Starting phenix.real_space_refine on Wed Mar 4 03:27:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v68_31738/03_2026/7v68_31738.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v68_31738/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7v68_31738/03_2026/7v68_31738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v68_31738/03_2026/7v68_31738.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v68_31738/03_2026/7v68_31738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v68_31738/03_2026/7v68_31738.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 2.04, per 1000 atoms: 0.24 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: 0.69 Conformation dependent library (CDL) restraints added in 367.1 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: 0.30 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: 1.45 Time building geometry restraints manager: 0.94 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 - 22.59: 4861 22.59 - 45.17: 260 45.17 - 67.76: 10 67.76 - 90.35: 8 90.35 - 112.94: 1 Dihedral angle restraints: 5140 sinusoidal: 1881 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 5137 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.800 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 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 : 12.843 112.936 3027 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 covalent geometry : bond 0.00715 ( 8763) covalent geometry : angle 0.83408 (11917) SS BOND : bond 0.00306 ( 3) SS BOND : angle 1.37550 ( 6) hydrogen bonds : bond 0.17351 ( 414) hydrogen bonds : angle 6.95374 ( 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 : 0.308 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: 0.0961 time to fit residues: 40.7776 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 : 0.255 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4066 r_free = 0.4066 target = 0.156289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.136945 restraints weight = 14439.715| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 3.01 r_work: 0.3712 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8766 Z= 0.161 Angle : 0.667 8.892 11923 Z= 0.344 Chirality : 0.045 0.280 1386 Planarity : 0.005 0.058 1484 Dihedral : 5.827 82.757 1226 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.57 % Allowed : 14.32 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.25), residues: 1104 helix: 1.38 (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 0.000 ARG S 148 TYR 0.022 0.002 TYR S 216 PHE 0.017 0.002 PHE A 191 TRP 0.017 0.002 TRP R 435 HIS 0.012 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 8763) covalent geometry : angle 0.66705 (11917) SS BOND : bond 0.00366 ( 3) SS BOND : angle 1.17536 ( 6) hydrogen bonds : bond 0.04091 ( 414) hydrogen bonds : angle 5.49976 ( 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 324 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 310 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7754 (tm-30) REVERT: A 35 LYS cc_start: 0.7967 (mtmm) cc_final: 0.7458 (mtmm) REVERT: A 198 MET cc_start: 0.7104 (ttm) cc_final: 0.6821 (ttm) REVERT: A 251 ASP cc_start: 0.7378 (t70) cc_final: 0.6758 (t0) REVERT: A 270 LYS cc_start: 0.7985 (mtmm) cc_final: 0.7542 (mtmm) REVERT: A 271 LYS cc_start: 0.6756 (ptpp) cc_final: 0.6305 (ptpp) REVERT: A 274 PHE cc_start: 0.6768 (t80) cc_final: 0.6288 (t80) REVERT: A 330 LYS cc_start: 0.8264 (mppt) cc_final: 0.8059 (mppt) REVERT: A 347 ASN cc_start: 0.7536 (m-40) cc_final: 0.7018 (m-40) REVERT: B 45 MET cc_start: 0.8136 (mtm) cc_final: 0.7904 (mtp) REVERT: B 63 TRP cc_start: 0.8040 (m100) cc_final: 0.7664 (m100) REVERT: B 65 THR cc_start: 0.7902 (m) cc_final: 0.7640 (p) REVERT: B 114 CYS cc_start: 0.6950 (t) cc_final: 0.6407 (p) REVERT: B 170 ASP cc_start: 0.7648 (t0) cc_final: 0.7396 (t0) REVERT: B 175 GLN cc_start: 0.7851 (pp30) cc_final: 0.7570 (pp30) REVERT: B 176 GLN cc_start: 0.8283 (pt0) cc_final: 0.7769 (pt0) REVERT: B 220 GLN cc_start: 0.6662 (mt0) cc_final: 0.6438 (mt0) REVERT: B 237 ASN cc_start: 0.8195 (p0) cc_final: 0.7990 (p0) REVERT: B 246 ASP cc_start: 0.8312 (t0) cc_final: 0.7666 (t0) REVERT: B 253 PHE cc_start: 0.7939 (m-10) cc_final: 0.7572 (m-80) REVERT: B 259 GLN cc_start: 0.7733 (pt0) cc_final: 0.7385 (pt0) REVERT: B 275 SER cc_start: 0.8123 (m) cc_final: 0.7850 (p) REVERT: B 335 PHE cc_start: 0.7977 (m-80) cc_final: 0.7766 (m-80) REVERT: C 15 LEU cc_start: 0.8110 (mt) cc_final: 0.7725 (mt) REVERT: S 176 LEU cc_start: 0.8510 (mm) cc_final: 0.8264 (mm) REVERT: S 182 ASN cc_start: 0.6938 (m110) cc_final: 0.6563 (m110) REVERT: R 52 LEU cc_start: 0.7267 (mt) cc_final: 0.7023 (mt) REVERT: R 54 MET cc_start: 0.6546 (ptp) cc_final: 0.6260 (ptp) REVERT: R 84 PHE cc_start: 0.6579 (m-80) cc_final: 0.6133 (m-80) REVERT: R 86 MET cc_start: 0.4808 (mmp) cc_final: 0.4310 (mmp) REVERT: R 89 TYR cc_start: 0.6799 (t80) cc_final: 0.6320 (t80) REVERT: R 93 ILE cc_start: 0.6155 (mt) cc_final: 0.5793 (mt) REVERT: R 111 LEU cc_start: 0.7659 (tt) cc_final: 0.7413 (tp) REVERT: R 121 MET cc_start: 0.8058 (mtt) cc_final: 0.7621 (mtt) REVERT: R 173 PHE cc_start: 0.6924 (t80) cc_final: 0.6632 (t80) REVERT: R 187 ILE cc_start: 0.7357 (tp) cc_final: 0.7117 (tp) REVERT: R 449 ASN cc_start: 0.7475 (m-40) cc_final: 0.7020 (m-40) outliers start: 14 outliers final: 12 residues processed: 314 average time/residue: 0.0945 time to fit residues: 40.3739 Evaluate side-chains 304 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 292 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 15 optimal weight: 0.0670 chunk 53 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 75 optimal weight: 0.3980 chunk 66 optimal weight: 0.7980 chunk 58 optimal weight: 0.0270 chunk 69 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 67 optimal weight: 0.0970 chunk 22 optimal weight: 2.9990 overall best weight: 0.2574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 241 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.158213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.139227 restraints weight = 14371.466| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.92 r_work: 0.3748 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8766 Z= 0.125 Angle : 0.625 8.188 11923 Z= 0.320 Chirality : 0.043 0.223 1386 Planarity : 0.004 0.049 1484 Dihedral : 5.127 48.776 1226 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.91 % Allowed : 17.79 % Favored : 79.31 % 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: -0.21 (0.25), residues: 1104 helix: 1.48 (0.25), residues: 396 sheet: -0.84 (0.30), residues: 267 loop : -1.12 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 251 TYR 0.020 0.001 TYR B 264 PHE 0.012 0.001 PHE B 235 TRP 0.021 0.001 TRP B 82 HIS 0.012 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8763) covalent geometry : angle 0.62444 (11917) SS BOND : bond 0.00090 ( 3) SS BOND : angle 1.02139 ( 6) hydrogen bonds : bond 0.03828 ( 414) hydrogen bonds : angle 5.29676 ( 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 333 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 307 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.7871 (mtmm) cc_final: 0.7337 (mtmm) REVERT: A 251 ASP cc_start: 0.7352 (t70) cc_final: 0.6693 (t0) REVERT: A 270 LYS cc_start: 0.8026 (mtmm) cc_final: 0.7580 (mtmm) REVERT: A 274 PHE cc_start: 0.6719 (t80) cc_final: 0.6203 (t80) REVERT: A 330 LYS cc_start: 0.8239 (mppt) cc_final: 0.7997 (mppt) REVERT: A 345 LYS cc_start: 0.8523 (tptt) cc_final: 0.8231 (tptt) REVERT: A 347 ASN cc_start: 0.7491 (m-40) cc_final: 0.7017 (m-40) REVERT: A 353 LEU cc_start: 0.8078 (tp) cc_final: 0.7781 (tt) REVERT: B 45 MET cc_start: 0.8135 (mtm) cc_final: 0.7896 (mtp) REVERT: B 49 ARG cc_start: 0.7841 (mpt180) cc_final: 0.7582 (mmt90) REVERT: B 65 THR cc_start: 0.7857 (m) cc_final: 0.7591 (p) REVERT: B 110 ASN cc_start: 0.8036 (m-40) cc_final: 0.7744 (m110) REVERT: B 146 LEU cc_start: 0.7852 (mm) cc_final: 0.7643 (mt) REVERT: B 170 ASP cc_start: 0.7525 (t0) cc_final: 0.7316 (t0) REVERT: B 175 GLN cc_start: 0.7793 (pp30) cc_final: 0.7542 (pp30) REVERT: B 237 ASN cc_start: 0.8144 (p0) cc_final: 0.7909 (p0) REVERT: B 249 THR cc_start: 0.8291 (p) cc_final: 0.8075 (p) REVERT: B 259 GLN cc_start: 0.7822 (pt0) cc_final: 0.7562 (pt0) REVERT: B 304 ARG cc_start: 0.8135 (ttp80) cc_final: 0.7918 (ttt-90) REVERT: C 15 LEU cc_start: 0.8096 (mt) cc_final: 0.7701 (mt) REVERT: C 27 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7467 (mtm180) REVERT: S 165 PHE cc_start: 0.8188 (m-10) cc_final: 0.7672 (m-80) REVERT: S 167 GLN cc_start: 0.7962 (tt0) cc_final: 0.7762 (tt0) REVERT: S 176 LEU cc_start: 0.8479 (mm) cc_final: 0.8051 (mm) REVERT: S 182 ASN cc_start: 0.6845 (m110) cc_final: 0.6481 (m110) REVERT: R 52 LEU cc_start: 0.7261 (mt) cc_final: 0.7020 (mt) REVERT: R 54 MET cc_start: 0.6235 (ptp) cc_final: 0.5978 (ptp) REVERT: R 84 PHE cc_start: 0.6489 (m-80) cc_final: 0.6012 (m-80) REVERT: R 86 MET cc_start: 0.4709 (mmp) cc_final: 0.4291 (mmp) REVERT: R 109 LEU cc_start: 0.7596 (mm) cc_final: 0.7275 (pp) REVERT: R 111 LEU cc_start: 0.7627 (tt) cc_final: 0.7409 (tp) REVERT: R 121 MET cc_start: 0.7882 (mtt) cc_final: 0.7524 (mtt) REVERT: R 173 PHE cc_start: 0.6784 (t80) cc_final: 0.6504 (t80) REVERT: R 449 ASN cc_start: 0.7394 (m-40) cc_final: 0.7116 (m-40) outliers start: 26 outliers final: 22 residues processed: 316 average time/residue: 0.0924 time to fit residues: 39.7779 Evaluate side-chains 314 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 291 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL 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 102 THR Chi-restraints excluded: chain B residue 239 ASN 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 C residue 27 ARG Chi-restraints excluded: chain S residue 69 THR 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 148 MET Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 441 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: 0.0070 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 0.0470 chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 157 ASN ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.157786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.138525 restraints weight = 14629.884| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 3.05 r_work: 0.3732 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.217 8766 Z= 0.173 Angle : 0.636 10.396 11923 Z= 0.325 Chirality : 0.043 0.222 1386 Planarity : 0.004 0.049 1484 Dihedral : 5.410 48.778 1226 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.68 % Allowed : 21.48 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.25), residues: 1104 helix: 1.47 (0.25), residues: 396 sheet: -0.84 (0.30), residues: 267 loop : -1.12 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.020 0.001 TYR B 264 PHE 0.012 0.001 PHE B 235 TRP 0.020 0.001 TRP B 82 HIS 0.012 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8763) covalent geometry : angle 0.62627 (11917) SS BOND : bond 0.12540 ( 3) SS BOND : angle 4.87494 ( 6) hydrogen bonds : bond 0.03829 ( 414) hydrogen bonds : angle 5.29686 ( 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 315 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 291 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.7864 (mtmm) cc_final: 0.7329 (mtmm) REVERT: A 251 ASP cc_start: 0.7390 (t70) cc_final: 0.6720 (t0) REVERT: A 270 LYS cc_start: 0.8030 (mtmm) cc_final: 0.7579 (mtmm) REVERT: A 274 PHE cc_start: 0.6747 (t80) cc_final: 0.6225 (t80) REVERT: A 330 LYS cc_start: 0.8259 (mppt) cc_final: 0.8014 (mppt) REVERT: A 345 LYS cc_start: 0.8528 (tptt) cc_final: 0.8239 (tptt) REVERT: A 347 ASN cc_start: 0.7498 (m-40) cc_final: 0.7021 (m-40) REVERT: A 353 LEU cc_start: 0.8075 (tp) cc_final: 0.7784 (tt) REVERT: B 45 MET cc_start: 0.8166 (mtm) cc_final: 0.7926 (mtp) REVERT: B 49 ARG cc_start: 0.7819 (mpt180) cc_final: 0.7573 (mmt90) REVERT: B 65 THR cc_start: 0.7840 (m) cc_final: 0.7587 (p) REVERT: B 110 ASN cc_start: 0.8064 (m-40) cc_final: 0.7779 (m110) REVERT: B 146 LEU cc_start: 0.7839 (mm) cc_final: 0.7632 (mt) REVERT: B 170 ASP cc_start: 0.7541 (t0) cc_final: 0.7327 (t0) REVERT: B 175 GLN cc_start: 0.7782 (pp30) cc_final: 0.7542 (pp30) REVERT: B 237 ASN cc_start: 0.8168 (p0) cc_final: 0.7921 (p0) REVERT: B 249 THR cc_start: 0.8309 (p) cc_final: 0.8083 (p) REVERT: B 259 GLN cc_start: 0.7867 (pt0) cc_final: 0.7583 (pt0) REVERT: B 304 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7937 (ttt-90) REVERT: C 15 LEU cc_start: 0.8089 (mt) cc_final: 0.7704 (mt) REVERT: C 27 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7476 (mtm180) REVERT: S 165 PHE cc_start: 0.8212 (m-10) cc_final: 0.7693 (m-80) REVERT: S 176 LEU cc_start: 0.8471 (mm) cc_final: 0.8066 (mm) REVERT: S 182 ASN cc_start: 0.6850 (m110) cc_final: 0.6481 (m110) REVERT: R 52 LEU cc_start: 0.7268 (mt) cc_final: 0.7029 (mt) REVERT: R 54 MET cc_start: 0.6272 (ptp) cc_final: 0.6007 (ptp) REVERT: R 84 PHE cc_start: 0.6511 (m-80) cc_final: 0.6027 (m-80) REVERT: R 86 MET cc_start: 0.4722 (mmp) cc_final: 0.4313 (mmp) REVERT: R 109 LEU cc_start: 0.7614 (mm) cc_final: 0.7285 (pp) REVERT: R 111 LEU cc_start: 0.7650 (tt) cc_final: 0.7430 (tp) REVERT: R 121 MET cc_start: 0.7920 (mtt) cc_final: 0.7566 (mtt) REVERT: R 173 PHE cc_start: 0.6780 (t80) cc_final: 0.6498 (t80) REVERT: R 449 ASN cc_start: 0.7410 (m-40) cc_final: 0.7119 (m-40) outliers start: 24 outliers final: 22 residues processed: 299 average time/residue: 0.0917 time to fit residues: 37.2961 Evaluate side-chains 314 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 291 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL 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 102 THR Chi-restraints excluded: chain B residue 239 ASN 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 C residue 27 ARG Chi-restraints excluded: chain S residue 69 THR 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 148 MET Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 441 LEU 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: 1.9990 chunk 25 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS B 132 ASN B 239 ASN B 313 ASN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 157 ASN S 167 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.154037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.134773 restraints weight = 14413.726| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 3.03 r_work: 0.3684 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.2285 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= 0.189 Angle : 0.646 8.034 11923 Z= 0.336 Chirality : 0.045 0.234 1386 Planarity : 0.004 0.047 1484 Dihedral : 5.233 43.258 1226 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.47 % Allowed : 20.36 % Favored : 75.17 % 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: -0.22 (0.25), residues: 1104 helix: 1.59 (0.26), residues: 396 sheet: -0.97 (0.30), residues: 277 loop : -1.15 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 52 TYR 0.017 0.002 TYR S 103 PHE 0.018 0.002 PHE B 235 TRP 0.039 0.002 TRP B 82 HIS 0.013 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8763) covalent geometry : angle 0.64572 (11917) SS BOND : bond 0.00267 ( 3) SS BOND : angle 1.02722 ( 6) hydrogen bonds : bond 0.03838 ( 414) hydrogen bonds : angle 5.29854 ( 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 335 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 295 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7692 (tm-30) REVERT: A 35 LYS cc_start: 0.8155 (mtmm) cc_final: 0.7597 (mtmm) REVERT: A 198 MET cc_start: 0.7201 (ttm) cc_final: 0.6896 (ttm) REVERT: A 251 ASP cc_start: 0.7400 (t70) cc_final: 0.6737 (t0) REVERT: A 345 LYS cc_start: 0.8541 (tptt) cc_final: 0.8251 (tptt) REVERT: A 347 ASN cc_start: 0.7510 (m-40) cc_final: 0.7034 (m-40) REVERT: B 45 MET cc_start: 0.8247 (mtm) cc_final: 0.7970 (mtp) REVERT: B 65 THR cc_start: 0.7976 (m) cc_final: 0.7671 (p) REVERT: B 83 ASP cc_start: 0.7909 (t0) cc_final: 0.7585 (t0) REVERT: B 132 ASN cc_start: 0.7608 (OUTLIER) cc_final: 0.7288 (p0) REVERT: B 170 ASP cc_start: 0.7568 (t0) cc_final: 0.7367 (t0) REVERT: B 175 GLN cc_start: 0.7849 (pp30) cc_final: 0.7605 (pp30) REVERT: B 211 TRP cc_start: 0.8059 (m100) cc_final: 0.7768 (m-10) REVERT: B 212 ASP cc_start: 0.7882 (t70) cc_final: 0.7322 (p0) REVERT: B 249 THR cc_start: 0.8317 (p) cc_final: 0.8070 (p) REVERT: B 253 PHE cc_start: 0.7983 (m-10) cc_final: 0.7627 (m-80) REVERT: B 259 GLN cc_start: 0.7950 (pt0) cc_final: 0.7718 (pt0) REVERT: B 304 ARG cc_start: 0.8285 (ttp80) cc_final: 0.8027 (ttp80) REVERT: C 15 LEU cc_start: 0.8155 (mt) cc_final: 0.7740 (mt) REVERT: C 27 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7518 (mtm180) REVERT: S 176 LEU cc_start: 0.8569 (mm) cc_final: 0.8235 (mm) REVERT: S 182 ASN cc_start: 0.7195 (m110) cc_final: 0.6794 (m-40) REVERT: R 54 MET cc_start: 0.6442 (ptp) cc_final: 0.6111 (ptp) REVERT: R 84 PHE cc_start: 0.6546 (m-80) cc_final: 0.6040 (m-80) REVERT: R 86 MET cc_start: 0.5442 (mmp) cc_final: 0.4769 (mmp) REVERT: R 89 TYR cc_start: 0.6759 (t80) cc_final: 0.6434 (t80) REVERT: R 111 LEU cc_start: 0.7693 (tt) cc_final: 0.7449 (tp) REVERT: R 121 MET cc_start: 0.7986 (mtt) cc_final: 0.7578 (mtt) REVERT: R 173 PHE cc_start: 0.6963 (t80) cc_final: 0.6648 (t80) REVERT: R 214 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6756 (tt) REVERT: R 441 LEU cc_start: 0.5518 (OUTLIER) cc_final: 0.5217 (pp) REVERT: R 449 ASN cc_start: 0.7463 (m-40) cc_final: 0.7228 (m-40) outliers start: 40 outliers final: 27 residues processed: 310 average time/residue: 0.0931 time to fit residues: 39.1165 Evaluate side-chains 319 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 288 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 132 ASN 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 246 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 27 ARG 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 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 148 MET Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 441 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 39 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 157 ASN ** S 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.154606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.135936 restraints weight = 14296.323| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.94 r_work: 0.3692 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.2379 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= 0.190 Angle : 0.646 8.034 11923 Z= 0.336 Chirality : 0.045 0.234 1386 Planarity : 0.004 0.047 1484 Dihedral : 5.232 43.258 1226 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 25.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.47 % Allowed : 22.93 % Favored : 73.60 % 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: -0.22 (0.25), residues: 1104 helix: 1.59 (0.26), residues: 396 sheet: -0.97 (0.30), residues: 277 loop : -1.15 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 52 TYR 0.017 0.002 TYR S 103 PHE 0.018 0.002 PHE B 235 TRP 0.039 0.002 TRP B 82 HIS 0.013 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 8763) covalent geometry : angle 0.64580 (11917) SS BOND : bond 0.00267 ( 3) SS BOND : angle 1.02722 ( 6) hydrogen bonds : bond 0.03838 ( 414) hydrogen bonds : angle 5.29854 ( 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 319 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 288 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7688 (tm-30) REVERT: A 35 LYS cc_start: 0.8146 (mtmm) cc_final: 0.7597 (mtmm) REVERT: A 198 MET cc_start: 0.7148 (ttm) cc_final: 0.6862 (ttm) REVERT: A 251 ASP cc_start: 0.7366 (t70) cc_final: 0.6706 (t0) REVERT: A 345 LYS cc_start: 0.8520 (tptt) cc_final: 0.8223 (tptt) REVERT: A 347 ASN cc_start: 0.7501 (m-40) cc_final: 0.7020 (m-40) REVERT: B 45 MET cc_start: 0.8250 (mtm) cc_final: 0.7966 (mtp) REVERT: B 65 THR cc_start: 0.7985 (m) cc_final: 0.7661 (p) REVERT: B 83 ASP cc_start: 0.7903 (t0) cc_final: 0.7595 (t0) REVERT: B 132 ASN cc_start: 0.7605 (OUTLIER) cc_final: 0.7299 (p0) REVERT: B 175 GLN cc_start: 0.7838 (pp30) cc_final: 0.7587 (pp30) REVERT: B 211 TRP cc_start: 0.8039 (m100) cc_final: 0.7741 (m-10) REVERT: B 212 ASP cc_start: 0.7873 (t70) cc_final: 0.7314 (p0) REVERT: B 249 THR cc_start: 0.8350 (p) cc_final: 0.8074 (p) REVERT: B 253 PHE cc_start: 0.7960 (m-10) cc_final: 0.7633 (m-80) REVERT: B 259 GLN cc_start: 0.7982 (pt0) cc_final: 0.7729 (pt0) REVERT: B 304 ARG cc_start: 0.8226 (ttp80) cc_final: 0.7985 (ttp80) REVERT: B 323 ASP cc_start: 0.7976 (p0) cc_final: 0.7771 (p0) REVERT: C 15 LEU cc_start: 0.8146 (mt) cc_final: 0.7734 (mt) REVERT: C 27 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7500 (mtm180) REVERT: S 176 LEU cc_start: 0.8609 (mm) cc_final: 0.8229 (mm) REVERT: S 182 ASN cc_start: 0.7200 (m110) cc_final: 0.6791 (m-40) REVERT: R 54 MET cc_start: 0.6394 (ptp) cc_final: 0.6054 (ptp) REVERT: R 84 PHE cc_start: 0.6506 (m-80) cc_final: 0.6017 (m-80) REVERT: R 86 MET cc_start: 0.5364 (mmp) cc_final: 0.4689 (mmp) REVERT: R 89 TYR cc_start: 0.6714 (t80) cc_final: 0.6418 (t80) REVERT: R 111 LEU cc_start: 0.7680 (tt) cc_final: 0.7433 (tp) REVERT: R 121 MET cc_start: 0.7941 (mtt) cc_final: 0.7534 (mtt) REVERT: R 173 PHE cc_start: 0.6913 (t80) cc_final: 0.6616 (t80) REVERT: R 214 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6753 (tt) REVERT: R 441 LEU cc_start: 0.5510 (OUTLIER) cc_final: 0.5213 (pp) REVERT: R 449 ASN cc_start: 0.7436 (m-40) cc_final: 0.7224 (m-40) outliers start: 31 outliers final: 27 residues processed: 296 average time/residue: 0.0948 time to fit residues: 38.0563 Evaluate side-chains 318 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 287 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 132 ASN 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 246 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 27 ARG 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 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 148 MET Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 441 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 48 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS B 110 ASN B 132 ASN B 239 ASN B 313 ASN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 157 ASN S 167 GLN ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.154226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.134921 restraints weight = 14430.690| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 3.01 r_work: 0.3682 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2531 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= 0.181 Angle : 0.695 13.788 11923 Z= 0.352 Chirality : 0.046 0.227 1386 Planarity : 0.004 0.044 1484 Dihedral : 5.250 42.005 1226 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.81 % Allowed : 21.70 % Favored : 73.49 % 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: -0.25 (0.25), residues: 1104 helix: 1.60 (0.25), residues: 396 sheet: -1.02 (0.30), residues: 281 loop : -1.19 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.018 0.002 TYR B 264 PHE 0.023 0.002 PHE R 403 TRP 0.026 0.002 TRP B 82 HIS 0.012 0.002 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 8763) covalent geometry : angle 0.69517 (11917) SS BOND : bond 0.00314 ( 3) SS BOND : angle 0.97130 ( 6) hydrogen bonds : bond 0.03815 ( 414) hydrogen bonds : angle 5.27403 ( 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 334 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 291 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7687 (tm-30) REVERT: A 35 LYS cc_start: 0.8160 (mtmm) cc_final: 0.7612 (mtmm) REVERT: A 198 MET cc_start: 0.7204 (ttm) cc_final: 0.6917 (ttm) REVERT: A 251 ASP cc_start: 0.7334 (t70) cc_final: 0.6685 (t0) REVERT: A 345 LYS cc_start: 0.8548 (tptt) cc_final: 0.8262 (tptt) REVERT: A 347 ASN cc_start: 0.7514 (m-40) cc_final: 0.7033 (m-40) REVERT: B 45 MET cc_start: 0.8215 (mtm) cc_final: 0.7918 (mtp) REVERT: B 65 THR cc_start: 0.7869 (m) cc_final: 0.7614 (p) REVERT: B 83 ASP cc_start: 0.7917 (t0) cc_final: 0.7588 (t0) REVERT: B 175 GLN cc_start: 0.7874 (pp30) cc_final: 0.7614 (pp30) REVERT: B 212 ASP cc_start: 0.7939 (t70) cc_final: 0.7430 (p0) REVERT: B 249 THR cc_start: 0.8379 (p) cc_final: 0.8118 (p) REVERT: B 259 GLN cc_start: 0.7857 (pt0) cc_final: 0.7618 (pt0) REVERT: B 304 ARG cc_start: 0.8330 (ttp80) cc_final: 0.8054 (ttp80) REVERT: B 323 ASP cc_start: 0.8028 (p0) cc_final: 0.7819 (p0) REVERT: C 11 GLN cc_start: 0.8144 (tm130) cc_final: 0.7624 (tm130) REVERT: C 15 LEU cc_start: 0.8170 (mt) cc_final: 0.7533 (mt) REVERT: C 27 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7511 (mtm180) REVERT: S 176 LEU cc_start: 0.8574 (mm) cc_final: 0.8159 (mm) REVERT: S 180 MET cc_start: 0.5710 (ttp) cc_final: 0.5228 (ttm) REVERT: S 182 ASN cc_start: 0.7223 (m110) cc_final: 0.6797 (m-40) REVERT: R 54 MET cc_start: 0.6466 (ptp) cc_final: 0.6092 (ptp) REVERT: R 84 PHE cc_start: 0.6390 (m-80) cc_final: 0.5927 (m-80) REVERT: R 111 LEU cc_start: 0.7689 (tt) cc_final: 0.7431 (tp) REVERT: R 121 MET cc_start: 0.7933 (mtt) cc_final: 0.7564 (mtt) REVERT: R 151 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6658 (pp) REVERT: R 173 PHE cc_start: 0.6938 (t80) cc_final: 0.6625 (t80) REVERT: R 183 ASN cc_start: 0.6732 (OUTLIER) cc_final: 0.6482 (p0) REVERT: R 214 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6717 (tt) outliers start: 43 outliers final: 31 residues processed: 304 average time/residue: 0.0935 time to fit residues: 38.4329 Evaluate side-chains 315 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 280 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 271 LYS 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 143 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 C residue 27 ARG 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 119 SER Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 219 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 101 optimal weight: 3.9990 chunk 94 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 65 optimal weight: 0.0370 chunk 47 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 157 ASN S 167 GLN ** 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 = 0.4055 r_free = 0.4055 target = 0.155593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.136308 restraints weight = 14212.919| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 3.03 r_work: 0.3695 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2663 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= 0.144 Angle : 0.676 13.227 11923 Z= 0.341 Chirality : 0.045 0.227 1386 Planarity : 0.004 0.043 1484 Dihedral : 5.191 43.147 1226 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.14 % Allowed : 23.38 % Favored : 72.48 % 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: -0.21 (0.25), residues: 1104 helix: 1.67 (0.26), residues: 396 sheet: -0.98 (0.30), residues: 271 loop : -1.23 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 251 TYR 0.019 0.002 TYR S 103 PHE 0.017 0.002 PHE R 403 TRP 0.021 0.002 TRP B 82 HIS 0.020 0.002 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8763) covalent geometry : angle 0.67574 (11917) SS BOND : bond 0.00566 ( 3) SS BOND : angle 1.30451 ( 6) hydrogen bonds : bond 0.03656 ( 414) hydrogen bonds : angle 5.19528 ( 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 332 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 295 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7672 (tm-30) REVERT: A 35 LYS cc_start: 0.8146 (mtmm) cc_final: 0.7595 (mtmm) REVERT: A 198 MET cc_start: 0.7182 (ttm) cc_final: 0.6903 (ttm) REVERT: A 251 ASP cc_start: 0.7296 (t70) cc_final: 0.6648 (t0) REVERT: A 345 LYS cc_start: 0.8544 (tptt) cc_final: 0.8273 (tptt) REVERT: A 347 ASN cc_start: 0.7529 (m-40) cc_final: 0.7036 (m-40) REVERT: B 45 MET cc_start: 0.8187 (mtm) cc_final: 0.7911 (mtp) REVERT: B 65 THR cc_start: 0.7824 (m) cc_final: 0.7587 (p) REVERT: B 83 ASP cc_start: 0.7901 (t0) cc_final: 0.7540 (t0) REVERT: B 175 GLN cc_start: 0.7896 (pp30) cc_final: 0.7603 (pp30) REVERT: B 211 TRP cc_start: 0.7970 (m100) cc_final: 0.7444 (m100) REVERT: B 212 ASP cc_start: 0.7917 (t70) cc_final: 0.7566 (p0) REVERT: B 222 PHE cc_start: 0.8608 (m-10) cc_final: 0.8242 (m-80) REVERT: B 249 THR cc_start: 0.8389 (p) cc_final: 0.8179 (p) REVERT: B 253 PHE cc_start: 0.7900 (m-10) cc_final: 0.7475 (m-80) REVERT: B 289 TYR cc_start: 0.8398 (m-80) cc_final: 0.8118 (m-80) REVERT: C 11 GLN cc_start: 0.8192 (tm130) cc_final: 0.7607 (tm130) REVERT: C 15 LEU cc_start: 0.8187 (mt) cc_final: 0.7550 (mt) REVERT: S 60 TYR cc_start: 0.7747 (m-80) cc_final: 0.7226 (m-80) REVERT: S 176 LEU cc_start: 0.8488 (mm) cc_final: 0.8183 (mt) REVERT: S 180 MET cc_start: 0.5597 (ttp) cc_final: 0.5158 (ttm) REVERT: S 182 ASN cc_start: 0.7195 (m110) cc_final: 0.6769 (m-40) REVERT: R 54 MET cc_start: 0.6436 (ptp) cc_final: 0.6047 (ptp) REVERT: R 84 PHE cc_start: 0.6334 (m-80) cc_final: 0.5844 (m-80) REVERT: R 86 MET cc_start: 0.5218 (mmt) cc_final: 0.4829 (mmt) REVERT: R 109 LEU cc_start: 0.7643 (mm) cc_final: 0.7280 (pp) REVERT: R 111 LEU cc_start: 0.7656 (tt) cc_final: 0.7371 (tp) REVERT: R 121 MET cc_start: 0.7927 (mtt) cc_final: 0.7529 (mtt) REVERT: R 140 TYR cc_start: 0.8051 (t80) cc_final: 0.7534 (t80) REVERT: R 151 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6560 (pp) REVERT: R 173 PHE cc_start: 0.6877 (t80) cc_final: 0.6570 (t80) outliers start: 37 outliers final: 29 residues processed: 307 average time/residue: 0.0929 time to fit residues: 38.7945 Evaluate side-chains 309 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 279 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 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 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 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 166 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 151 LEU Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 219 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 0.0030 chunk 70 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 chunk 50 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 213 HIS B 259 GLN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4057 r_free = 0.4057 target = 0.155669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.136352 restraints weight = 14296.456| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 3.04 r_work: 0.3696 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8766 Z= 0.150 Angle : 0.697 12.831 11923 Z= 0.353 Chirality : 0.046 0.248 1386 Planarity : 0.004 0.043 1484 Dihedral : 5.236 43.689 1226 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.91 % Allowed : 24.72 % Favored : 71.36 % 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: -0.27 (0.25), residues: 1104 helix: 1.63 (0.26), residues: 396 sheet: -1.01 (0.30), residues: 271 loop : -1.27 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 251 TYR 0.020 0.002 TYR S 216 PHE 0.021 0.002 PHE A 274 TRP 0.019 0.002 TRP B 82 HIS 0.014 0.002 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8763) covalent geometry : angle 0.69631 (11917) SS BOND : bond 0.00214 ( 3) SS BOND : angle 1.88211 ( 6) hydrogen bonds : bond 0.03719 ( 414) hydrogen bonds : angle 5.24060 ( 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 318 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 283 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8137 (mtmm) cc_final: 0.7575 (mtmm) REVERT: A 198 MET cc_start: 0.7190 (ttm) cc_final: 0.6917 (ttm) REVERT: A 251 ASP cc_start: 0.7277 (t70) cc_final: 0.6643 (t0) REVERT: A 345 LYS cc_start: 0.8537 (tptt) cc_final: 0.8269 (tptt) REVERT: A 347 ASN cc_start: 0.7538 (m-40) cc_final: 0.7049 (m-40) REVERT: B 45 MET cc_start: 0.8162 (mtm) cc_final: 0.7922 (mtp) REVERT: B 65 THR cc_start: 0.7810 (m) cc_final: 0.7590 (p) REVERT: B 82 TRP cc_start: 0.7884 (m-10) cc_final: 0.7677 (m-10) REVERT: B 83 ASP cc_start: 0.7895 (t0) cc_final: 0.7529 (t0) REVERT: B 175 GLN cc_start: 0.7866 (pp30) cc_final: 0.7581 (pp30) REVERT: B 212 ASP cc_start: 0.7907 (t70) cc_final: 0.7585 (p0) REVERT: B 249 THR cc_start: 0.8435 (p) cc_final: 0.8188 (p) REVERT: B 253 PHE cc_start: 0.7876 (m-10) cc_final: 0.7531 (m-80) REVERT: B 289 TYR cc_start: 0.8409 (m-80) cc_final: 0.8116 (m-80) REVERT: C 11 GLN cc_start: 0.8197 (tm130) cc_final: 0.7610 (tm130) REVERT: C 15 LEU cc_start: 0.8197 (mt) cc_final: 0.7544 (mt) REVERT: S 176 LEU cc_start: 0.8491 (mm) cc_final: 0.8178 (mt) REVERT: S 180 MET cc_start: 0.5620 (ttp) cc_final: 0.5175 (ttm) REVERT: S 182 ASN cc_start: 0.7187 (m110) cc_final: 0.6750 (m-40) REVERT: R 54 MET cc_start: 0.6457 (ptp) cc_final: 0.6064 (ptp) REVERT: R 74 LEU cc_start: 0.8192 (tp) cc_final: 0.7870 (tt) REVERT: R 84 PHE cc_start: 0.6332 (m-80) cc_final: 0.5827 (m-80) REVERT: R 86 MET cc_start: 0.5233 (mmt) cc_final: 0.4854 (mmt) REVERT: R 111 LEU cc_start: 0.7705 (tt) cc_final: 0.7457 (tp) REVERT: R 121 MET cc_start: 0.7903 (mtt) cc_final: 0.7525 (mtt) REVERT: R 140 TYR cc_start: 0.8033 (t80) cc_final: 0.7534 (t80) REVERT: R 173 PHE cc_start: 0.6917 (t80) cc_final: 0.6603 (t80) outliers start: 35 outliers final: 30 residues processed: 294 average time/residue: 0.0951 time to fit residues: 38.3652 Evaluate side-chains 307 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 277 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 271 LYS 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 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 286 LEU 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 166 LEU Chi-restraints excluded: chain S residue 207 LEU 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 219 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.9990 chunk 93 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 21 optimal weight: 0.0980 chunk 81 optimal weight: 0.0670 chunk 85 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.4720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS B 259 GLN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4058 r_free = 0.4058 target = 0.155838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.136609 restraints weight = 14339.645| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 3.03 r_work: 0.3698 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8766 Z= 0.150 Angle : 0.711 12.730 11923 Z= 0.357 Chirality : 0.046 0.229 1386 Planarity : 0.004 0.042 1484 Dihedral : 5.244 43.830 1226 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.69 % Allowed : 25.06 % Favored : 71.25 % 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: -0.27 (0.25), residues: 1104 helix: 1.61 (0.26), residues: 396 sheet: -1.01 (0.30), residues: 271 loop : -1.26 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 251 TYR 0.022 0.002 TYR S 216 PHE 0.021 0.002 PHE A 274 TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8763) covalent geometry : angle 0.70973 (11917) SS BOND : bond 0.00459 ( 3) SS BOND : angle 1.90533 ( 6) hydrogen bonds : bond 0.03712 ( 414) hydrogen bonds : angle 5.23097 ( 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 314 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 281 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8141 (mtmm) cc_final: 0.7582 (mtmm) REVERT: A 198 MET cc_start: 0.7207 (ttm) cc_final: 0.6931 (ttm) REVERT: A 251 ASP cc_start: 0.7255 (t70) cc_final: 0.6629 (t0) REVERT: A 345 LYS cc_start: 0.8548 (tptt) cc_final: 0.8281 (tptt) REVERT: A 347 ASN cc_start: 0.7539 (m-40) cc_final: 0.7049 (m-40) REVERT: B 45 MET cc_start: 0.8166 (mtm) cc_final: 0.7931 (mtp) REVERT: B 65 THR cc_start: 0.7803 (m) cc_final: 0.7586 (p) REVERT: B 82 TRP cc_start: 0.7889 (m-10) cc_final: 0.7685 (m-10) REVERT: B 83 ASP cc_start: 0.7892 (t0) cc_final: 0.7522 (t0) REVERT: B 175 GLN cc_start: 0.7862 (pp30) cc_final: 0.7576 (pp30) REVERT: B 212 ASP cc_start: 0.7898 (t70) cc_final: 0.7587 (p0) REVERT: B 249 THR cc_start: 0.8430 (p) cc_final: 0.8194 (p) REVERT: B 289 TYR cc_start: 0.8405 (m-80) cc_final: 0.8115 (m-80) REVERT: C 11 GLN cc_start: 0.8185 (tm130) cc_final: 0.7603 (tm130) REVERT: C 15 LEU cc_start: 0.8192 (mt) cc_final: 0.7539 (mt) REVERT: S 176 LEU cc_start: 0.8491 (mm) cc_final: 0.8171 (mt) REVERT: S 180 MET cc_start: 0.5599 (ttp) cc_final: 0.5149 (ttm) REVERT: S 182 ASN cc_start: 0.7187 (m110) cc_final: 0.6747 (m-40) REVERT: R 54 MET cc_start: 0.6462 (ptp) cc_final: 0.6063 (ptp) REVERT: R 84 PHE cc_start: 0.6305 (m-80) cc_final: 0.5801 (m-80) REVERT: R 111 LEU cc_start: 0.7693 (tt) cc_final: 0.7441 (tp) REVERT: R 121 MET cc_start: 0.7907 (mtt) cc_final: 0.7525 (mtt) REVERT: R 140 TYR cc_start: 0.8023 (t80) cc_final: 0.7527 (t80) REVERT: R 173 PHE cc_start: 0.6888 (t80) cc_final: 0.6577 (t80) REVERT: R 214 LEU cc_start: 0.6957 (mp) cc_final: 0.6697 (mp) outliers start: 33 outliers final: 28 residues processed: 289 average time/residue: 0.0924 time to fit residues: 36.7316 Evaluate side-chains 306 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 278 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 257 LYS 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 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 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 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 166 LEU Chi-restraints excluded: chain S residue 207 LEU 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 219 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 39 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 106 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 90 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS B 259 GLN ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4058 r_free = 0.4058 target = 0.155804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.136584 restraints weight = 14304.369| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 3.02 r_work: 0.3700 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8766 Z= 0.150 Angle : 0.711 12.730 11923 Z= 0.358 Chirality : 0.046 0.229 1386 Planarity : 0.004 0.042 1484 Dihedral : 5.243 43.830 1226 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.47 % Allowed : 25.50 % Favored : 71.03 % 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: -0.27 (0.25), residues: 1104 helix: 1.61 (0.26), residues: 396 sheet: -1.01 (0.30), residues: 271 loop : -1.26 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 251 TYR 0.022 0.002 TYR S 216 PHE 0.021 0.002 PHE A 274 TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8763) covalent geometry : angle 0.70972 (11917) SS BOND : bond 0.00724 ( 3) SS BOND : angle 2.25157 ( 6) hydrogen bonds : bond 0.03712 ( 414) hydrogen bonds : angle 5.23097 ( 1182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1937.55 seconds wall clock time: 34 minutes 6.37 seconds (2046.37 seconds total)