen bonds : angle 6.45933 / 4.51 ( 2976) metal coordination : bond 0.12049 / 7.65 ( 32) metal coordination : angle 6.25366 / 3.52 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 343 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8395 (m-40) REVERT: E 3 ASP cc_start: 0.6556 (OUTLIER) cc_final: 0.6157 (m-30) REVERT: N 271 TYR cc_start: 0.8002 (t80) cc_final: 0.7601 (t80) REVERT: L 154 MET cc_start: 0.7117 (mmt) cc_final: 0.6873 (mmp) REVERT: L 171 LYS cc_start: 0.7352 (mttt) cc_final: 0.6936 (mttp) REVERT: K 42 LYS cc_start: 0.8590 (mmmt) cc_final: 0.8138 (mmtp) REVERT: K 63 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7234 (ttm) REVERT: K 131 TRP cc_start: 0.7692 (t60) cc_final: 0.7484 (t60) REVERT: K 154 MET cc_start: 0.7996 (mmt) cc_final: 0.7711 (mmt) REVERT: J 11 GLU cc_start: 0.7428 (tp30) cc_final: 0.7195 (mm-30) REVERT: M 15 TYR cc_start: 0.8310 (m-80) cc_final: 0.7946 (m-80) REVERT: F 251 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8824 (pt) REVERT: D 154 MET cc_start: 0.7147 (mmt) cc_final: 0.6881 (mmp) REVERT: C 42 LYS cc_start: 0.8618 (mmmt) cc_final: 0.8344 (mmtp) REVERT: C 63 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7158 (ttm) REVERT: C 134 GLN cc_start: 0.7761 (mt0) cc_final: 0.7508 (mt0) REVERT: B 11 GLU cc_start: 0.7515 (tp30) cc_final: 0.7302 (mm-30) REVERT: B 93 THR cc_start: 0.6842 (t) cc_final: 0.6082 (p) outliers start: 64 outliers final: 14 residues processed: 394 average time/residue: 0.1475 time to fit residues: 85.3395 Evaluate side-chains 265 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 246 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 63 MET Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain M residue 3 ASP Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain B residue 151 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 ASN E 39 GLN L 216 GLN K 18 ASN K 168 GLN J 9 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 155 ASN I 216 GLN M 17 ASN M 39 GLN D 216 GLN C 18 ASN C 168 GLN B 9 GLN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.159814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.128496 restraints weight = 20958.586| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.90 r_work: 0.3033 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18908 Z= 0.158 Angle : 0.552 7.640 25884 Z= 0.314 Chirality : 0.044 0.139 2850 Planarity : 0.005 0.047 3014 Dihedral : 18.605 87.184 3260 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.83 % Allowed : 8.92 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.17), residues: 2032 helix: 0.96 (0.16), residues: 958 sheet: 0.49 (0.23), residues: 440 loop : -3.11 (0.20), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 263 TYR 0.016 0.002 TYR E 15 PHE 0.011 0.001 PHE A 26 TRP 0.013 0.001 TRP A 19 HIS 0.007 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (18876) covalent geometry : angle 0.54865 / 0.31 (25874) hydrogen bonds : bond 0.06420 / 4.36 ( 1056) hydrogen bonds : angle 4.86908 / 3.41 ( 2976) metal coordination : bond 0.01281 / 0.82 ( 32) metal coordination : angle 3.14711 / 1.65 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 243 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 22 MET cc_start: 0.8482 (mtm) cc_final: 0.8226 (mtm) REVERT: N 228 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8506 (ttp-170) REVERT: L 154 MET cc_start: 0.7742 (mmt) cc_final: 0.7342 (mmt) REVERT: K 42 LYS cc_start: 0.8557 (mmmt) cc_final: 0.7897 (mmtp) REVERT: K 63 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7861 (ttm) REVERT: K 154 MET cc_start: 0.8211 (mmt) cc_final: 0.7868 (mmt) REVERT: F 228 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8497 (ttp-170) REVERT: D 154 MET cc_start: 0.7695 (mmt) cc_final: 0.7317 (mmt) REVERT: B 11 GLU cc_start: 0.7896 (tp30) cc_final: 0.7670 (mm-30) outliers start: 32 outliers final: 24 residues processed: 264 average time/residue: 0.1433 time to fit residues: 56.0145 Evaluate side-chains 228 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 228 ARG Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 63 MET Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 228 ARG Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain B residue 206 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 82 optimal weight: 7.9990 chunk 209 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 202 optimal weight: 0.1980 chunk 17 optimal weight: 3.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.157858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.126219 restraints weight = 21007.052| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.93 r_work: 0.3015 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18908 Z= 0.175 Angle : 0.542 7.498 25884 Z= 0.308 Chirality : 0.044 0.141 2850 Planarity : 0.004 0.047 3014 Dihedral : 18.721 87.529 3243 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.77 % Allowed : 10.93 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2032 helix: 1.74 (0.16), residues: 960 sheet: 0.61 (0.23), residues: 436 loop : -2.94 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 263 TYR 0.015 0.002 TYR A 194 PHE 0.017 0.002 PHE M 1 TRP 0.016 0.001 TRP B 19 HIS 0.005 0.001 HIS J 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (18876) covalent geometry : angle 0.53531 / 0.31 (25874) hydrogen bonds : bond 0.06466 / 4.40 ( 1056) hydrogen bonds : angle 4.60867 / 3.22 ( 2976) metal coordination : bond 0.01383 / 0.91 ( 32) metal coordination : angle 4.21957 / 2.31 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7854 (mmtt) cc_final: 0.7414 (mptt) REVERT: E 22 MET cc_start: 0.8499 (mtm) cc_final: 0.8279 (mtm) REVERT: N 271 TYR cc_start: 0.7907 (t80) cc_final: 0.7644 (t80) REVERT: L 154 MET cc_start: 0.7914 (mmt) cc_final: 0.7647 (mmp) REVERT: K 63 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8141 (ttm) REVERT: K 154 MET cc_start: 0.8307 (mmt) cc_final: 0.7940 (mmt) REVERT: J 11 GLU cc_start: 0.7909 (tp30) cc_final: 0.7621 (mm-30) REVERT: I 264 LYS cc_start: 0.7686 (mmtt) cc_final: 0.7291 (mptt) REVERT: M 45 VAL cc_start: 0.8343 (OUTLIER) cc_final: 0.8059 (t) REVERT: F 271 TYR cc_start: 0.7915 (t80) cc_final: 0.7703 (t80) REVERT: D 154 MET cc_start: 0.7791 (mmt) cc_final: 0.7360 (mmt) REVERT: B 11 GLU cc_start: 0.7932 (tp30) cc_final: 0.7646 (mm-30) REVERT: B 266 LYS cc_start: 0.7053 (ptpt) cc_final: 0.6848 (ptpt) outliers start: 31 outliers final: 28 residues processed: 233 average time/residue: 0.1427 time to fit residues: 49.8373 Evaluate side-chains 230 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 63 MET Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 206 SER Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 206 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 72 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 176 optimal weight: 0.2980 chunk 156 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 252 GLN L 233 GLN K 112 HIS J 39 GLN F 252 GLN ** B 39 GLN ** 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 = 0.3797 r_free = 0.3797 target = 0.160061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.130664 restraints weight = 21019.218| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.84 r_work: 0.3061 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18908 Z= 0.128 Angle : 0.486 7.324 25884 Z= 0.278 Chirality : 0.042 0.143 2850 Planarity : 0.004 0.043 3014 Dihedral : 18.730 88.393 3239 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.17 % Allowed : 11.73 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.19), residues: 2032 helix: 2.17 (0.17), residues: 958 sheet: 0.68 (0.23), residues: 446 loop : -2.67 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 231 TYR 0.012 0.001 TYR A 194 PHE 0.012 0.001 PHE N 223 TRP 0.014 0.001 TRP B 19 HIS 0.005 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (18876) covalent geometry : angle 0.47944 / 0.28 (25874) hydrogen bonds : bond 0.05314 / 3.62 ( 1056) hydrogen bonds : angle 4.41508 / 3.08 ( 2976) metal coordination : bond 0.00996 / 0.65 ( 32) metal coordination : angle 4.12012 / 2.14 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7696 (mmtt) cc_final: 0.7334 (mptt) REVERT: E 22 MET cc_start: 0.8454 (mtm) cc_final: 0.8192 (mtm) REVERT: E 45 VAL cc_start: 0.8263 (OUTLIER) cc_final: 0.8057 (t) REVERT: N 271 TYR cc_start: 0.7911 (t80) cc_final: 0.7652 (t80) REVERT: L 154 MET cc_start: 0.7852 (mmt) cc_final: 0.7636 (mmt) REVERT: K 63 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.8028 (ttm) REVERT: K 154 MET cc_start: 0.8360 (mmt) cc_final: 0.8036 (mmt) REVERT: J 11 GLU cc_start: 0.7871 (tp30) cc_final: 0.7590 (mm-30) REVERT: J 221 GLN cc_start: 0.8142 (mt0) cc_final: 0.7462 (mm-40) REVERT: I 264 LYS cc_start: 0.7640 (mmtt) cc_final: 0.7337 (mptt) REVERT: M 45 VAL cc_start: 0.8320 (OUTLIER) cc_final: 0.8056 (t) REVERT: F 251 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.8953 (pp) REVERT: F 271 TYR cc_start: 0.7906 (t80) cc_final: 0.7706 (t80) REVERT: D 63 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.7897 (mtm) REVERT: D 154 MET cc_start: 0.7732 (mmt) cc_final: 0.7481 (mmp) REVERT: B 11 GLU cc_start: 0.7869 (tp30) cc_final: 0.7605 (mm-30) REVERT: B 136 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7360 (mt-10) REVERT: B 221 GLN cc_start: 0.8040 (mt0) cc_final: 0.7559 (mm-40) outliers start: 38 outliers final: 25 residues processed: 248 average time/residue: 0.1435 time to fit residues: 52.9407 Evaluate side-chains 243 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 63 MET Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 206 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 23 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 165 optimal weight: 0.0270 chunk 168 optimal weight: 0.0970 chunk 19 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 182 optimal weight: 1.9990 overall best weight: 1.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 GLN ** 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 = 0.3801 r_free = 0.3801 target = 0.160403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.127428 restraints weight = 20840.175| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.02 r_work: 0.2974 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 18908 Z= 0.128 Angle : 0.480 7.272 25884 Z= 0.274 Chirality : 0.042 0.141 2850 Planarity : 0.004 0.040 3014 Dihedral : 18.701 88.967 3239 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.06 % Allowed : 12.36 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.19), residues: 2032 helix: 2.34 (0.17), residues: 958 sheet: 0.71 (0.23), residues: 446 loop : -2.58 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 231 TYR 0.012 0.001 TYR A 194 PHE 0.008 0.001 PHE E 1 TRP 0.014 0.001 TRP B 19 HIS 0.004 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (18876) covalent geometry : angle 0.47300 / 0.27 (25874) hydrogen bonds : bond 0.05225 / 3.55 ( 1056) hydrogen bonds : angle 4.31819 / 3.01 ( 2976) metal coordination : bond 0.00920 / 0.59 ( 32) metal coordination : angle 4.11066 / 2.21 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 22 MET cc_start: 0.8561 (mtm) cc_final: 0.8298 (mtm) REVERT: E 45 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8170 (t) REVERT: N 271 TYR cc_start: 0.8012 (t80) cc_final: 0.7777 (t80) REVERT: L 63 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8016 (mtm) REVERT: K 63 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8150 (ttm) REVERT: K 154 MET cc_start: 0.8418 (mmt) cc_final: 0.8112 (mmt) REVERT: J 11 GLU cc_start: 0.8112 (tp30) cc_final: 0.7847 (mm-30) REVERT: J 221 GLN cc_start: 0.8150 (mt0) cc_final: 0.7717 (mm-40) REVERT: I 264 LYS cc_start: 0.7623 (mmtt) cc_final: 0.7362 (mptt) REVERT: M 45 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8149 (t) REVERT: F 251 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9003 (pp) REVERT: F 271 TYR cc_start: 0.8037 (t80) cc_final: 0.7827 (t80) REVERT: D 63 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8030 (mtm) REVERT: D 154 MET cc_start: 0.7734 (mmt) cc_final: 0.7454 (mmt) REVERT: B 11 GLU cc_start: 0.8071 (tp30) cc_final: 0.7818 (mm-30) REVERT: B 22 MET cc_start: 0.9051 (mtm) cc_final: 0.8846 (mtp) REVERT: B 221 GLN cc_start: 0.8154 (mt0) cc_final: 0.7644 (mm-40) outliers start: 36 outliers final: 28 residues processed: 233 average time/residue: 0.1446 time to fit residues: 50.3607 Evaluate side-chains 238 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain L residue 63 MET Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 63 MET Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 266 LYS Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 206 SER Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 206 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 152 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 115 optimal weight: 0.1980 chunk 122 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN D 233 GLN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.159800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.126343 restraints weight = 20855.856| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.07 r_work: 0.2976 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18908 Z= 0.142 Angle : 0.485 7.287 25884 Z= 0.276 Chirality : 0.042 0.141 2850 Planarity : 0.004 0.041 3014 Dihedral : 18.706 89.076 3239 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.40 % Allowed : 12.01 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.19), residues: 2032 helix: 2.41 (0.17), residues: 958 sheet: 0.78 (0.24), residues: 440 loop : -2.56 (0.22), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 231 TYR 0.013 0.001 TYR A 194 PHE 0.013 0.001 PHE E 1 TRP 0.014 0.001 TRP J 19 HIS 0.004 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (18876) covalent geometry : angle 0.47873 / 0.28 (25874) hydrogen bonds : bond 0.05451 / 3.71 ( 1056) hydrogen bonds : angle 4.29432 / 2.99 ( 2976) metal coordination : bond 0.00933 / 0.59 ( 32) metal coordination : angle 4.03326 / 2.16 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 210 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 22 MET cc_start: 0.8568 (mtm) cc_final: 0.8316 (mtm) REVERT: N 271 TYR cc_start: 0.7957 (t80) cc_final: 0.7732 (t80) REVERT: L 63 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8026 (mtm) REVERT: L 158 LEU cc_start: 0.7163 (mm) cc_final: 0.6800 (mm) REVERT: K 63 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8127 (ttm) REVERT: K 154 MET cc_start: 0.8460 (mmt) cc_final: 0.8153 (mmt) REVERT: J 11 GLU cc_start: 0.8089 (tp30) cc_final: 0.7867 (mm-30) REVERT: J 22 MET cc_start: 0.9071 (mtm) cc_final: 0.8863 (mtp) REVERT: J 221 GLN cc_start: 0.8102 (mt0) cc_final: 0.7689 (mm-40) REVERT: I 264 LYS cc_start: 0.7604 (mmtt) cc_final: 0.7371 (mptt) REVERT: M 45 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8201 (t) REVERT: F 251 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.9003 (pp) REVERT: F 271 TYR cc_start: 0.8029 (t80) cc_final: 0.7826 (t80) REVERT: C 7 LYS cc_start: 0.6252 (mtmt) cc_final: 0.5971 (pttt) REVERT: B 11 GLU cc_start: 0.8049 (tp30) cc_final: 0.7842 (mm-30) REVERT: B 221 GLN cc_start: 0.8085 (mt0) cc_final: 0.7672 (mm-40) outliers start: 42 outliers final: 31 residues processed: 237 average time/residue: 0.1360 time to fit residues: 48.7074 Evaluate side-chains 238 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain L residue 63 MET Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 63 MET Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 206 SER Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 206 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 12 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 29 optimal weight: 30.0000 chunk 52 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 252 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN ** B 39 GLN ** 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 = 0.3809 r_free = 0.3809 target = 0.161073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.127701 restraints weight = 21037.608| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.08 r_work: 0.3072 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18908 Z= 0.119 Angle : 0.467 6.989 25884 Z= 0.266 Chirality : 0.042 0.145 2850 Planarity : 0.004 0.050 3014 Dihedral : 18.662 89.579 3238 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.12 % Allowed : 12.24 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.19), residues: 2032 helix: 2.55 (0.17), residues: 958 sheet: 0.72 (0.24), residues: 442 loop : -2.42 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 231 TYR 0.012 0.001 TYR A 194 PHE 0.008 0.001 PHE M 1 TRP 0.014 0.001 TRP J 19 HIS 0.004 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (18876) covalent geometry : angle 0.46032 / 0.27 (25874) hydrogen bonds : bond 0.04927 / 3.35 ( 1056) hydrogen bonds : angle 4.23089 / 2.95 ( 2976) metal coordination : bond 0.00920 / 0.60 ( 32) metal coordination : angle 3.93023 / 2.07 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 22 MET cc_start: 0.8477 (mtm) cc_final: 0.8274 (mtm) REVERT: N 271 TYR cc_start: 0.7842 (t80) cc_final: 0.7630 (t80) REVERT: L 63 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7907 (mtm) REVERT: K 154 MET cc_start: 0.8326 (mmt) cc_final: 0.8028 (mmt) REVERT: K 178 MET cc_start: 0.8609 (mtp) cc_final: 0.8336 (mtt) REVERT: J 221 GLN cc_start: 0.7931 (mt0) cc_final: 0.7566 (mm-40) REVERT: D 63 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7906 (mtm) REVERT: C 178 MET cc_start: 0.8619 (mtp) cc_final: 0.8347 (mtt) REVERT: B 221 GLN cc_start: 0.8022 (mt0) cc_final: 0.7601 (mm-40) outliers start: 37 outliers final: 29 residues processed: 240 average time/residue: 0.1442 time to fit residues: 51.3035 Evaluate side-chains 245 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain L residue 63 MET Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 266 LYS Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 206 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 141 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 201 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** B 39 GLN ** 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 = 0.3797 r_free = 0.3797 target = 0.159870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.131351 restraints weight = 20952.157| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.70 r_work: 0.3064 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18908 Z= 0.147 Angle : 0.490 6.781 25884 Z= 0.278 Chirality : 0.043 0.144 2850 Planarity : 0.004 0.044 3014 Dihedral : 18.649 89.310 3234 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.17 % Allowed : 12.36 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.19), residues: 2032 helix: 2.53 (0.17), residues: 958 sheet: 0.72 (0.24), residues: 446 loop : -2.44 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 231 TYR 0.014 0.001 TYR A 194 PHE 0.010 0.001 PHE E 1 TRP 0.015 0.001 TRP B 19 HIS 0.004 0.001 HIS B 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (18876) covalent geometry : angle 0.48515 / 0.28 (25874) hydrogen bonds : bond 0.05488 / 3.73 ( 1056) hydrogen bonds : angle 4.25035 / 2.96 ( 2976) metal coordination : bond 0.00929 / 0.61 ( 32) metal coordination : angle 3.67692 / 1.99 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 271 TYR cc_start: 0.7857 (t80) cc_final: 0.7657 (t80) REVERT: L 63 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7902 (mtm) REVERT: K 154 MET cc_start: 0.8376 (mmt) cc_final: 0.8080 (mmt) REVERT: K 178 MET cc_start: 0.8600 (mtp) cc_final: 0.8387 (mtt) REVERT: J 221 GLN cc_start: 0.7947 (mt0) cc_final: 0.7587 (mm-40) REVERT: F 251 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.8972 (pp) REVERT: F 271 TYR cc_start: 0.7820 (t80) cc_final: 0.7582 (t80) REVERT: D 63 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7926 (mtm) REVERT: C 178 MET cc_start: 0.8620 (mtp) cc_final: 0.8409 (mtt) REVERT: B 221 GLN cc_start: 0.7702 (mt0) cc_final: 0.7458 (mm-40) outliers start: 38 outliers final: 33 residues processed: 237 average time/residue: 0.1478 time to fit residues: 52.2198 Evaluate side-chains 242 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain L residue 63 MET Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 206 SER Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 206 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 200 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 149 optimal weight: 20.0000 chunk 176 optimal weight: 0.4980 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** B 39 GLN ** 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 = 0.3789 r_free = 0.3789 target = 0.158969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.130153 restraints weight = 20801.746| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.76 r_work: 0.3054 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18908 Z= 0.144 Angle : 0.491 6.765 25884 Z= 0.278 Chirality : 0.043 0.148 2850 Planarity : 0.004 0.043 3014 Dihedral : 18.664 89.033 3234 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.17 % Allowed : 12.64 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.19), residues: 2032 helix: 2.53 (0.17), residues: 960 sheet: 0.77 (0.24), residues: 446 loop : -2.42 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 231 TYR 0.014 0.001 TYR A 194 PHE 0.009 0.001 PHE M 1 TRP 0.016 0.001 TRP B 19 HIS 0.004 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (18876) covalent geometry : angle 0.48595 / 0.28 (25874) hydrogen bonds : bond 0.05458 / 3.71 ( 1056) hydrogen bonds : angle 4.23810 / 2.95 ( 2976) metal coordination : bond 0.00971 / 0.64 ( 32) metal coordination : angle 3.76417 / 2.03 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 63 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7909 (mtm) REVERT: K 39 GLN cc_start: 0.8473 (mm-40) cc_final: 0.7796 (mp10) REVERT: K 154 MET cc_start: 0.8414 (mmt) cc_final: 0.8114 (mmt) REVERT: J 27 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8019 (mm-40) REVERT: J 221 GLN cc_start: 0.7694 (mt0) cc_final: 0.7481 (mm-40) REVERT: F 251 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.8981 (pp) REVERT: F 271 TYR cc_start: 0.7884 (t80) cc_final: 0.7650 (t80) REVERT: D 63 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7922 (mtm) REVERT: C 39 GLN cc_start: 0.8428 (mm-40) cc_final: 0.7776 (mp10) REVERT: C 178 MET cc_start: 0.8620 (mtp) cc_final: 0.8418 (mtt) REVERT: B 27 GLN cc_start: 0.8313 (mm-40) cc_final: 0.8014 (mm-40) outliers start: 38 outliers final: 35 residues processed: 237 average time/residue: 0.1428 time to fit residues: 50.5924 Evaluate side-chains 249 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain L residue 63 MET Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 266 LYS Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 206 SER Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 206 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 46 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 149 optimal weight: 30.0000 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN ** B 39 GLN ** 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 = 0.3774 r_free = 0.3774 target = 0.157777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.128016 restraints weight = 21031.122| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.84 r_work: 0.3012 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 18908 Z= 0.197 Angle : 0.542 7.016 25884 Z= 0.305 Chirality : 0.045 0.149 2850 Planarity : 0.004 0.055 3014 Dihedral : 18.730 87.495 3234 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.23 % Allowed : 12.93 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.19), residues: 2032 helix: 2.41 (0.16), residues: 956 sheet: 0.69 (0.24), residues: 442 loop : -2.46 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 231 TYR 0.017 0.002 TYR A 194 PHE 0.013 0.002 PHE E 1 TRP 0.019 0.002 TRP B 19 HIS 0.005 0.001 HIS B 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (18876) covalent geometry : angle 0.53692 / 0.30 (25874) hydrogen bonds : bond 0.06419 / 4.35 ( 1056) hydrogen bonds : angle 4.33264 / 3.03 ( 2976) metal coordination : bond 0.01057 / 0.71 ( 32) metal coordination : angle 3.87226 / 2.15 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 271 TYR cc_start: 0.7920 (t80) cc_final: 0.7676 (t80) REVERT: L 63 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7945 (mtm) REVERT: K 39 GLN cc_start: 0.8485 (mm-40) cc_final: 0.7814 (mp10) REVERT: K 154 MET cc_start: 0.8446 (mmt) cc_final: 0.8140 (mmt) REVERT: J 27 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8062 (mm-40) REVERT: F 251 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.8992 (pp) REVERT: F 271 TYR cc_start: 0.7916 (t80) cc_final: 0.7687 (t80) REVERT: D 63 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7962 (mtm) REVERT: C 178 MET cc_start: 0.8658 (mtp) cc_final: 0.8426 (mtt) REVERT: B 27 GLN cc_start: 0.8291 (mm-40) cc_final: 0.7978 (mm-40) outliers start: 39 outliers final: 34 residues processed: 240 average time/residue: 0.1476 time to fit residues: 52.6919 Evaluate side-chains 250 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain L residue 63 MET Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 206 SER Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 206 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 62 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 203 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 184 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN ** B 39 GLN ** 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 = 0.3806 r_free = 0.3806 target = 0.160699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.126934 restraints weight = 20935.266| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.93 r_work: 0.2995 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18908 Z= 0.119 Angle : 0.481 7.061 25884 Z= 0.271 Chirality : 0.042 0.159 2850 Planarity : 0.004 0.057 3014 Dihedral : 18.651 88.041 3234 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.06 % Allowed : 13.16 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.19), residues: 2032 helix: 2.60 (0.17), residues: 958 sheet: 0.74 (0.24), residues: 442 loop : -2.35 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 231 TYR 0.012 0.001 TYR A 194 PHE 0.008 0.001 PHE L 100 TRP 0.015 0.001 TRP J 19 HIS 0.004 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (18876) covalent geometry : angle 0.47412 / 0.27 (25874) hydrogen bonds : bond 0.04935 / 3.35 ( 1056) hydrogen bonds : angle 4.22026 / 2.95 ( 2976) metal coordination : bond 0.00958 / 0.64 ( 32) metal coordination : angle 4.00728 / 2.06 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3810.98 seconds wall clock time: 66 minutes 13.80 seconds (3973.80 seconds total)