Starting phenix.real_space_refine on Sun Oct 25 20:14:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rwm_10042/10_2026/6rwm_10042.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rwm_10042/10_2026/6rwm_10042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rwm_10042/10_2026/6rwm_10042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rwm_10042/10_2026/6rwm_10042.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rwm_10042/10_2026/6rwm_10042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rwm_10042/10_2026/6rwm_10042.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6rwm_10042/10_2026/6rwm_10042.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rwm_10042/10_2026/6rwm_10042.cif" } resolution = 2.81 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= 0.172 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 11354 2.51 5 N 3278 2.21 5 O 3640 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18450 Number of models: 1 Model: "" Number of chains: 24 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: "B" 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: "C" 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: "D" 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: "F" 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: "M" 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: "T" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 408 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "S" 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: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {' CL': 1, ' MG': 2, ' ZN': 1, 'KLQ': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "S" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "Q" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Restraints were copied for chains: I, J, K, L, N, E, W, Q List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 335 SG CYS A 40 79.792 61.576 30.481 1.00 17.41 S ATOM 357 SG CYS A 43 76.742 63.586 31.856 1.00 17.29 S ATOM 2468 SG CYS B 40 71.227 142.884 58.209 1.00 47.60 S ATOM 2490 SG CYS B 43 73.085 141.223 55.153 1.00 49.95 S ATOM 4455 SG CYS C 40 106.007 124.964 21.006 1.00 59.27 S ATOM 4477 SG CYS C 43 103.780 127.438 23.073 1.00 53.33 S ATOM 8211 SG CYS M 40 37.412 132.358 52.505 1.00 39.13 S ATOM 8233 SG CYS M 43 35.342 130.439 55.372 1.00 44.52 S ATOM 9467 SG CYS I 40 49.758 111.197 30.545 1.00 17.24 S ATOM 9489 SG CYS I 43 52.809 109.190 31.922 1.00 17.31 S ATOM 11600 SG CYS J 40 58.389 29.873 58.207 1.00 47.92 S ATOM 11622 SG CYS J 43 56.532 31.535 55.151 1.00 49.94 S ATOM 13587 SG CYS K 40 23.626 47.787 20.983 1.00 58.79 S ATOM 13609 SG CYS K 43 25.854 45.313 23.050 1.00 53.12 S ATOM 17343 SG CYS E 40 92.165 40.468 52.549 1.00 39.18 S ATOM 17365 SG CYS E 43 94.229 42.385 55.423 1.00 44.27 S Time building chain proxies: 4.98, per 1000 atoms: 0.27 Number of scatterers: 18450 At special positions: 0 Unit cell: (130.68, 173.88, 98.28, 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 6 9.00 O 3640 8.00 N 3278 7.00 C 11354 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: 1.71 Conformation dependent library (CDL) restraints added in 541.9 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 43 " pdb="ZN ZN C 500 " - pdb=" SG CYS C 40 " 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: 74 helices and 18 sheets defined 49.8% alpha, 19.1% beta 34 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 1 through 16 Processing helix chain 'A' and resid 18 through 26 Processing helix chain 'A' and resid 29 through 39 Processing helix chain 'A' and resid 93 through 108 removed outlier: 3.807A 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: 3.738A pdb=" N GLU A 152 " --> pdb=" O GLN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 169 removed outlier: 3.589A 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: 3.718A 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 '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 93 through 108 removed outlier: 3.710A 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: 3.760A pdb=" N ALA B 175 " --> pdb=" O LYS B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 221 Processing helix chain 'C' and resid 5 through 16 Processing helix chain 'C' and resid 18 through 27 Processing helix chain 'C' and resid 29 through 39 removed outlier: 3.604A pdb=" N ALA C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 108 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: 3.690A 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: 3.587A 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 'D' and resid 93 through 108 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: 3.844A 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: 3.597A pdb=" N ALA D 175 " --> pdb=" O LYS D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 221 removed outlier: 3.526A pdb=" N ARG D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 221 removed outlier: 4.226A pdb=" N GLN F 221 " --> pdb=" O ILE F 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 1 through 16 Processing helix chain 'M' and resid 18 through 27 Processing helix chain 'M' and resid 29 through 40 removed outlier: 3.544A pdb=" N ALA M 33 " --> pdb=" O PRO M 29 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS M 40 " --> pdb=" O ILE M 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 16 Processing helix chain 'I' and resid 18 through 26 Processing helix chain 'I' and resid 29 through 39 Processing helix chain 'I' and resid 93 through 108 removed outlier: 3.807A 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: 3.738A pdb=" N GLU I 152 " --> pdb=" O GLN I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 169 removed outlier: 3.588A 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: 3.717A 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 '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 93 through 108 removed outlier: 3.710A 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: 3.760A pdb=" N ALA J 175 " --> pdb=" O LYS J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 221 Processing helix chain 'K' and resid 5 through 16 Processing helix chain 'K' and resid 18 through 27 Processing helix chain 'K' and resid 29 through 39 removed outlier: 3.603A pdb=" N ALA K 33 " --> pdb=" O PRO K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 108 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: 3.690A 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: 3.586A 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 'L' and resid 93 through 108 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: 3.843A 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: 3.598A pdb=" N ALA L 175 " --> pdb=" O LYS L 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 221 removed outlier: 3.525A pdb=" N ARG L 199 " --> pdb=" O SER L 195 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER L 218 " --> pdb=" O GLN L 214 " (cutoff:3.500A) Processing helix chain 'N' and resid 204 through 221 removed outlier: 4.228A pdb=" N GLN N 221 " --> pdb=" O ILE N 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 16 Processing helix chain 'E' and resid 18 through 27 Processing helix chain 'E' and resid 29 through 40 removed outlier: 3.545A pdb=" N ALA E 33 " --> pdb=" O PRO E 29 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 89 removed outlier: 4.373A 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: 6.343A pdb=" N GLN A 252 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LEU A 241 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 239 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 83 through 89 removed outlier: 4.385A pdb=" N VAL B 72 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 256 through 261 removed outlier: 6.141A pdb=" N GLN B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU B 241 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N PHE B 227 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL B 225 " --> pdb=" O PRO B 238 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N THR B 240 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N PHE B 223 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 89 removed outlier: 4.338A pdb=" N VAL C 72 " --> pdb=" O LEU C 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 83 through 89 removed outlier: 4.226A pdb=" N VAL D 72 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 257 through 261 removed outlier: 5.986A pdb=" N GLN D 252 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LEU D 241 " --> pdb=" O GLN D 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 234 through 236 removed outlier: 3.703A pdb=" N GLN F 234 " --> pdb=" O GLU F 229 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU F 229 " --> pdb=" O GLN F 234 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE F 227 " --> pdb=" O LYS F 236 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 240 through 244 removed outlier: 5.687A pdb=" N LEU F 241 " --> pdb=" O GLN F 252 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLN F 252 " --> pdb=" O LEU F 241 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 83 through 89 removed outlier: 4.373A pdb=" N VAL I 72 " --> pdb=" O LEU I 89 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 256 through 261 removed outlier: 6.342A pdb=" N GLN I 252 " --> pdb=" O LEU I 241 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LEU I 241 " --> pdb=" O GLN I 252 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA I 239 " --> pdb=" O VAL I 225 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 83 through 89 removed outlier: 4.384A pdb=" N VAL J 72 " --> pdb=" O LEU J 89 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 256 through 261 removed outlier: 6.141A pdb=" N GLN J 252 " --> pdb=" O LEU J 241 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU J 241 " --> pdb=" O GLN J 252 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N PHE J 227 " --> pdb=" O LYS J 236 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL J 225 " --> pdb=" O PRO J 238 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N THR J 240 " --> pdb=" O PHE J 223 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N PHE J 223 " --> pdb=" O THR J 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 83 through 89 removed outlier: 4.338A pdb=" N VAL K 72 " --> pdb=" O LEU K 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 83 through 89 removed outlier: 4.226A pdb=" N VAL L 72 " --> pdb=" O LEU L 89 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 257 through 261 removed outlier: 5.986A pdb=" N GLN L 252 " --> pdb=" O LEU L 241 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU L 241 " --> pdb=" O GLN L 252 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 234 through 236 removed outlier: 3.704A pdb=" N GLN N 234 " --> pdb=" O GLU N 229 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU N 229 " --> pdb=" O GLN N 234 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE N 227 " --> pdb=" O LYS N 236 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 240 through 244 removed outlier: 5.688A pdb=" N LEU N 241 " --> pdb=" O GLN N 252 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLN N 252 " --> pdb=" O LEU N 241 " (cutoff:3.500A) 980 hydrogen bonds defined for protein. 2850 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 3.10 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4466 1.33 - 1.46: 4963 1.46 - 1.58: 9183 1.58 - 1.71: 162 1.71 - 1.84: 108 Bond restraints: 18882 Sorted by residual: bond pdb=" C1' DC Q 3 " pdb=" N1 DC Q 3 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.36e+01 bond pdb=" C1' DC S 3 " pdb=" N1 DC S 3 " ideal model delta sigma weight residual 1.468 1.519 -0.051 1.40e-02 5.10e+03 1.31e+01 bond pdb=" C3' DA T 21 " pdb=" C2' DA T 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.48e+00 bond pdb=" C3' DA Q 1 " pdb=" O3' DA Q 1 " ideal model delta sigma weight residual 1.435 1.395 0.040 1.30e-02 5.92e+03 9.44e+00 bond pdb=" C3' DA W 21 " pdb=" C2' DA W 21 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.27e+00 ... (remaining 18877 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 24878 1.85 - 3.70: 942 3.70 - 5.55: 59 5.55 - 7.41: 1 7.41 - 9.26: 6 Bond angle restraints: 25886 Sorted by residual: angle pdb=" N3 DT T 17 " pdb=" C4 DT T 17 " pdb=" O4 DT T 17 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT T 4 " pdb=" C4 DT T 4 " pdb=" O4 DT T 4 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT W 17 " pdb=" C4 DT W 17 " pdb=" O4 DT W 17 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT W 4 " pdb=" C4 DT W 4 " pdb=" O4 DT W 4 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT Q 7 " pdb=" C4 DT Q 7 " pdb=" O4 DT Q 7 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 ... (remaining 25881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 9693 17.36 - 34.71: 910 34.71 - 52.07: 439 52.07 - 69.43: 92 69.43 - 86.79: 10 Dihedral angle restraints: 11144 sinusoidal: 5186 harmonic: 5958 Sorted by residual: dihedral pdb=" CA TYR A 194 " pdb=" C TYR A 194 " pdb=" N SER A 195 " pdb=" CA SER A 195 " ideal model delta harmonic sigma weight residual 180.00 158.10 21.90 0 5.00e+00 4.00e-02 1.92e+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 180.00 158.15 21.85 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA LYS M 14 " pdb=" C LYS M 14 " pdb=" N TYR M 15 " pdb=" CA TYR M 15 " ideal model delta harmonic sigma weight residual 180.00 -159.60 -20.40 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 11141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1574 0.038 - 0.075: 878 0.075 - 0.113: 281 0.113 - 0.150: 89 0.150 - 0.188: 30 Chirality restraints: 2852 Sorted by residual: chirality pdb=" CB ILE B 74 " pdb=" CA ILE B 74 " pdb=" CG1 ILE B 74 " pdb=" CG2 ILE B 74 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CB ILE J 74 " pdb=" CA ILE J 74 " pdb=" CG1 ILE J 74 " pdb=" CG2 ILE J 74 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.56e-01 chirality pdb=" CA ILE L 268 " pdb=" N ILE L 268 " pdb=" C ILE L 268 " pdb=" CB ILE L 268 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.28e-01 ... (remaining 2849 not shown) Planarity restraints: 3012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL I 45 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" C VAL I 45 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL I 45 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS I 46 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 45 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.80e+00 pdb=" C VAL A 45 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL A 45 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS A 46 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 28 " 0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO E 29 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 29 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 29 " 0.031 5.00e-02 4.00e+02 ... (remaining 3009 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 131 2.58 - 3.16: 12952 3.16 - 3.74: 26485 3.74 - 4.32: 39412 4.32 - 4.90: 63934 Nonbonded interactions: 142914 Sorted by model distance: nonbonded pdb="MG MG A 303 " pdb=" OAC KLQ A 304 " model vdw 2.005 2.170 nonbonded pdb="MG MG I 303 " pdb=" OAC KLQ I 304 " model vdw 2.010 2.170 nonbonded pdb="MG MG I 302 " pdb=" O HOH I 404 " model vdw 2.011 2.170 nonbonded pdb="MG MG A 302 " pdb=" O HOH A 403 " model vdw 2.011 2.170 nonbonded pdb="MG MG A 303 " pdb=" O HOH T 103 " model vdw 2.021 2.170 ... (remaining 142909 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'N' } ncs_group { reference = chain 'M' selection = chain 'E' } ncs_group { reference = chain 'T' selection = chain 'W' } ncs_group { reference = chain 'S' selection = chain 'Q' } 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: 5.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.770 Find NCS groups from input model: 0.290 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:7.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.008 0.181 18914 Z= 0.414 Angle : 0.777 9.257 25896 Z= 0.523 Chirality : 0.052 0.188 2852 Planarity : 0.006 0.055 3012 Dihedral : 16.838 86.786 7280 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.20 % Allowed : 5.26 % Favored : 91.53 % 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: -2.80 (0.15), residues: 2032 helix: -1.77 (0.12), residues: 954 sheet: 0.11 (0.23), residues: 446 loop : -3.28 (0.19), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 228 TYR 0.011 0.002 TYR K 83 PHE 0.016 0.002 PHE A 1 TRP 0.014 0.002 TRP E 19 HIS 0.005 0.001 HIS I 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.39 (18882) covalent geometry : angle 0.76861 / 0.52 (25886) hydrogen bonds : bond 0.16273 / 11.12 ( 1062) hydrogen bonds : angle 6.57742 / 4.75 ( 3014) metal coordination : bond 0.12654 / 8.09 ( 32) metal coordination : angle 5.98522 / 3.29 ( 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 373 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 317 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8813 (mtm) cc_final: 0.8449 (mtp) REVERT: B 154 MET cc_start: 0.7468 (mmt) cc_final: 0.7051 (mmt) REVERT: C 62 GLN cc_start: 0.7430 (mt0) cc_final: 0.7126 (mt0) REVERT: C 194 TYR cc_start: 0.6580 (OUTLIER) cc_final: 0.5792 (t80) REVERT: D 234 GLN cc_start: 0.7653 (mt0) cc_final: 0.7410 (mp10) REVERT: M 7 LYS cc_start: 0.8180 (mttt) cc_final: 0.7801 (mtmt) REVERT: M 35 GLU cc_start: 0.7884 (tp30) cc_final: 0.7575 (tp30) REVERT: I 10 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7259 (mt-10) REVERT: I 22 MET cc_start: 0.8936 (mtm) cc_final: 0.8666 (mtp) REVERT: I 50 MET cc_start: 0.8776 (ppp) cc_final: 0.8549 (ppp) REVERT: I 154 MET cc_start: 0.8689 (mmt) cc_final: 0.8283 (mmt) REVERT: J 39 GLN cc_start: 0.7365 (mt0) cc_final: 0.7130 (mm110) REVERT: J 154 MET cc_start: 0.7558 (mmt) cc_final: 0.7302 (mmt) REVERT: J 224 ARG cc_start: 0.7610 (tpp80) cc_final: 0.7076 (mmt-90) REVERT: K 62 GLN cc_start: 0.7511 (mt0) cc_final: 0.7179 (mt0) REVERT: K 194 TYR cc_start: 0.6545 (OUTLIER) cc_final: 0.5549 (t80) REVERT: L 194 TYR cc_start: 0.5764 (m-80) cc_final: 0.5334 (m-80) REVERT: L 234 GLN cc_start: 0.7643 (mt0) cc_final: 0.7407 (mp10) REVERT: E 7 LYS cc_start: 0.8135 (mttt) cc_final: 0.7758 (mtmt) REVERT: E 32 VAL cc_start: 0.8342 (OUTLIER) cc_final: 0.8041 (t) REVERT: E 35 GLU cc_start: 0.7882 (tp30) cc_final: 0.7578 (tp30) outliers start: 56 outliers final: 13 residues processed: 363 average time/residue: 0.7019 time to fit residues: 281.7124 Evaluate side-chains 210 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 194 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain F residue 229 GLU Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 77, 122] chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 GLN A 216 GLN B 9 GLN B 157 GLN C 17 ASN C 112 HIS C 114 HIS C 168 GLN C 214 GLN C 216 GLN D 67 HIS M 17 ASN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 127 GLN I 216 GLN J 9 GLN J 157 GLN K 112 HIS K 114 HIS K 168 GLN K 214 GLN K 216 GLN L 67 HIS L 157 GLN E 17 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.197201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.157553 restraints weight = 17970.110| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.51 r_work: 0.3296 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18914 Z= 0.149 Angle : 0.551 5.459 25896 Z= 0.322 Chirality : 0.045 0.157 2852 Planarity : 0.005 0.050 3012 Dihedral : 18.409 89.507 3271 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.80 % Allowed : 12.81 % Favored : 84.38 % 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: -0.51 (0.18), residues: 2032 helix: 0.96 (0.16), residues: 964 sheet: 0.49 (0.23), residues: 446 loop : -3.14 (0.19), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 224 TYR 0.009 0.001 TYR B 83 PHE 0.018 0.001 PHE M 1 TRP 0.011 0.001 TRP M 19 HIS 0.007 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (18882) covalent geometry : angle 0.54968 / 0.32 (25886) hydrogen bonds : bond 0.06738 / 4.73 ( 1062) hydrogen bonds : angle 4.94574 / 3.58 ( 3014) metal coordination : bond 0.01803 / 1.23 ( 32) metal coordination : angle 2.16085 / 1.09 ( 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 260 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 211 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7902 (tt0) REVERT: B 154 MET cc_start: 0.8037 (mmt) cc_final: 0.7516 (mmt) REVERT: B 273 ARG cc_start: 0.7844 (mpt180) cc_final: 0.7559 (mpt180) REVERT: C 194 TYR cc_start: 0.6631 (OUTLIER) cc_final: 0.5325 (t80) REVERT: D 68 LEU cc_start: 0.7095 (tp) cc_final: 0.6828 (tt) REVERT: D 231 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7651 (ttm170) REVERT: D 234 GLN cc_start: 0.8505 (mt0) cc_final: 0.8119 (mp10) REVERT: M 7 LYS cc_start: 0.7887 (mttt) cc_final: 0.7329 (mtmt) REVERT: M 35 GLU cc_start: 0.8412 (tp30) cc_final: 0.8100 (tp30) REVERT: J 39 GLN cc_start: 0.7314 (mt0) cc_final: 0.7111 (mm110) REVERT: J 87 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: J 154 MET cc_start: 0.8064 (mmt) cc_final: 0.7382 (mmt) REVERT: K 62 GLN cc_start: 0.7713 (mt0) cc_final: 0.7295 (mt0) REVERT: L 68 LEU cc_start: 0.7124 (tp) cc_final: 0.6788 (tt) REVERT: L 194 TYR cc_start: 0.5957 (m-80) cc_final: 0.4972 (m-80) REVERT: L 234 GLN cc_start: 0.8516 (mt0) cc_final: 0.8182 (mp10) REVERT: N 224 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7288 (mtp-110) REVERT: N 252 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: E 7 LYS cc_start: 0.7812 (mttt) cc_final: 0.7224 (mtmt) REVERT: E 35 GLU cc_start: 0.8413 (tp30) cc_final: 0.8135 (tp30) outliers start: 49 outliers final: 21 residues processed: 240 average time/residue: 0.6616 time to fit residues: 176.4451 Evaluate side-chains 222 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain J residue 87 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 221 GLN Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain L residue 63 MET Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain N residue 224 ARG Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [145, 177, 206, 26, 135, 209, 164, 139, 115, 120, 92] chunk 145 optimal weight: 4.9990 chunk 177 optimal weight: 10.0000 chunk 206 optimal weight: 40.0000 chunk 26 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 209 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 139 optimal weight: 0.0870 chunk 115 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 GLN A 155 ASN A 216 GLN B 112 HIS C 62 GLN C 214 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 127 GLN I 155 ASN I 216 GLN J 112 HIS K 214 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.194353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.154716 restraints weight = 17914.306| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.68 r_work: 0.3266 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18914 Z= 0.210 Angle : 0.601 6.047 25896 Z= 0.343 Chirality : 0.048 0.177 2852 Planarity : 0.005 0.050 3012 Dihedral : 18.587 88.778 3262 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.55 % Allowed : 13.22 % Favored : 83.24 % 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: 0.06 (0.18), residues: 2032 helix: 1.61 (0.16), residues: 962 sheet: 0.70 (0.23), residues: 434 loop : -3.07 (0.19), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 263 TYR 0.011 0.002 TYR K 83 PHE 0.021 0.002 PHE E 1 TRP 0.014 0.002 TRP M 19 HIS 0.005 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (18882) covalent geometry : angle 0.59819 / 0.34 (25886) hydrogen bonds : bond 0.07604 / 5.33 ( 1062) hydrogen bonds : angle 4.78219 / 3.45 ( 3014) metal coordination : bond 0.02051 / 1.36 ( 32) metal coordination : angle 2.85146 / 1.61 ( 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 263 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 201 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8498 (p) REVERT: B 112 HIS cc_start: 0.8713 (t70) cc_final: 0.8098 (m90) REVERT: B 136 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8115 (mm-30) REVERT: C 17 ASN cc_start: 0.7912 (m-40) cc_final: 0.7602 (m110) REVERT: C 62 GLN cc_start: 0.7727 (mt0) cc_final: 0.7284 (mt0) REVERT: C 194 TYR cc_start: 0.6676 (OUTLIER) cc_final: 0.5311 (t80) REVERT: D 68 LEU cc_start: 0.7083 (tp) cc_final: 0.6816 (tt) REVERT: D 73 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7439 (mm) REVERT: D 234 GLN cc_start: 0.8526 (mt0) cc_final: 0.8129 (mp10) REVERT: M 7 LYS cc_start: 0.7914 (mttt) cc_final: 0.7322 (mtmt) REVERT: M 35 GLU cc_start: 0.8329 (tp30) cc_final: 0.8056 (tp30) REVERT: I 264 LYS cc_start: 0.7187 (mttt) cc_final: 0.6772 (mtpp) REVERT: J 112 HIS cc_start: 0.8743 (t70) cc_final: 0.8105 (m90) REVERT: J 136 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8109 (mm-30) REVERT: J 154 MET cc_start: 0.8057 (mmt) cc_final: 0.7837 (mmt) REVERT: K 17 ASN cc_start: 0.7984 (m-40) cc_final: 0.7734 (m-40) REVERT: L 68 LEU cc_start: 0.7075 (tp) cc_final: 0.6751 (tt) REVERT: L 234 GLN cc_start: 0.8486 (mt0) cc_final: 0.8135 (mp10) REVERT: N 224 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7356 (ttp-110) REVERT: N 252 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: E 7 LYS cc_start: 0.7906 (mttt) cc_final: 0.7306 (mtmt) REVERT: E 17 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.7788 (m110) outliers start: 62 outliers final: 31 residues processed: 243 average time/residue: 0.6471 time to fit residues: 174.8139 Evaluate side-chains 232 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 171 LYS Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 221 GLN Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain N residue 224 ARG Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [194, 127, 170, 7, 138, 6, 76, 201, 189, 166, 58] chunk 194 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 189 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 GLN A 216 GLN C 214 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 127 GLN I 216 GLN K 62 GLN K 214 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.194584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.153717 restraints weight = 17969.784| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.76 r_work: 0.3272 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18914 Z= 0.202 Angle : 0.589 5.948 25896 Z= 0.337 Chirality : 0.047 0.173 2852 Planarity : 0.005 0.051 3012 Dihedral : 18.643 87.900 3262 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.83 % Allowed : 14.65 % Favored : 81.52 % 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: 0.29 (0.18), residues: 2032 helix: 1.82 (0.16), residues: 962 sheet: 0.75 (0.23), residues: 438 loop : -2.99 (0.20), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 166 TYR 0.010 0.002 TYR K 83 PHE 0.020 0.002 PHE M 1 TRP 0.015 0.002 TRP M 19 HIS 0.004 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (18882) covalent geometry : angle 0.58676 / 0.34 (25886) hydrogen bonds : bond 0.07281 / 5.11 ( 1062) hydrogen bonds : angle 4.71079 / 3.40 ( 3014) metal coordination : bond 0.01848 / 1.26 ( 32) metal coordination : angle 2.62444 / 1.47 ( 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 257 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 190 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7235 (mttt) cc_final: 0.6775 (mtpp) REVERT: B 112 HIS cc_start: 0.8717 (t70) cc_final: 0.8135 (m90) REVERT: B 136 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8088 (mm-30) REVERT: C 62 GLN cc_start: 0.7654 (mt0) cc_final: 0.7203 (mt0) REVERT: D 68 LEU cc_start: 0.7040 (tp) cc_final: 0.6788 (tt) REVERT: D 73 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7399 (mm) REVERT: D 234 GLN cc_start: 0.8574 (mt0) cc_final: 0.8227 (mp10) REVERT: M 7 LYS cc_start: 0.7931 (mttt) cc_final: 0.7338 (mtmt) REVERT: M 35 GLU cc_start: 0.8330 (tp30) cc_final: 0.8061 (tp30) REVERT: I 264 LYS cc_start: 0.7199 (mttt) cc_final: 0.6757 (mtpp) REVERT: J 112 HIS cc_start: 0.8730 (t70) cc_final: 0.8130 (m90) REVERT: J 136 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8090 (mm-30) REVERT: J 154 MET cc_start: 0.8058 (mmt) cc_final: 0.7625 (mmt) REVERT: K 62 GLN cc_start: 0.7728 (mt0) cc_final: 0.7271 (mt0) REVERT: K 103 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7176 (mtmm) REVERT: L 68 LEU cc_start: 0.7031 (tp) cc_final: 0.6757 (tt) REVERT: L 234 GLN cc_start: 0.8565 (mt0) cc_final: 0.8228 (mp10) REVERT: N 224 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7395 (mtp-110) REVERT: N 252 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: E 7 LYS cc_start: 0.7919 (mttt) cc_final: 0.7316 (mtmt) REVERT: E 17 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.7872 (m110) outliers start: 67 outliers final: 39 residues processed: 228 average time/residue: 0.6499 time to fit residues: 164.7999 Evaluate side-chains 239 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 221 GLN Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain N residue 203 ILE Chi-restraints excluded: chain N residue 224 ARG Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [5, 202, 94, 147, 154, 156, 38, 47, 203, 84, 122] chunk 5 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 203 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN C 214 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN K 214 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.195981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.155134 restraints weight = 17896.453| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.68 r_work: 0.3302 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18914 Z= 0.156 Angle : 0.537 5.388 25896 Z= 0.309 Chirality : 0.045 0.154 2852 Planarity : 0.004 0.049 3012 Dihedral : 18.624 87.934 3262 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.20 % Allowed : 16.42 % Favored : 80.38 % 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: 0.54 (0.18), residues: 2032 helix: 2.06 (0.16), residues: 966 sheet: 0.81 (0.23), residues: 438 loop : -2.90 (0.20), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 166 TYR 0.011 0.001 TYR B 83 PHE 0.015 0.001 PHE E 1 TRP 0.014 0.001 TRP M 19 HIS 0.004 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (18882) covalent geometry : angle 0.53405 / 0.31 (25886) hydrogen bonds : bond 0.06348 / 4.47 ( 1062) hydrogen bonds : angle 4.60093 / 3.33 ( 3014) metal coordination : bond 0.01598 / 1.09 ( 32) metal coordination : angle 2.92699 / 1.55 ( 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 253 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 197 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7244 (mttt) cc_final: 0.6775 (mtpp) REVERT: B 87 GLU cc_start: 0.7945 (tt0) cc_final: 0.7727 (tt0) REVERT: B 112 HIS cc_start: 0.8740 (t70) cc_final: 0.8224 (m90) REVERT: B 136 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8063 (mm-30) REVERT: C 62 GLN cc_start: 0.7708 (mt0) cc_final: 0.7278 (mt0) REVERT: C 159 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7491 (mtpt) REVERT: D 68 LEU cc_start: 0.7086 (tp) cc_final: 0.6864 (tt) REVERT: D 73 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7377 (mm) REVERT: D 234 GLN cc_start: 0.8592 (mt0) cc_final: 0.8219 (mp10) REVERT: M 7 LYS cc_start: 0.7900 (mttt) cc_final: 0.7300 (mtmt) REVERT: M 17 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.7879 (m110) REVERT: I 264 LYS cc_start: 0.7214 (mttt) cc_final: 0.6773 (mtpp) REVERT: J 112 HIS cc_start: 0.8731 (t70) cc_final: 0.8210 (m90) REVERT: J 136 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8055 (mm-30) REVERT: K 62 GLN cc_start: 0.7737 (mt0) cc_final: 0.7296 (mt0) REVERT: K 103 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7154 (mtmm) REVERT: L 68 LEU cc_start: 0.7022 (tp) cc_final: 0.6751 (tt) REVERT: L 234 GLN cc_start: 0.8579 (mt0) cc_final: 0.8237 (mp10) REVERT: N 224 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7498 (mtp-110) REVERT: N 252 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: E 7 LYS cc_start: 0.7899 (mttt) cc_final: 0.7289 (mtmt) REVERT: E 17 ASN cc_start: 0.8665 (OUTLIER) cc_final: 0.7889 (m110) outliers start: 56 outliers final: 32 residues processed: 231 average time/residue: 0.6843 time to fit residues: 175.0461 Evaluate side-chains 233 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 159 LYS Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 224 ARG Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 221 GLN Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain N residue 203 ILE Chi-restraints excluded: chain N residue 224 ARG Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [124, 181, 205, 105, 149, 33, 51, 77, 145, 17, 139] chunk 124 optimal weight: 6.9990 chunk 181 optimal weight: 7.9990 chunk 205 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 77 optimal weight: 0.0040 chunk 145 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 overall best weight: 2.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN K 214 GLN ** E 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 = 0.4215 r_free = 0.4215 target = 0.195254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.153539 restraints weight = 17501.094| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.62 r_work: 0.3282 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18914 Z= 0.156 Angle : 0.532 5.260 25896 Z= 0.306 Chirality : 0.045 0.152 2852 Planarity : 0.004 0.047 3012 Dihedral : 18.638 87.896 3262 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.06 % Allowed : 16.19 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.18), residues: 2032 helix: 2.21 (0.16), residues: 966 sheet: 0.82 (0.23), residues: 438 loop : -2.84 (0.21), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 166 TYR 0.011 0.002 TYR B 83 PHE 0.015 0.001 PHE E 1 TRP 0.013 0.001 TRP M 19 HIS 0.003 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (18882) covalent geometry : angle 0.52953 / 0.31 (25886) hydrogen bonds : bond 0.06230 / 4.38 ( 1062) hydrogen bonds : angle 4.54790 / 3.30 ( 3014) metal coordination : bond 0.01517 / 1.03 ( 32) metal coordination : angle 2.74232 / 1.51 ( 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 269 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 198 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7225 (mttt) cc_final: 0.6767 (mtpp) REVERT: B 112 HIS cc_start: 0.8756 (t70) cc_final: 0.8210 (m90) REVERT: B 136 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8046 (mm-30) REVERT: C 62 GLN cc_start: 0.7686 (mt0) cc_final: 0.7248 (mt0) REVERT: D 68 LEU cc_start: 0.7102 (tp) cc_final: 0.6884 (tt) REVERT: D 73 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7404 (mm) REVERT: D 234 GLN cc_start: 0.8575 (mt0) cc_final: 0.8177 (mp10) REVERT: M 7 LYS cc_start: 0.7844 (mttt) cc_final: 0.7229 (mtmt) REVERT: M 17 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.7824 (m110) REVERT: I 264 LYS cc_start: 0.7187 (mttt) cc_final: 0.6746 (mtpp) REVERT: J 25 ASP cc_start: 0.7260 (m-30) cc_final: 0.7044 (m-30) REVERT: J 112 HIS cc_start: 0.8743 (t70) cc_final: 0.8195 (m90) REVERT: J 136 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8047 (mm-30) REVERT: K 62 GLN cc_start: 0.7729 (mt0) cc_final: 0.7303 (mt0) REVERT: K 103 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7132 (mtmm) REVERT: K 132 TRP cc_start: 0.8676 (t60) cc_final: 0.8338 (t60) REVERT: K 159 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7481 (mtpt) REVERT: L 68 LEU cc_start: 0.7019 (tp) cc_final: 0.6752 (tt) REVERT: L 234 GLN cc_start: 0.8567 (mt0) cc_final: 0.8205 (mp10) REVERT: N 252 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: E 7 LYS cc_start: 0.7839 (mttt) cc_final: 0.7215 (mtmt) REVERT: E 17 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.7875 (m110) outliers start: 71 outliers final: 45 residues processed: 244 average time/residue: 0.6566 time to fit residues: 178.1614 Evaluate side-chains 249 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 196 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 224 ARG Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 221 GLN Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 159 LYS Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain N residue 203 ILE Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [141, 21, 137, 15, 89, 114, 75, 87, 187, 31, 18] chunk 141 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 114 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN C 214 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN K 214 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.197359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.156021 restraints weight = 17587.252| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.61 r_work: 0.3316 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18914 Z= 0.154 Angle : 0.529 6.156 25896 Z= 0.303 Chirality : 0.044 0.150 2852 Planarity : 0.004 0.047 3012 Dihedral : 18.647 87.631 3262 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.00 % Allowed : 16.53 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 2032 helix: 2.28 (0.16), residues: 966 sheet: 0.87 (0.23), residues: 438 loop : -2.77 (0.21), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 166 TYR 0.011 0.002 TYR B 83 PHE 0.015 0.001 PHE M 1 TRP 0.014 0.001 TRP M 19 HIS 0.003 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (18882) covalent geometry : angle 0.52566 / 0.30 (25886) hydrogen bonds : bond 0.06131 / 4.31 ( 1062) hydrogen bonds : angle 4.51436 / 3.27 ( 3014) metal coordination : bond 0.01518 / 1.03 ( 32) metal coordination : angle 2.87444 / 1.55 ( 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 267 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 197 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7238 (mttt) cc_final: 0.6773 (mtpp) REVERT: B 87 GLU cc_start: 0.8015 (tt0) cc_final: 0.7779 (tt0) REVERT: B 112 HIS cc_start: 0.8750 (t70) cc_final: 0.8217 (m90) REVERT: B 136 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8073 (mm-30) REVERT: C 62 GLN cc_start: 0.7673 (mt0) cc_final: 0.7235 (mt0) REVERT: C 159 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7440 (mtpt) REVERT: D 68 LEU cc_start: 0.7082 (tp) cc_final: 0.6870 (tt) REVERT: D 73 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7374 (mm) REVERT: D 234 GLN cc_start: 0.8632 (mt0) cc_final: 0.8078 (mp10) REVERT: M 7 LYS cc_start: 0.7898 (mttt) cc_final: 0.7294 (mtmt) REVERT: M 17 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.7856 (m110) REVERT: I 87 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8361 (tp30) REVERT: I 264 LYS cc_start: 0.7180 (mttt) cc_final: 0.6738 (mtpp) REVERT: J 112 HIS cc_start: 0.8706 (t70) cc_final: 0.8191 (m90) REVERT: J 136 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8017 (mm-30) REVERT: K 62 GLN cc_start: 0.7750 (mt0) cc_final: 0.7299 (mt0) REVERT: K 103 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7136 (mtmm) REVERT: K 132 TRP cc_start: 0.8657 (t60) cc_final: 0.8326 (t60) REVERT: K 159 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7452 (mtpt) REVERT: L 68 LEU cc_start: 0.7008 (tp) cc_final: 0.6752 (tt) REVERT: L 234 GLN cc_start: 0.8603 (mt0) cc_final: 0.8247 (mp10) REVERT: N 229 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7344 (pp20) REVERT: N 252 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: E 7 LYS cc_start: 0.7882 (mttt) cc_final: 0.7264 (mtmt) REVERT: E 17 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.7899 (m110) outliers start: 70 outliers final: 44 residues processed: 244 average time/residue: 0.6462 time to fit residues: 175.3522 Evaluate side-chains 251 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 197 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 159 LYS Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 224 ARG Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 221 GLN Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 159 LYS Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain N residue 203 ILE Chi-restraints excluded: chain N residue 229 GLU Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [34, 5, 3, 162, 48, 115, 62, 22, 196, 63, 146] chunk 34 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 162 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 196 optimal weight: 0.0670 chunk 63 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN K 214 GLN ** E 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 = 0.4274 r_free = 0.4274 target = 0.200217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.159407 restraints weight = 17525.191| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.45 r_work: 0.3346 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18914 Z= 0.118 Angle : 0.482 6.836 25896 Z= 0.279 Chirality : 0.042 0.140 2852 Planarity : 0.004 0.044 3012 Dihedral : 18.581 88.401 3262 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.26 % Allowed : 17.33 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.19), residues: 2032 helix: 2.49 (0.16), residues: 968 sheet: 0.93 (0.23), residues: 442 loop : -2.65 (0.22), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 166 TYR 0.011 0.001 TYR J 83 PHE 0.010 0.001 PHE E 1 TRP 0.014 0.001 TRP A 19 HIS 0.003 0.001 HIS A 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.12 (18882) covalent geometry : angle 0.47893 / 0.28 (25886) hydrogen bonds : bond 0.05052 / 3.56 ( 1062) hydrogen bonds : angle 4.42450 / 3.21 ( 3014) metal coordination : bond 0.01118 / 0.77 ( 32) metal coordination : angle 2.76932 / 1.49 ( 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 271 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 214 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7184 (mttt) cc_final: 0.6738 (mtpp) REVERT: B 87 GLU cc_start: 0.8033 (tt0) cc_final: 0.7803 (tt0) REVERT: B 112 HIS cc_start: 0.8798 (t70) cc_final: 0.8251 (m90) REVERT: C 62 GLN cc_start: 0.7672 (mt0) cc_final: 0.7245 (mt0) REVERT: C 159 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7440 (mtpt) REVERT: D 68 LEU cc_start: 0.7099 (tp) cc_final: 0.6889 (tt) REVERT: D 73 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7448 (mm) REVERT: D 234 GLN cc_start: 0.8629 (mt0) cc_final: 0.8095 (mp10) REVERT: M 7 LYS cc_start: 0.7858 (mttt) cc_final: 0.7241 (mtmt) REVERT: M 17 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.7725 (m-40) REVERT: I 264 LYS cc_start: 0.7114 (mttt) cc_final: 0.6682 (mtpp) REVERT: J 25 ASP cc_start: 0.7224 (m-30) cc_final: 0.6972 (m-30) REVERT: J 112 HIS cc_start: 0.8743 (t70) cc_final: 0.8212 (m90) REVERT: K 62 GLN cc_start: 0.7802 (mt0) cc_final: 0.7335 (mt0) REVERT: K 103 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7131 (mtmm) REVERT: K 159 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7441 (mtpt) REVERT: L 68 LEU cc_start: 0.7029 (tp) cc_final: 0.6773 (tt) REVERT: L 234 GLN cc_start: 0.8602 (mt0) cc_final: 0.8043 (mp10) REVERT: E 7 LYS cc_start: 0.7906 (mttt) cc_final: 0.7300 (mtmt) REVERT: E 17 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.7824 (m110) outliers start: 57 outliers final: 34 residues processed: 252 average time/residue: 0.6515 time to fit residues: 182.6507 Evaluate side-chains 250 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 159 LYS Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 224 ARG Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 221 GLN Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 159 LYS Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [186, 107, 9, 147, 11, 163, 93, 112, 42, 82, 98] chunk 186 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 147 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 163 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN C 214 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN K 214 GLN N 252 GLN ** E 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 = 0.4252 r_free = 0.4252 target = 0.198223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.157028 restraints weight = 17563.660| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.61 r_work: 0.3312 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18914 Z= 0.147 Angle : 0.518 6.828 25896 Z= 0.296 Chirality : 0.044 0.147 2852 Planarity : 0.004 0.076 3012 Dihedral : 18.615 88.300 3261 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.03 % Allowed : 17.51 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.19), residues: 2032 helix: 2.50 (0.16), residues: 966 sheet: 1.01 (0.23), residues: 434 loop : -2.65 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 166 TYR 0.012 0.001 TYR B 83 PHE 0.016 0.001 PHE M 1 TRP 0.012 0.001 TRP E 19 HIS 0.003 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (18882) covalent geometry : angle 0.51549 / 0.30 (25886) hydrogen bonds : bond 0.05741 / 4.04 ( 1062) hydrogen bonds : angle 4.43790 / 3.22 ( 3014) metal coordination : bond 0.01423 / 0.98 ( 32) metal coordination : angle 2.75650 / 1.49 ( 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 257 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 204 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7177 (mttt) cc_final: 0.6729 (mtpp) REVERT: B 87 GLU cc_start: 0.8026 (tt0) cc_final: 0.7793 (tt0) REVERT: B 112 HIS cc_start: 0.8764 (t70) cc_final: 0.8221 (m90) REVERT: B 273 ARG cc_start: 0.7824 (mpt180) cc_final: 0.7405 (mmt90) REVERT: C 62 GLN cc_start: 0.7661 (mt0) cc_final: 0.7229 (mt0) REVERT: C 132 TRP cc_start: 0.8682 (t60) cc_final: 0.8406 (t60) REVERT: C 159 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7435 (mtpt) REVERT: D 68 LEU cc_start: 0.7096 (tp) cc_final: 0.6871 (tt) REVERT: D 73 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7445 (mm) REVERT: D 111 LYS cc_start: 0.7887 (tppt) cc_final: 0.7686 (tppt) REVERT: D 234 GLN cc_start: 0.8629 (mt0) cc_final: 0.8087 (mp10) REVERT: M 7 LYS cc_start: 0.7900 (mttt) cc_final: 0.7289 (mtmt) REVERT: M 17 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.7840 (m110) REVERT: I 264 LYS cc_start: 0.7179 (mttt) cc_final: 0.6737 (mtpp) REVERT: J 25 ASP cc_start: 0.7149 (m-30) cc_final: 0.6872 (m-30) REVERT: J 112 HIS cc_start: 0.8717 (t70) cc_final: 0.8187 (m90) REVERT: K 62 GLN cc_start: 0.7775 (mt0) cc_final: 0.7305 (mt0) REVERT: K 103 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7179 (mtmm) REVERT: K 159 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7447 (mtpt) REVERT: L 68 LEU cc_start: 0.7002 (tp) cc_final: 0.6745 (tt) REVERT: L 217 ILE cc_start: 0.8594 (mm) cc_final: 0.8377 (mt) REVERT: L 234 GLN cc_start: 0.8614 (mt0) cc_final: 0.8228 (mp10) REVERT: N 252 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8681 (tp-100) REVERT: E 7 LYS cc_start: 0.7879 (mttt) cc_final: 0.7260 (mtmt) REVERT: E 17 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.7869 (m110) outliers start: 53 outliers final: 39 residues processed: 238 average time/residue: 0.6573 time to fit residues: 173.8771 Evaluate side-chains 250 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 159 LYS Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 224 ARG Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 221 GLN Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 159 LYS Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain L residue 63 MET Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain N residue 203 ILE Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [130, 95, 82, 165, 160, 120, 71, 58, 32, 89, 39] chunk 130 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 160 optimal weight: 0.0370 chunk 120 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN F 252 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN K 214 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.196586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.155118 restraints weight = 17536.143| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.63 r_work: 0.3296 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18914 Z= 0.193 Angle : 0.569 6.977 25896 Z= 0.323 Chirality : 0.046 0.165 2852 Planarity : 0.005 0.093 3012 Dihedral : 18.649 87.401 3259 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.20 % Allowed : 17.68 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 2032 helix: 2.36 (0.16), residues: 966 sheet: 0.97 (0.23), residues: 434 loop : -2.71 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG L 166 TYR 0.013 0.002 TYR C 83 PHE 0.019 0.002 PHE E 1 TRP 0.012 0.001 TRP M 19 HIS 0.004 0.001 HIS C 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (18882) covalent geometry : angle 0.56709 / 0.32 (25886) hydrogen bonds : bond 0.06551 / 4.60 ( 1062) hydrogen bonds : angle 4.50546 / 3.26 ( 3014) metal coordination : bond 0.01558 / 1.06 ( 32) metal coordination : angle 2.64917 / 1.48 ( 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 258 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 202 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7216 (mttt) cc_final: 0.6753 (mtpp) REVERT: B 87 GLU cc_start: 0.8023 (tt0) cc_final: 0.7790 (tt0) REVERT: B 112 HIS cc_start: 0.8753 (t70) cc_final: 0.8216 (m90) REVERT: B 273 ARG cc_start: 0.7858 (mpt180) cc_final: 0.7418 (mmt90) REVERT: C 62 GLN cc_start: 0.7680 (mt0) cc_final: 0.7239 (mt0) REVERT: C 132 TRP cc_start: 0.8688 (t60) cc_final: 0.8418 (t60) REVERT: C 154 MET cc_start: 0.8238 (mmm) cc_final: 0.7477 (mmt) REVERT: C 159 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7457 (mtpt) REVERT: D 68 LEU cc_start: 0.7085 (tp) cc_final: 0.6862 (tt) REVERT: D 73 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7380 (mm) REVERT: D 111 LYS cc_start: 0.7904 (tppt) cc_final: 0.7700 (tppt) REVERT: D 234 GLN cc_start: 0.8650 (mt0) cc_final: 0.8097 (mp10) REVERT: F 252 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8763 (tp-100) REVERT: M 7 LYS cc_start: 0.7920 (mttt) cc_final: 0.7312 (mtmt) REVERT: M 17 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.7883 (m110) REVERT: I 264 LYS cc_start: 0.7227 (mttt) cc_final: 0.6768 (mtpp) REVERT: J 112 HIS cc_start: 0.8731 (t70) cc_final: 0.8204 (m90) REVERT: K 62 GLN cc_start: 0.7757 (mt0) cc_final: 0.7304 (mt0) REVERT: K 103 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7150 (mtmm) REVERT: L 68 LEU cc_start: 0.7016 (tp) cc_final: 0.6754 (tt) REVERT: L 234 GLN cc_start: 0.8663 (mt0) cc_final: 0.8258 (mp10) REVERT: E 7 LYS cc_start: 0.7923 (mttt) cc_final: 0.7306 (mtmt) REVERT: E 17 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.7930 (m110) outliers start: 56 outliers final: 44 residues processed: 237 average time/residue: 0.6298 time to fit residues: 166.5576 Evaluate side-chains 250 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 200 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 159 LYS Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 224 ARG Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 221 GLN Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain L residue 63 MET Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain N residue 203 ILE Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [133, 125, 189, 123, 142, 176, 132, 74, 71, 208, 148] chunk 133 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 208 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN F 252 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN K 214 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.196659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.155200 restraints weight = 17554.525| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.53 r_work: 0.3300 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.183 18914 Z= 0.212 Angle : 0.771 59.199 25896 Z= 0.448 Chirality : 0.048 0.808 2852 Planarity : 0.005 0.088 3012 Dihedral : 18.651 87.393 3259 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.32 % Allowed : 17.73 % Favored : 78.95 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 2032 helix: 2.35 (0.16), residues: 966 sheet: 0.98 (0.23), residues: 434 loop : -2.72 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG L 166 TYR 0.013 0.002 TYR C 83 PHE 0.018 0.002 PHE E 1 TRP 0.013 0.001 TRP M 19 HIS 0.003 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (18882) covalent geometry : angle 0.76981 / 0.45 (25886) hydrogen bonds : bond 0.06506 / 4.56 ( 1062) hydrogen bonds : angle 4.50760 / 3.26 ( 3014) metal coordination : bond 0.01544 / 1.05 ( 32) metal coordination : angle 2.65636 / 1.48 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5910.18 seconds wall clock time: 101 minutes 21.52 seconds (6081.52 seconds total)