Starting phenix.real_space_refine on Thu Jul 2 21:53:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v68_31738/07_2026/7v68_31738.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v68_31738/07_2026/7v68_31738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7v68_31738/07_2026/7v68_31738.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v68_31738/07_2026/7v68_31738.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v68_31738/07_2026/7v68_31738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v68_31738/07_2026/7v68_31738.map" model { file = "/net/cci-nas-00/data/ceres_data/7v68_31738/07_2026/7v68_31738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v68_31738/07_2026/7v68_31738.cif" } resolution = 3.4 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2117 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 66 5.16 5 Cl 1 4.86 5 C 5496 2.51 5 N 1451 2.21 5 O 1563 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8577 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1646 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 8, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2553 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1746 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 2154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2154 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'2CU': 1, 'IXO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.00, per 1000 atoms: 0.23 Number of scatterers: 8577 At special positions: 0 Unit cell: (94.2936, 122.027, 123.414, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 66 16.00 O 1563 8.00 N 1451 7.00 C 5496 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 426 " - pdb=" SG CYS R 429 " distance=2.03 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: 0.77 Conformation dependent library (CDL) restraints added in 459.4 milliseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 39.1% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.663A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.976A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 241 through 256 Processing helix chain 'A' and resid 257 through 260 removed outlier: 3.762A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 260' Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.849A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.536A pdb=" N GLY A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 29 through 45 removed outlier: 3.515A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.896A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'R' and resid 30 through 60 Processing helix chain 'R' and resid 61 through 67 removed outlier: 3.525A pdb=" N THR R 65 " --> pdb=" O GLN R 62 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL R 66 " --> pdb=" O LEU R 63 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ASN R 67 " --> pdb=" O GLN R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 94 removed outlier: 3.858A pdb=" N MET R 86 " --> pdb=" O GLY R 82 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASN R 87 " --> pdb=" O ALA R 83 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU R 88 " --> pdb=" O PHE R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 136 Processing helix chain 'R' and resid 139 through 145 removed outlier: 3.974A pdb=" N THR R 145 " --> pdb=" O PRO R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 176 removed outlier: 3.782A pdb=" N GLY R 150 " --> pdb=" O THR R 146 " (cutoff:3.500A) Proline residue: R 166 - end of helix removed outlier: 5.018A pdb=" N GLN R 172 " --> pdb=" O ILE R 168 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE R 173 " --> pdb=" O LEU R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 191 Processing helix chain 'R' and resid 192 through 223 removed outlier: 3.873A pdb=" N THR R 196 " --> pdb=" O ASN R 192 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLY R 198 " --> pdb=" O ALA R 194 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N THR R 199 " --> pdb=" O VAL R 195 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU R 206 " --> pdb=" O ALA R 202 " (cutoff:3.500A) Proline residue: R 207 - end of helix Processing helix chain 'R' and resid 392 through 420 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 421 through 425 removed outlier: 3.964A pdb=" N PHE R 425 " --> pdb=" O VAL R 422 " (cutoff:3.500A) Processing helix chain 'R' and resid 433 through 456 removed outlier: 4.323A pdb=" N ILE R 437 " --> pdb=" O THR R 433 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY R 438 " --> pdb=" O VAL R 434 " (cutoff:3.500A) Proline residue: R 450 - end of helix Processing helix chain 'R' and resid 457 through 471 removed outlier: 3.798A pdb=" N LYS R 461 " --> pdb=" O ASN R 457 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 190 removed outlier: 3.834A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N THR A 324 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEU A 268 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.372A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 63 removed outlier: 6.875A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 6.027A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 149 removed outlier: 3.827A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 198 through 201 removed outlier: 3.708A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.530A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 Processing sheet with id=AA9, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.541A pdb=" N PHE S 80 " --> pdb=" O SER S 71 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.543A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.543A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 130 removed outlier: 3.595A pdb=" N PHE S 200 " --> pdb=" O CYS S 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.435A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'S' and resid 182 through 183 removed outlier: 3.990A pdb=" N ARG S 179 " --> pdb=" O ASN S 182 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N SER S 172 " --> pdb=" O ARG S 168 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ARG S 168 " --> pdb=" O SER S 172 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1182 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 5 1.20 - 1.35: 2720 1.35 - 1.51: 2564 1.51 - 1.66: 3377 1.66 - 1.82: 97 Bond restraints: 8763 Sorted by residual: bond pdb=" CG PRO R 181 " pdb=" CD PRO R 181 " ideal model delta sigma weight residual 1.503 1.042 0.461 3.40e-02 8.65e+02 1.83e+02 bond pdb=" C08 2CU R 502 " pdb=" N05 2CU R 502 " ideal model delta sigma weight residual 1.346 1.480 -0.134 2.00e-02 2.50e+03 4.51e+01 bond pdb=" C05 IXO R 501 " pdb=" C06 IXO R 501 " ideal model delta sigma weight residual 1.450 1.564 -0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C18 2CU R 502 " pdb=" N19 2CU R 502 " ideal model delta sigma weight residual 1.356 1.466 -0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C24 2CU R 502 " pdb=" N26 2CU R 502 " ideal model delta sigma weight residual 1.353 1.463 -0.110 2.00e-02 2.50e+03 3.01e+01 ... (remaining 8758 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.78: 11877 4.78 - 9.56: 32 9.56 - 14.34: 4 14.34 - 19.12: 1 19.12 - 23.90: 3 Bond angle restraints: 11917 Sorted by residual: angle pdb=" N PRO R 181 " pdb=" CD PRO R 181 " pdb=" CG PRO R 181 " ideal model delta sigma weight residual 103.20 79.30 23.90 1.50e+00 4.44e-01 2.54e+02 angle pdb=" CA PRO R 181 " pdb=" CB PRO R 181 " pdb=" CG PRO R 181 " ideal model delta sigma weight residual 104.50 85.23 19.27 1.90e+00 2.77e-01 1.03e+02 angle pdb=" CA PRO R 181 " pdb=" N PRO R 181 " pdb=" CD PRO R 181 " ideal model delta sigma weight residual 112.00 99.00 13.00 1.40e+00 5.10e-01 8.62e+01 angle pdb=" N TYR S 223 " pdb=" CA TYR S 223 " pdb=" C TYR S 223 " ideal model delta sigma weight residual 109.81 129.23 -19.42 2.21e+00 2.05e-01 7.72e+01 angle pdb=" CA PRO R 137 " pdb=" N PRO R 137 " pdb=" CD PRO R 137 " ideal model delta sigma weight residual 112.00 103.74 8.26 1.40e+00 5.10e-01 3.48e+01 ... (remaining 11912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 4725 17.74 - 35.48: 341 35.48 - 53.22: 60 53.22 - 70.96: 2 70.96 - 88.70: 7 Dihedral angle restraints: 5135 sinusoidal: 1876 harmonic: 3259 Sorted by residual: dihedral pdb=" CB CYS R 426 " pdb=" SG CYS R 426 " pdb=" SG CYS R 429 " pdb=" CB CYS R 429 " ideal model delta sinusoidal sigma weight residual -86.00 -134.56 48.56 1 1.00e+01 1.00e-02 3.25e+01 dihedral pdb=" N TYR S 223 " pdb=" C TYR S 223 " pdb=" CA TYR S 223 " pdb=" CB TYR S 223 " ideal model delta harmonic sigma weight residual 122.80 134.50 -11.70 0 2.50e+00 1.60e-01 2.19e+01 dihedral pdb=" C TYR S 223 " pdb=" N TYR S 223 " pdb=" CA TYR S 223 " pdb=" CB TYR S 223 " ideal model delta harmonic sigma weight residual -122.60 -134.18 11.58 0 2.50e+00 1.60e-01 2.15e+01 ... (remaining 5132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 1377 0.140 - 0.281: 7 0.281 - 0.421: 1 0.421 - 0.562: 0 0.562 - 0.702: 1 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA TYR S 223 " pdb=" N TYR S 223 " pdb=" C TYR S 223 " pdb=" CB TYR S 223 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CB VAL A 13 " pdb=" CA VAL A 13 " pdb=" CG1 VAL A 13 " pdb=" CG2 VAL A 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB THR B 164 " pdb=" CA THR B 164 " pdb=" OG1 THR B 164 " pdb=" CG2 THR B 164 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 1383 not shown) Planarity restraints: 1484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C04 2CU R 502 " 0.801 2.00e-02 2.50e+03 6.36e-01 6.06e+03 pdb=" C06 2CU R 502 " -0.695 2.00e-02 2.50e+03 pdb=" C08 2CU R 502 " -0.086 2.00e-02 2.50e+03 pdb=" C10 2CU R 502 " 0.746 2.00e-02 2.50e+03 pdb=" N05 2CU R 502 " 0.089 2.00e-02 2.50e+03 pdb=" O09 2CU R 502 " -0.854 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 180 " -0.083 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO R 181 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO R 181 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO R 181 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS R 136 " -0.060 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO R 137 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO R 137 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO R 137 " -0.047 5.00e-02 4.00e+02 ... (remaining 1481 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 256 2.70 - 3.25: 9058 3.25 - 3.80: 13988 3.80 - 4.35: 17572 4.35 - 4.90: 29186 Nonbonded interactions: 70060 Sorted by model distance: nonbonded pdb=" OH TYR B 59 " pdb=" OE1 GLN B 75 " model vdw 2.151 3.040 nonbonded pdb=" O ALA R 408 " pdb=" OG1 THR R 412 " model vdw 2.187 3.040 nonbonded pdb=" OG SER R 85 " pdb=" OD1 ASP R 112 " model vdw 2.205 3.040 nonbonded pdb=" O PHE S 29 " pdb=" NH2 ARG S 72 " model vdw 2.268 3.120 nonbonded pdb=" OD2 ASP R 112 " pdb=" OH TYR R 443 " model vdw 2.279 3.040 ... (remaining 70055 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.260 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.461 8766 Z= 0.285 Angle : 0.834 23.900 11923 Z= 0.437 Chirality : 0.049 0.702 1386 Planarity : 0.018 0.636 1484 Dihedral : 12.677 88.699 3022 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.08 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.10 % 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: -0.44 (0.25), residues: 1104 helix: 1.30 (0.26), residues: 395 sheet: -0.91 (0.31), residues: 261 loop : -1.31 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 313 TYR 0.026 0.002 TYR B 264 PHE 0.036 0.002 PHE B 253 TRP 0.058 0.003 TRP R 435 HIS 0.009 0.001 HIS R 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00715 / 0.28 ( 8763) covalent geometry : angle 0.83408 / 0.44 (11917) SS BOND : bond 0.00306 / 0.15 ( 3) SS BOND : angle 1.37550 / 0.60 ( 6) hydrogen bonds : bond 0.17351 / 11.98 ( 414) hydrogen bonds : angle 6.95374 / 5.05 ( 1182) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7450 (tm-30) REVERT: A 35 LYS cc_start: 0.7829 (mtmm) cc_final: 0.7421 (mtmm) REVERT: A 251 ASP cc_start: 0.7115 (t70) cc_final: 0.6572 (t0) REVERT: A 270 LYS cc_start: 0.7859 (mtmm) cc_final: 0.7409 (mtmm) REVERT: A 345 LYS cc_start: 0.8076 (tptt) cc_final: 0.7613 (tptt) REVERT: A 347 ASN cc_start: 0.7334 (m-40) cc_final: 0.6825 (m-40) REVERT: B 175 GLN cc_start: 0.7638 (pp30) cc_final: 0.7227 (pp30) REVERT: B 176 GLN cc_start: 0.7915 (pt0) cc_final: 0.7482 (pt0) REVERT: B 187 VAL cc_start: 0.8095 (t) cc_final: 0.7541 (t) REVERT: B 188 MET cc_start: 0.6979 (mmt) cc_final: 0.6750 (mmt) REVERT: B 220 GLN cc_start: 0.5820 (mt0) cc_final: 0.5496 (mt0) REVERT: B 253 PHE cc_start: 0.7849 (m-10) cc_final: 0.7445 (m-80) REVERT: B 277 SER cc_start: 0.7818 (t) cc_final: 0.7471 (t) REVERT: C 15 LEU cc_start: 0.8011 (mt) cc_final: 0.7621 (mt) REVERT: C 20 LYS cc_start: 0.7695 (pttm) cc_final: 0.7490 (pttm) REVERT: S 78 THR cc_start: 0.7827 (p) cc_final: 0.7593 (p) REVERT: S 182 ASN cc_start: 0.6684 (m110) cc_final: 0.6445 (m110) REVERT: S 192 SER cc_start: 0.7622 (t) cc_final: 0.7348 (t) REVERT: R 54 MET cc_start: 0.6286 (ptp) cc_final: 0.6039 (ptp) REVERT: R 84 PHE cc_start: 0.6220 (m-80) cc_final: 0.5727 (m-80) REVERT: R 86 MET cc_start: 0.4847 (mmp) cc_final: 0.4551 (mmp) REVERT: R 111 LEU cc_start: 0.7683 (tt) cc_final: 0.7470 (tp) REVERT: R 131 TYR cc_start: 0.7977 (t80) cc_final: 0.7769 (t80) REVERT: R 173 PHE cc_start: 0.6519 (t80) cc_final: 0.6226 (t80) REVERT: R 187 ILE cc_start: 0.6825 (tp) cc_final: 0.6614 (tp) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.0869 time to fit residues: 37.1732 Evaluate side-chains 286 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS B 239 ASN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN R 417 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.156238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.136770 restraints weight = 14456.390| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 3.02 r_work: 0.3708 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8766 Z= 0.162 Angle : 0.670 9.272 11923 Z= 0.347 Chirality : 0.045 0.292 1386 Planarity : 0.005 0.060 1484 Dihedral : 5.004 44.051 1221 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.90 % Allowed : 14.21 % Favored : 83.89 % 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: -0.34 (0.25), residues: 1104 helix: 1.39 (0.25), residues: 397 sheet: -0.89 (0.30), residues: 268 loop : -1.24 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 148 TYR 0.020 0.002 TYR S 216 PHE 0.018 0.002 PHE A 191 TRP 0.017 0.002 TRP R 435 HIS 0.011 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 8763) covalent geometry : angle 0.67017 / 0.35 (11917) SS BOND : bond 0.00746 / 0.36 ( 3) SS BOND : angle 1.08464 / 0.47 ( 6) hydrogen bonds : bond 0.04225 / 2.91 ( 414) hydrogen bonds : angle 5.55057 / 4.12 ( 1182) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 310 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7754 (tm-30) REVERT: A 35 LYS cc_start: 0.7974 (mtmm) cc_final: 0.7463 (mtmm) REVERT: A 198 MET cc_start: 0.7106 (ttm) cc_final: 0.6835 (ttm) REVERT: A 251 ASP cc_start: 0.7367 (t70) cc_final: 0.6752 (t0) REVERT: A 270 LYS cc_start: 0.7994 (mtmm) cc_final: 0.7533 (mtmm) REVERT: A 271 LYS cc_start: 0.6740 (ptpp) cc_final: 0.6299 (ptpp) REVERT: A 274 PHE cc_start: 0.6769 (t80) cc_final: 0.6290 (t80) REVERT: A 347 ASN cc_start: 0.7533 (m-40) cc_final: 0.7010 (m-40) REVERT: B 45 MET cc_start: 0.8131 (mtm) cc_final: 0.7901 (mtp) REVERT: B 63 TRP cc_start: 0.8041 (m100) cc_final: 0.7681 (m100) REVERT: B 65 THR cc_start: 0.7906 (m) cc_final: 0.7642 (p) REVERT: B 170 ASP cc_start: 0.7634 (t0) cc_final: 0.7391 (t0) REVERT: B 175 GLN cc_start: 0.7850 (pp30) cc_final: 0.7572 (pp30) REVERT: B 176 GLN cc_start: 0.8283 (pt0) cc_final: 0.7767 (pt0) REVERT: B 220 GLN cc_start: 0.6657 (mt0) cc_final: 0.6426 (mt0) REVERT: B 233 CYS cc_start: 0.8006 (t) cc_final: 0.7803 (t) REVERT: B 253 PHE cc_start: 0.7935 (m-10) cc_final: 0.7556 (m-80) REVERT: B 259 GLN cc_start: 0.7723 (pt0) cc_final: 0.7369 (pt0) REVERT: B 275 SER cc_start: 0.8167 (m) cc_final: 0.7820 (p) REVERT: C 15 LEU cc_start: 0.8109 (mt) cc_final: 0.7723 (mt) REVERT: S 176 LEU cc_start: 0.8541 (mm) cc_final: 0.8289 (mm) REVERT: S 182 ASN cc_start: 0.6988 (m110) cc_final: 0.6624 (m110) REVERT: R 52 LEU cc_start: 0.7259 (mt) cc_final: 0.7013 (mt) REVERT: R 54 MET cc_start: 0.6561 (ptp) cc_final: 0.6271 (ptp) REVERT: R 84 PHE cc_start: 0.6564 (m-80) cc_final: 0.6117 (m-80) REVERT: R 86 MET cc_start: 0.4757 (mmp) cc_final: 0.4365 (mmp) REVERT: R 89 TYR cc_start: 0.6836 (t80) cc_final: 0.6356 (t80) REVERT: R 93 ILE cc_start: 0.6164 (mt) cc_final: 0.5789 (mt) REVERT: R 111 LEU cc_start: 0.7657 (tt) cc_final: 0.7413 (tp) REVERT: R 121 MET cc_start: 0.7997 (mtt) cc_final: 0.7557 (mtt) REVERT: R 173 PHE cc_start: 0.6905 (t80) cc_final: 0.6614 (t80) REVERT: R 187 ILE cc_start: 0.7363 (tp) cc_final: 0.7140 (tp) REVERT: R 449 ASN cc_start: 0.7464 (m-40) cc_final: 0.7013 (m-40) outliers start: 17 outliers final: 14 residues processed: 314 average time/residue: 0.0904 time to fit residues: 38.8203 Evaluate side-chains 308 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 294 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 122 ASN Chi-restraints excluded: chain R residue 148 MET Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 407 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 15 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 58 optimal weight: 0.0070 chunk 69 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS A 346 ASN B 239 ASN S 39 GLN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN R 68 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.154981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.135675 restraints weight = 14323.077| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.00 r_work: 0.3692 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8766 Z= 0.166 Angle : 0.638 8.273 11923 Z= 0.331 Chirality : 0.044 0.232 1386 Planarity : 0.004 0.051 1484 Dihedral : 5.012 41.553 1221 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.02 % Allowed : 17.34 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.25), residues: 1104 helix: 1.48 (0.25), residues: 396 sheet: -0.98 (0.30), residues: 267 loop : -1.20 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.017 0.002 TYR B 264 PHE 0.016 0.002 PHE B 235 TRP 0.022 0.002 TRP B 82 HIS 0.015 0.002 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 ( 8763) covalent geometry : angle 0.63775 / 0.33 (11917) SS BOND : bond 0.00504 / 0.24 ( 3) SS BOND : angle 1.07385 / 0.48 ( 6) hydrogen bonds : bond 0.03936 / 2.68 ( 414) hydrogen bonds : angle 5.34800 / 3.97 ( 1182) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 310 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7700 (tm-30) REVERT: A 35 LYS cc_start: 0.8172 (mtmm) cc_final: 0.7624 (mtmm) REVERT: A 198 MET cc_start: 0.7172 (ttm) cc_final: 0.6858 (ttm) REVERT: A 251 ASP cc_start: 0.7395 (t70) cc_final: 0.6726 (t0) REVERT: A 270 LYS cc_start: 0.8044 (mtmm) cc_final: 0.7733 (mtmm) REVERT: A 274 PHE cc_start: 0.6739 (t80) cc_final: 0.6226 (t80) REVERT: A 345 LYS cc_start: 0.8540 (tptt) cc_final: 0.8133 (tppt) REVERT: A 347 ASN cc_start: 0.7518 (m-40) cc_final: 0.7049 (m-40) REVERT: B 45 MET cc_start: 0.8244 (mtm) cc_final: 0.7980 (mtp) REVERT: B 65 THR cc_start: 0.7950 (m) cc_final: 0.7638 (p) REVERT: B 146 LEU cc_start: 0.8042 (mm) cc_final: 0.7826 (mt) REVERT: B 175 GLN cc_start: 0.7841 (pp30) cc_final: 0.7569 (pp30) REVERT: B 176 GLN cc_start: 0.8360 (pt0) cc_final: 0.7803 (pt0) REVERT: B 188 MET cc_start: 0.7403 (mmm) cc_final: 0.7202 (mmm) REVERT: B 249 THR cc_start: 0.8330 (p) cc_final: 0.8034 (p) REVERT: B 251 ARG cc_start: 0.7418 (tpp80) cc_final: 0.6725 (tpp80) REVERT: B 259 GLN cc_start: 0.7865 (pt0) cc_final: 0.7647 (pt0) REVERT: B 275 SER cc_start: 0.8131 (m) cc_final: 0.7825 (p) REVERT: C 15 LEU cc_start: 0.8131 (mt) cc_final: 0.7739 (mt) REVERT: S 176 LEU cc_start: 0.8603 (mm) cc_final: 0.8224 (mm) REVERT: S 182 ASN cc_start: 0.7155 (m110) cc_final: 0.6782 (m-40) REVERT: R 54 MET cc_start: 0.6328 (ptp) cc_final: 0.6063 (ptp) REVERT: R 84 PHE cc_start: 0.6562 (m-80) cc_final: 0.6065 (m-80) REVERT: R 86 MET cc_start: 0.5015 (mmp) cc_final: 0.4473 (mmp) REVERT: R 89 TYR cc_start: 0.6795 (t80) cc_final: 0.6467 (t80) REVERT: R 111 LEU cc_start: 0.7660 (tt) cc_final: 0.7439 (tp) REVERT: R 121 MET cc_start: 0.7950 (mtt) cc_final: 0.7536 (mtt) REVERT: R 173 PHE cc_start: 0.6930 (t80) cc_final: 0.6618 (t80) REVERT: R 187 ILE cc_start: 0.7431 (tp) cc_final: 0.7216 (tp) REVERT: R 449 ASN cc_start: 0.7421 (m-40) cc_final: 0.7169 (m-40) outliers start: 27 outliers final: 22 residues processed: 318 average time/residue: 0.0947 time to fit residues: 41.0920 Evaluate side-chains 314 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 292 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 148 MET Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 407 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 0.0050 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS B 132 ASN B 239 ASN C 11 GLN S 39 GLN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 157 ASN S 167 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.154540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.135247 restraints weight = 14513.118| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 3.04 r_work: 0.3680 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8766 Z= 0.178 Angle : 0.660 13.217 11923 Z= 0.337 Chirality : 0.045 0.210 1386 Planarity : 0.004 0.046 1484 Dihedral : 5.104 42.517 1221 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.36 % Allowed : 19.91 % Favored : 75.73 % 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 (0.25), residues: 1104 helix: 1.53 (0.26), residues: 395 sheet: -1.08 (0.30), residues: 277 loop : -1.14 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.022 0.002 TYR B 264 PHE 0.017 0.002 PHE B 235 TRP 0.035 0.002 TRP B 82 HIS 0.013 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 ( 8763) covalent geometry : angle 0.65919 / 0.34 (11917) SS BOND : bond 0.00312 / 0.15 ( 3) SS BOND : angle 1.16569 / 0.51 ( 6) hydrogen bonds : bond 0.03845 / 2.60 ( 414) hydrogen bonds : angle 5.30344 / 3.94 ( 1182) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 298 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7695 (tm-30) REVERT: A 35 LYS cc_start: 0.8203 (mtmm) cc_final: 0.7645 (mtmm) REVERT: A 198 MET cc_start: 0.7242 (ttm) cc_final: 0.6944 (ttm) REVERT: A 251 ASP cc_start: 0.7388 (t70) cc_final: 0.6719 (t0) REVERT: A 270 LYS cc_start: 0.8024 (mtmm) cc_final: 0.7814 (mtmm) REVERT: A 274 PHE cc_start: 0.6727 (t80) cc_final: 0.6191 (t80) REVERT: A 345 LYS cc_start: 0.8549 (tptt) cc_final: 0.8274 (tptt) REVERT: A 347 ASN cc_start: 0.7519 (m-40) cc_final: 0.7212 (m-40) REVERT: A 353 LEU cc_start: 0.8295 (tp) cc_final: 0.8062 (tt) REVERT: B 45 MET cc_start: 0.8287 (mtm) cc_final: 0.8023 (mtp) REVERT: B 65 THR cc_start: 0.7942 (m) cc_final: 0.7619 (p) REVERT: B 83 ASP cc_start: 0.7895 (t0) cc_final: 0.7587 (t0) REVERT: B 175 GLN cc_start: 0.7834 (pp30) cc_final: 0.7553 (pp30) REVERT: B 249 THR cc_start: 0.8297 (p) cc_final: 0.8019 (p) REVERT: B 253 PHE cc_start: 0.7924 (m-10) cc_final: 0.7566 (m-80) REVERT: B 259 GLN cc_start: 0.7922 (pt0) cc_final: 0.7681 (pt0) REVERT: C 15 LEU cc_start: 0.8167 (mt) cc_final: 0.7761 (mt) REVERT: S 34 MET cc_start: 0.7192 (mmm) cc_final: 0.6809 (mmm) REVERT: S 91 THR cc_start: 0.5982 (OUTLIER) cc_final: 0.5754 (t) REVERT: S 176 LEU cc_start: 0.8561 (mm) cc_final: 0.8176 (mm) REVERT: S 180 MET cc_start: 0.5646 (ttp) cc_final: 0.5241 (ttm) REVERT: S 182 ASN cc_start: 0.7177 (m110) cc_final: 0.6764 (m-40) REVERT: R 54 MET cc_start: 0.6434 (ptp) cc_final: 0.6073 (ptp) REVERT: R 66 VAL cc_start: 0.7904 (p) cc_final: 0.7573 (t) REVERT: R 84 PHE cc_start: 0.6583 (m-80) cc_final: 0.6080 (m-80) REVERT: R 86 MET cc_start: 0.4736 (mmp) cc_final: 0.3925 (mmp) REVERT: R 111 LEU cc_start: 0.7665 (tt) cc_final: 0.7404 (tp) REVERT: R 121 MET cc_start: 0.7976 (mtt) cc_final: 0.7587 (mtt) REVERT: R 173 PHE cc_start: 0.6933 (t80) cc_final: 0.6627 (t80) REVERT: R 187 ILE cc_start: 0.7480 (tp) cc_final: 0.7253 (tp) REVERT: R 449 ASN cc_start: 0.7464 (m-40) cc_final: 0.7263 (m-40) outliers start: 39 outliers final: 29 residues processed: 308 average time/residue: 0.0947 time to fit residues: 39.6714 Evaluate side-chains 313 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 283 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 148 MET Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 217 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 157 ASN S 167 GLN R 417 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.152116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.132984 restraints weight = 14375.645| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.99 r_work: 0.3655 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8766 Z= 0.226 Angle : 0.673 11.163 11923 Z= 0.349 Chirality : 0.046 0.205 1386 Planarity : 0.004 0.044 1484 Dihedral : 5.214 42.770 1221 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.70 % Allowed : 21.92 % Favored : 73.38 % 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: -0.35 (0.25), residues: 1104 helix: 1.53 (0.26), residues: 395 sheet: -1.20 (0.30), residues: 278 loop : -1.14 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.019 0.002 TYR B 264 PHE 0.021 0.002 PHE R 403 TRP 0.021 0.002 TRP S 36 HIS 0.016 0.002 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.23 ( 8763) covalent geometry : angle 0.67239 / 0.35 (11917) SS BOND : bond 0.00293 / 0.14 ( 3) SS BOND : angle 1.33499 / 0.57 ( 6) hydrogen bonds : bond 0.03906 / 2.60 ( 414) hydrogen bonds : angle 5.36455 / 3.97 ( 1182) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 295 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7653 (tm-30) REVERT: A 35 LYS cc_start: 0.8203 (mtmm) cc_final: 0.7636 (mtmm) REVERT: A 198 MET cc_start: 0.7233 (ttm) cc_final: 0.6944 (ttm) REVERT: A 213 HIS cc_start: 0.8348 (OUTLIER) cc_final: 0.8088 (p-80) REVERT: A 243 MET cc_start: 0.7875 (mmm) cc_final: 0.7456 (mmm) REVERT: A 251 ASP cc_start: 0.7423 (t70) cc_final: 0.6754 (t0) REVERT: A 274 PHE cc_start: 0.6738 (t80) cc_final: 0.6172 (t80) REVERT: A 345 LYS cc_start: 0.8564 (tptt) cc_final: 0.8280 (tptt) REVERT: A 347 ASN cc_start: 0.7546 (m-40) cc_final: 0.7233 (m-40) REVERT: A 353 LEU cc_start: 0.8331 (tp) cc_final: 0.8114 (tt) REVERT: B 45 MET cc_start: 0.8298 (mtm) cc_final: 0.7986 (mtp) REVERT: B 83 ASP cc_start: 0.7932 (t0) cc_final: 0.7612 (t0) REVERT: B 175 GLN cc_start: 0.7929 (pp30) cc_final: 0.7640 (pp30) REVERT: B 234 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7635 (m-80) REVERT: B 249 THR cc_start: 0.8384 (p) cc_final: 0.8086 (p) REVERT: B 253 PHE cc_start: 0.7895 (m-10) cc_final: 0.7564 (m-80) REVERT: B 259 GLN cc_start: 0.8015 (pt0) cc_final: 0.7746 (pt0) REVERT: B 292 PHE cc_start: 0.7197 (OUTLIER) cc_final: 0.6721 (m-80) REVERT: C 11 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7652 (tm-30) REVERT: C 15 LEU cc_start: 0.8174 (mt) cc_final: 0.7515 (mt) REVERT: S 34 MET cc_start: 0.7325 (mmm) cc_final: 0.6891 (mmm) REVERT: S 176 LEU cc_start: 0.8531 (mm) cc_final: 0.8273 (mt) REVERT: S 190 ARG cc_start: 0.6789 (ptt-90) cc_final: 0.6405 (ptt-90) REVERT: R 54 MET cc_start: 0.6498 (ptp) cc_final: 0.6077 (ptp) REVERT: R 84 PHE cc_start: 0.6435 (m-80) cc_final: 0.5964 (m-80) REVERT: R 89 TYR cc_start: 0.6769 (t80) cc_final: 0.6496 (t80) REVERT: R 111 LEU cc_start: 0.7748 (tt) cc_final: 0.7486 (tp) REVERT: R 121 MET cc_start: 0.7969 (mtt) cc_final: 0.7583 (mtt) REVERT: R 140 TYR cc_start: 0.8141 (t80) cc_final: 0.7775 (t80) REVERT: R 173 PHE cc_start: 0.7024 (t80) cc_final: 0.6691 (t80) REVERT: R 187 ILE cc_start: 0.7512 (tp) cc_final: 0.7282 (tp) outliers start: 42 outliers final: 33 residues processed: 309 average time/residue: 0.0876 time to fit residues: 36.9065 Evaluate side-chains 324 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 288 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 122 ASN Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 437 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 39 optimal weight: 0.9980 chunk 64 optimal weight: 0.0670 chunk 99 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 chunk 56 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS S 39 GLN S 82 GLN S 167 GLN R 68 ASN ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 417 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.156020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.136763 restraints weight = 14265.845| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 3.00 r_work: 0.3708 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8766 Z= 0.128 Angle : 0.628 10.273 11923 Z= 0.320 Chirality : 0.044 0.211 1386 Planarity : 0.004 0.041 1484 Dihedral : 5.029 44.348 1221 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.25 % Allowed : 25.28 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.25), residues: 1104 helix: 1.64 (0.26), residues: 396 sheet: -0.98 (0.31), residues: 271 loop : -1.11 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 251 TYR 0.019 0.001 TYR B 264 PHE 0.012 0.001 PHE S 108 TRP 0.014 0.002 TRP B 211 HIS 0.009 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 8763) covalent geometry : angle 0.62817 / 0.32 (11917) SS BOND : bond 0.00215 / 0.10 ( 3) SS BOND : angle 0.91910 / 0.39 ( 6) hydrogen bonds : bond 0.03536 / 2.40 ( 414) hydrogen bonds : angle 5.11657 / 3.78 ( 1182) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 285 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7652 (tm-30) REVERT: A 35 LYS cc_start: 0.8165 (mtmm) cc_final: 0.7595 (mtmm) REVERT: A 198 MET cc_start: 0.7157 (ttm) cc_final: 0.6891 (ttm) REVERT: A 243 MET cc_start: 0.7883 (mmm) cc_final: 0.7350 (mmm) REVERT: A 251 ASP cc_start: 0.7349 (t70) cc_final: 0.6676 (t0) REVERT: A 345 LYS cc_start: 0.8504 (tptt) cc_final: 0.8217 (tptt) REVERT: A 347 ASN cc_start: 0.7551 (m-40) cc_final: 0.7062 (m-40) REVERT: A 353 LEU cc_start: 0.8273 (tp) cc_final: 0.8044 (tt) REVERT: B 83 ASP cc_start: 0.7936 (t0) cc_final: 0.7588 (t0) REVERT: B 101 MET cc_start: 0.8155 (mtp) cc_final: 0.7859 (mtm) REVERT: B 175 GLN cc_start: 0.7864 (pp30) cc_final: 0.7535 (pp30) REVERT: B 212 ASP cc_start: 0.7861 (t0) cc_final: 0.7367 (p0) REVERT: B 217 MET cc_start: 0.6667 (pmm) cc_final: 0.6444 (pmm) REVERT: B 218 CYS cc_start: 0.7639 (t) cc_final: 0.7428 (p) REVERT: B 234 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: B 259 GLN cc_start: 0.7919 (pt0) cc_final: 0.7719 (pt0) REVERT: C 11 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7612 (tm-30) REVERT: C 15 LEU cc_start: 0.8171 (mt) cc_final: 0.7498 (mt) REVERT: S 34 MET cc_start: 0.7065 (mmm) cc_final: 0.6628 (mmm) REVERT: S 176 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8218 (mt) REVERT: S 190 ARG cc_start: 0.6634 (ptt-90) cc_final: 0.6297 (ptt-90) REVERT: R 54 MET cc_start: 0.6471 (ptp) cc_final: 0.6064 (ptp) REVERT: R 84 PHE cc_start: 0.6365 (m-80) cc_final: 0.5905 (m-80) REVERT: R 109 LEU cc_start: 0.7685 (mm) cc_final: 0.7405 (pp) REVERT: R 111 LEU cc_start: 0.7644 (tt) cc_final: 0.7403 (tp) REVERT: R 121 MET cc_start: 0.7908 (mtt) cc_final: 0.7484 (mtt) REVERT: R 140 TYR cc_start: 0.8024 (t80) cc_final: 0.7723 (t80) REVERT: R 151 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6786 (pp) REVERT: R 173 PHE cc_start: 0.6905 (t80) cc_final: 0.6588 (t80) outliers start: 38 outliers final: 30 residues processed: 300 average time/residue: 0.0901 time to fit residues: 36.8025 Evaluate side-chains 308 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 275 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 176 LEU Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 437 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 48 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 72 optimal weight: 0.2980 chunk 86 optimal weight: 0.7980 chunk 108 optimal weight: 0.3980 chunk 30 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 213 HIS ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 417 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.155521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.136178 restraints weight = 14445.084| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 3.04 r_work: 0.3711 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8766 Z= 0.146 Angle : 0.646 9.750 11923 Z= 0.329 Chirality : 0.045 0.213 1386 Planarity : 0.004 0.040 1484 Dihedral : 5.015 44.450 1221 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.47 % Allowed : 26.51 % Favored : 69.02 % 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: -0.11 (0.25), residues: 1104 helix: 1.69 (0.26), residues: 396 sheet: -0.89 (0.31), residues: 271 loop : -1.12 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.019 0.001 TYR S 216 PHE 0.012 0.001 PHE S 108 TRP 0.047 0.002 TRP B 82 HIS 0.013 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 8763) covalent geometry : angle 0.64579 / 0.33 (11917) SS BOND : bond 0.00190 / 0.09 ( 3) SS BOND : angle 0.72343 / 0.33 ( 6) hydrogen bonds : bond 0.03509 / 2.37 ( 414) hydrogen bonds : angle 5.08566 / 3.76 ( 1182) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 282 time to evaluate : 0.331 Fit side-chains REVERT: A 35 LYS cc_start: 0.8174 (mtmm) cc_final: 0.7629 (mtmm) REVERT: A 198 MET cc_start: 0.7194 (ttm) cc_final: 0.6924 (ttm) REVERT: A 243 MET cc_start: 0.8006 (mmm) cc_final: 0.7632 (mmm) REVERT: A 251 ASP cc_start: 0.7313 (t70) cc_final: 0.6902 (t0) REVERT: A 274 PHE cc_start: 0.6709 (t80) cc_final: 0.6089 (t80) REVERT: A 345 LYS cc_start: 0.8487 (tptt) cc_final: 0.8112 (tptt) REVERT: A 347 ASN cc_start: 0.7564 (m-40) cc_final: 0.7083 (m-40) REVERT: A 353 LEU cc_start: 0.8302 (tp) cc_final: 0.8068 (tt) REVERT: B 70 LEU cc_start: 0.7827 (mt) cc_final: 0.7553 (mp) REVERT: B 83 ASP cc_start: 0.7838 (t0) cc_final: 0.7482 (t0) REVERT: B 101 MET cc_start: 0.8119 (mtp) cc_final: 0.7816 (mtm) REVERT: B 156 GLN cc_start: 0.7138 (mt0) cc_final: 0.6877 (mt0) REVERT: B 170 ASP cc_start: 0.7586 (t0) cc_final: 0.7143 (t70) REVERT: B 175 GLN cc_start: 0.7866 (pp30) cc_final: 0.7490 (pp30) REVERT: B 207 SER cc_start: 0.6895 (t) cc_final: 0.6396 (p) REVERT: B 212 ASP cc_start: 0.7844 (t0) cc_final: 0.7375 (p0) REVERT: B 234 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7555 (m-80) REVERT: B 251 ARG cc_start: 0.7409 (ttm-80) cc_final: 0.6585 (tpp80) REVERT: B 253 PHE cc_start: 0.7819 (m-10) cc_final: 0.7419 (m-80) REVERT: B 259 GLN cc_start: 0.7969 (pt0) cc_final: 0.7762 (pt0) REVERT: B 289 TYR cc_start: 0.8375 (m-80) cc_final: 0.8125 (m-80) REVERT: B 292 PHE cc_start: 0.6858 (OUTLIER) cc_final: 0.6500 (m-80) REVERT: C 11 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7626 (tm-30) REVERT: C 15 LEU cc_start: 0.8177 (mt) cc_final: 0.7496 (mt) REVERT: S 34 MET cc_start: 0.7122 (mmm) cc_final: 0.6696 (mmm) REVERT: S 176 LEU cc_start: 0.8512 (mm) cc_final: 0.8217 (mt) REVERT: S 190 ARG cc_start: 0.6671 (ptt-90) cc_final: 0.6257 (ptt-90) REVERT: R 54 MET cc_start: 0.6462 (ptp) cc_final: 0.6056 (ptp) REVERT: R 84 PHE cc_start: 0.6308 (m-80) cc_final: 0.5862 (m-80) REVERT: R 109 LEU cc_start: 0.7692 (mm) cc_final: 0.7421 (pp) REVERT: R 111 LEU cc_start: 0.7656 (tt) cc_final: 0.7406 (tp) REVERT: R 121 MET cc_start: 0.7899 (mtt) cc_final: 0.7469 (mtt) REVERT: R 140 TYR cc_start: 0.7995 (t80) cc_final: 0.7759 (t80) REVERT: R 173 PHE cc_start: 0.6945 (t80) cc_final: 0.6622 (t80) outliers start: 40 outliers final: 29 residues processed: 298 average time/residue: 0.0935 time to fit residues: 37.7397 Evaluate side-chains 311 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 280 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 437 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 101 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS B 313 ASN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN R 68 ASN R 417 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.154115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.134801 restraints weight = 14215.982| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.99 r_work: 0.3690 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8766 Z= 0.177 Angle : 0.672 9.669 11923 Z= 0.343 Chirality : 0.046 0.220 1386 Planarity : 0.004 0.040 1484 Dihedral : 5.110 46.968 1221 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.36 % Allowed : 27.40 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.26), residues: 1104 helix: 1.67 (0.26), residues: 396 sheet: -0.87 (0.31), residues: 274 loop : -1.11 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.019 0.002 TYR S 216 PHE 0.016 0.002 PHE S 108 TRP 0.076 0.003 TRP B 82 HIS 0.014 0.002 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 ( 8763) covalent geometry : angle 0.67038 / 0.34 (11917) SS BOND : bond 0.00288 / 0.14 ( 3) SS BOND : angle 1.95656 / 0.85 ( 6) hydrogen bonds : bond 0.03521 / 2.35 ( 414) hydrogen bonds : angle 5.15641 / 3.81 ( 1182) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 288 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8204 (mtmm) cc_final: 0.7644 (mtmm) REVERT: A 198 MET cc_start: 0.7213 (ttm) cc_final: 0.6942 (ttm) REVERT: A 243 MET cc_start: 0.8105 (mmm) cc_final: 0.7686 (mmm) REVERT: A 251 ASP cc_start: 0.7602 (t70) cc_final: 0.6914 (t0) REVERT: A 345 LYS cc_start: 0.8494 (tptt) cc_final: 0.8141 (tptt) REVERT: A 347 ASN cc_start: 0.7597 (m-40) cc_final: 0.7315 (m-40) REVERT: A 353 LEU cc_start: 0.8339 (tp) cc_final: 0.8103 (tt) REVERT: B 83 ASP cc_start: 0.7804 (t0) cc_final: 0.7425 (t0) REVERT: B 101 MET cc_start: 0.8122 (mtp) cc_final: 0.7814 (mtm) REVERT: B 156 GLN cc_start: 0.7160 (mt0) cc_final: 0.6833 (mt0) REVERT: B 175 GLN cc_start: 0.7928 (pp30) cc_final: 0.7556 (pp30) REVERT: B 207 SER cc_start: 0.6978 (t) cc_final: 0.6517 (p) REVERT: B 212 ASP cc_start: 0.7866 (t0) cc_final: 0.7425 (p0) REVERT: B 234 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: B 251 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.6605 (tpp80) REVERT: B 259 GLN cc_start: 0.7926 (pt0) cc_final: 0.7707 (pt0) REVERT: B 292 PHE cc_start: 0.6944 (OUTLIER) cc_final: 0.6546 (m-80) REVERT: C 11 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7634 (tm-30) REVERT: C 15 LEU cc_start: 0.8208 (mt) cc_final: 0.7529 (mt) REVERT: S 34 MET cc_start: 0.7257 (mmm) cc_final: 0.6811 (mmm) REVERT: S 176 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8181 (mt) REVERT: S 190 ARG cc_start: 0.6579 (ptt-90) cc_final: 0.6174 (ptt-90) REVERT: R 54 MET cc_start: 0.6514 (ptp) cc_final: 0.6103 (ptp) REVERT: R 84 PHE cc_start: 0.6281 (m-80) cc_final: 0.5807 (m-80) REVERT: R 121 MET cc_start: 0.7920 (mtt) cc_final: 0.7488 (mtt) REVERT: R 173 PHE cc_start: 0.6969 (t80) cc_final: 0.6635 (t80) REVERT: R 184 GLN cc_start: 0.7972 (pm20) cc_final: 0.7749 (pm20) REVERT: R 436 SER cc_start: 0.8513 (m) cc_final: 0.8276 (t) REVERT: R 449 ASN cc_start: 0.7524 (m-40) cc_final: 0.7272 (m-40) outliers start: 39 outliers final: 32 residues processed: 302 average time/residue: 0.0931 time to fit residues: 38.4001 Evaluate side-chains 311 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 276 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 176 LEU Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 437 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS B 142 HIS S 39 GLN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN R 68 ASN R 417 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.154640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.135235 restraints weight = 14352.030| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.99 r_work: 0.3684 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8766 Z= 0.160 Angle : 0.680 10.189 11923 Z= 0.343 Chirality : 0.045 0.222 1386 Planarity : 0.004 0.041 1484 Dihedral : 5.166 47.242 1221 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.14 % Allowed : 28.52 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.26), residues: 1104 helix: 1.63 (0.26), residues: 396 sheet: -0.79 (0.32), residues: 265 loop : -1.15 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.026 0.002 TYR R 140 PHE 0.018 0.002 PHE R 186 TRP 0.066 0.002 TRP B 82 HIS 0.015 0.002 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 8763) covalent geometry : angle 0.67944 / 0.34 (11917) SS BOND : bond 0.00192 / 0.10 ( 3) SS BOND : angle 1.69274 / 0.76 ( 6) hydrogen bonds : bond 0.03467 / 2.32 ( 414) hydrogen bonds : angle 5.11814 / 3.78 ( 1182) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 294 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8174 (mtmm) cc_final: 0.7602 (mtmm) REVERT: A 198 MET cc_start: 0.7141 (ttm) cc_final: 0.6878 (ttm) REVERT: A 243 MET cc_start: 0.8115 (mmm) cc_final: 0.7678 (mmm) REVERT: A 251 ASP cc_start: 0.7584 (t70) cc_final: 0.6904 (t0) REVERT: A 345 LYS cc_start: 0.8507 (tptt) cc_final: 0.8138 (tptt) REVERT: A 347 ASN cc_start: 0.7603 (m-40) cc_final: 0.7131 (m-40) REVERT: A 353 LEU cc_start: 0.8339 (tp) cc_final: 0.8087 (tt) REVERT: B 171 ILE cc_start: 0.7826 (mm) cc_final: 0.7067 (mt) REVERT: B 175 GLN cc_start: 0.7923 (pp30) cc_final: 0.7613 (pp30) REVERT: B 207 SER cc_start: 0.6942 (t) cc_final: 0.6502 (p) REVERT: B 212 ASP cc_start: 0.7835 (t0) cc_final: 0.7287 (p0) REVERT: B 234 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7529 (m-80) REVERT: B 259 GLN cc_start: 0.7950 (pt0) cc_final: 0.7734 (pt0) REVERT: B 289 TYR cc_start: 0.8417 (m-80) cc_final: 0.8206 (m-80) REVERT: B 292 PHE cc_start: 0.6900 (OUTLIER) cc_final: 0.6616 (m-80) REVERT: B 293 ASN cc_start: 0.7498 (t0) cc_final: 0.7283 (t0) REVERT: C 11 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7619 (tm-30) REVERT: C 15 LEU cc_start: 0.8197 (mt) cc_final: 0.7529 (mt) REVERT: S 34 MET cc_start: 0.7226 (mmm) cc_final: 0.6749 (mmm) REVERT: S 176 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8124 (mm) REVERT: S 190 ARG cc_start: 0.6571 (ptt-90) cc_final: 0.6156 (ptt-90) REVERT: R 54 MET cc_start: 0.6517 (ptp) cc_final: 0.6174 (ptp) REVERT: R 84 PHE cc_start: 0.6291 (m-80) cc_final: 0.5833 (m-80) REVERT: R 121 MET cc_start: 0.7915 (mtt) cc_final: 0.7502 (mtt) REVERT: R 123 LEU cc_start: 0.8199 (mt) cc_final: 0.7612 (mt) REVERT: R 173 PHE cc_start: 0.6956 (t80) cc_final: 0.6585 (t80) REVERT: R 436 SER cc_start: 0.8614 (m) cc_final: 0.8391 (t) REVERT: R 449 ASN cc_start: 0.7462 (m-40) cc_final: 0.7232 (m-40) outliers start: 37 outliers final: 32 residues processed: 305 average time/residue: 0.0953 time to fit residues: 39.7744 Evaluate side-chains 319 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 284 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 176 LEU Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 437 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.6980 chunk 93 optimal weight: 0.0060 chunk 42 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 35 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 417 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.156000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.136874 restraints weight = 14350.704| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.99 r_work: 0.3699 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8766 Z= 0.143 Angle : 0.680 10.438 11923 Z= 0.342 Chirality : 0.045 0.223 1386 Planarity : 0.004 0.043 1484 Dihedral : 5.163 52.375 1221 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.47 % Allowed : 28.19 % Favored : 67.34 % 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: -0.13 (0.26), residues: 1104 helix: 1.66 (0.26), residues: 396 sheet: -0.92 (0.31), residues: 276 loop : -1.10 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 251 TYR 0.017 0.001 TYR S 103 PHE 0.012 0.002 PHE A 250 TRP 0.060 0.002 TRP B 82 HIS 0.009 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 8763) covalent geometry : angle 0.67968 / 0.34 (11917) SS BOND : bond 0.00213 / 0.11 ( 3) SS BOND : angle 1.59008 / 0.73 ( 6) hydrogen bonds : bond 0.03411 / 2.30 ( 414) hydrogen bonds : angle 5.05477 / 3.74 ( 1182) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 289 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8080 (mtmm) cc_final: 0.7554 (mtmm) REVERT: A 198 MET cc_start: 0.7129 (ttm) cc_final: 0.6885 (ttm) REVERT: A 243 MET cc_start: 0.8115 (mmm) cc_final: 0.7677 (mmm) REVERT: A 251 ASP cc_start: 0.7569 (t70) cc_final: 0.6888 (t0) REVERT: A 317 LYS cc_start: 0.8432 (mtmm) cc_final: 0.8096 (mtpp) REVERT: A 345 LYS cc_start: 0.8470 (tptt) cc_final: 0.8087 (tptt) REVERT: A 347 ASN cc_start: 0.7597 (m-40) cc_final: 0.7146 (m-40) REVERT: B 114 CYS cc_start: 0.7388 (t) cc_final: 0.6329 (p) REVERT: B 171 ILE cc_start: 0.7757 (mm) cc_final: 0.6988 (mt) REVERT: B 175 GLN cc_start: 0.7885 (pp30) cc_final: 0.7587 (pp30) REVERT: B 207 SER cc_start: 0.6903 (t) cc_final: 0.6470 (p) REVERT: B 212 ASP cc_start: 0.7821 (t0) cc_final: 0.7295 (p0) REVERT: B 234 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7510 (m-80) REVERT: B 247 ASP cc_start: 0.7523 (m-30) cc_final: 0.7305 (m-30) REVERT: B 292 PHE cc_start: 0.6749 (OUTLIER) cc_final: 0.6473 (m-80) REVERT: B 295 ASN cc_start: 0.8581 (m-40) cc_final: 0.8247 (m-40) REVERT: B 304 ARG cc_start: 0.8249 (ttp-170) cc_final: 0.7685 (ttp-170) REVERT: C 11 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7609 (tm-30) REVERT: C 15 LEU cc_start: 0.8186 (mt) cc_final: 0.7507 (mt) REVERT: S 34 MET cc_start: 0.7258 (mmm) cc_final: 0.6741 (mmm) REVERT: S 165 PHE cc_start: 0.8459 (m-10) cc_final: 0.8219 (m-80) REVERT: S 176 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8144 (mm) REVERT: S 190 ARG cc_start: 0.6524 (ptt-90) cc_final: 0.6202 (ptt-90) REVERT: R 54 MET cc_start: 0.6490 (ptp) cc_final: 0.6148 (ptp) REVERT: R 84 PHE cc_start: 0.6277 (m-80) cc_final: 0.5809 (m-80) REVERT: R 121 MET cc_start: 0.7883 (mtt) cc_final: 0.7458 (mtt) REVERT: R 130 ARG cc_start: 0.8071 (mmt90) cc_final: 0.7849 (tpp80) REVERT: R 140 TYR cc_start: 0.8015 (t80) cc_final: 0.7730 (t80) REVERT: R 173 PHE cc_start: 0.6969 (t80) cc_final: 0.6607 (t80) REVERT: R 436 SER cc_start: 0.8603 (m) cc_final: 0.8371 (t) REVERT: R 449 ASN cc_start: 0.7462 (m-40) cc_final: 0.7240 (m-40) outliers start: 40 outliers final: 30 residues processed: 300 average time/residue: 0.0928 time to fit residues: 38.3174 Evaluate side-chains 321 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 288 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 176 LEU Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 122 ASN Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 437 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 39 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS A 256 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 417 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.154443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.135040 restraints weight = 14287.924| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.99 r_work: 0.3683 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8766 Z= 0.173 Angle : 0.706 10.801 11923 Z= 0.356 Chirality : 0.046 0.224 1386 Planarity : 0.004 0.042 1484 Dihedral : 5.208 54.993 1221 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.91 % Allowed : 29.75 % Favored : 66.33 % 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: -0.17 (0.26), residues: 1104 helix: 1.50 (0.26), residues: 401 sheet: -0.93 (0.31), residues: 275 loop : -1.03 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 251 TYR 0.019 0.002 TYR S 216 PHE 0.023 0.002 PHE R 128 TRP 0.060 0.002 TRP B 82 HIS 0.008 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 8763) covalent geometry : angle 0.70520 / 0.36 (11917) SS BOND : bond 0.00232 / 0.11 ( 3) SS BOND : angle 1.33192 / 0.59 ( 6) hydrogen bonds : bond 0.03512 / 2.36 ( 414) hydrogen bonds : angle 5.13547 / 3.78 ( 1182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1945.42 seconds wall clock time: 34 minutes 20.16 seconds (2060.16 seconds total)