Starting phenix.real_space_refine on Fri Feb 14 18:08:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v68_31738/02_2025/7v68_31738.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v68_31738/02_2025/7v68_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7v68_31738/02_2025/7v68_31738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v68_31738/02_2025/7v68_31738.map" model { file = "/net/cci-nas-00/data/ceres_data/7v68_31738/02_2025/7v68_31738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v68_31738/02_2025/7v68_31738.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8} 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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 3} 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: {'GLN:plan1': 1, 'ARG:plan': 4} 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: 4.80, per 1000 atoms: 0.56 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: 2.23 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.96 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: 2.49 Time building geometry restraints manager: 2.54 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.280 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.120 ------------------------------------------------------------------------------- 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 8763 Z= 0.481 Angle : 0.834 23.900 11917 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.058 0.003 TRP R 435 HIS 0.009 0.001 HIS R 217 PHE 0.036 0.002 PHE B 253 TYR 0.026 0.002 TYR B 264 ARG 0.010 0.001 ARG A 313 *********************** 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 : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7451 (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: 0.6520 (t80) cc_final: 0.6227 (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: 0.2246 time to fit residues: 94.5538 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 : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 0.0980 chunk 98 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** 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 = 0.4063 r_free = 0.4063 target = 0.156163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.136873 restraints weight = 14261.942| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.98 r_work: 0.3706 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8763 Z= 0.237 Angle : 0.673 9.282 11917 Z= 0.347 Chirality : 0.046 0.282 1386 Planarity : 0.005 0.058 1484 Dihedral : 5.345 50.994 1226 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.90 % Allowed : 14.09 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.25), residues: 1104 helix: 1.38 (0.25), residues: 397 sheet: -0.88 (0.30), residues: 268 loop : -1.23 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 435 HIS 0.012 0.001 HIS A 188 PHE 0.019 0.002 PHE A 191 TYR 0.021 0.002 TYR S 216 ARG 0.006 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 310 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7737 (tm-30) REVERT: A 35 LYS cc_start: 0.7971 (mtmm) cc_final: 0.7458 (mtmm) REVERT: A 197 LYS cc_start: 0.7991 (mmtt) cc_final: 0.7771 (mmtt) REVERT: A 198 MET cc_start: 0.7105 (ttm) cc_final: 0.6826 (ttm) REVERT: A 251 ASP cc_start: 0.7376 (t70) cc_final: 0.6763 (t0) REVERT: A 270 LYS cc_start: 0.7986 (mtmm) cc_final: 0.7542 (mtmm) REVERT: A 271 LYS cc_start: 0.6736 (ptpp) cc_final: 0.6299 (ptpp) REVERT: A 274 PHE cc_start: 0.6771 (t80) cc_final: 0.6297 (t80) REVERT: A 330 LYS cc_start: 0.8265 (mppt) cc_final: 0.8060 (mppt) REVERT: A 347 ASN cc_start: 0.7531 (m-40) cc_final: 0.7016 (m-40) REVERT: B 45 MET cc_start: 0.8142 (mtm) cc_final: 0.7912 (mtp) REVERT: B 63 TRP cc_start: 0.8039 (m100) cc_final: 0.7663 (m100) REVERT: B 65 THR cc_start: 0.7915 (m) cc_final: 0.7649 (p) REVERT: B 114 CYS cc_start: 0.6972 (t) cc_final: 0.6413 (p) REVERT: B 163 ASP cc_start: 0.7502 (p0) cc_final: 0.7301 (p0) REVERT: B 170 ASP cc_start: 0.7632 (t0) cc_final: 0.7379 (t0) REVERT: B 175 GLN cc_start: 0.7849 (pp30) cc_final: 0.7575 (pp30) REVERT: B 176 GLN cc_start: 0.8279 (pt0) cc_final: 0.7767 (pt0) REVERT: B 188 MET cc_start: 0.7444 (mmt) cc_final: 0.7221 (mmm) REVERT: B 220 GLN cc_start: 0.6659 (mt0) cc_final: 0.6439 (mt0) REVERT: B 233 CYS cc_start: 0.8014 (t) cc_final: 0.7808 (t) REVERT: B 237 ASN cc_start: 0.8182 (p0) cc_final: 0.7981 (p0) REVERT: B 253 PHE cc_start: 0.7935 (m-10) cc_final: 0.7559 (m-80) REVERT: B 259 GLN cc_start: 0.7720 (pt0) cc_final: 0.7369 (pt0) REVERT: B 275 SER cc_start: 0.8114 (m) cc_final: 0.7835 (p) REVERT: B 335 PHE cc_start: 0.7989 (m-80) cc_final: 0.7783 (m-80) REVERT: C 15 LEU cc_start: 0.8106 (mt) cc_final: 0.7718 (mt) REVERT: S 78 THR cc_start: 0.8072 (p) cc_final: 0.7822 (p) REVERT: S 176 LEU cc_start: 0.8539 (mm) cc_final: 0.8292 (mm) REVERT: S 182 ASN cc_start: 0.6998 (m110) cc_final: 0.6633 (m110) REVERT: R 52 LEU cc_start: 0.7265 (mt) cc_final: 0.7021 (mt) REVERT: R 54 MET cc_start: 0.6556 (ptp) cc_final: 0.6265 (ptp) REVERT: R 84 PHE cc_start: 0.6563 (m-80) cc_final: 0.6116 (m-80) REVERT: R 86 MET cc_start: 0.4753 (mmp) cc_final: 0.4376 (mmp) REVERT: R 89 TYR cc_start: 0.6847 (t80) cc_final: 0.6368 (t80) REVERT: R 93 ILE cc_start: 0.6161 (mt) cc_final: 0.5783 (mt) REVERT: R 111 LEU cc_start: 0.7654 (tt) cc_final: 0.7408 (tp) REVERT: R 121 MET cc_start: 0.8043 (mtt) cc_final: 0.7598 (mtt) REVERT: R 173 PHE cc_start: 0.6921 (t80) cc_final: 0.6623 (t80) REVERT: R 187 ILE cc_start: 0.7351 (tp) cc_final: 0.7100 (tp) REVERT: R 449 ASN cc_start: 0.7461 (m-40) cc_final: 0.7007 (m-40) outliers start: 17 outliers final: 14 residues processed: 314 average time/residue: 0.2204 time to fit residues: 92.7679 Evaluate side-chains 306 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 292 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 122 ASN Chi-restraints excluded: chain R residue 148 MET Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 407 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 90 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 82 optimal weight: 0.0270 chunk 46 optimal weight: 0.5980 chunk 85 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 346 ASN B 239 ASN S 39 GLN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN R 68 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.156526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.137351 restraints weight = 14359.175| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 3.01 r_work: 0.3715 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8763 Z= 0.202 Angle : 0.628 8.241 11917 Z= 0.323 Chirality : 0.044 0.230 1386 Planarity : 0.004 0.050 1484 Dihedral : 5.123 48.497 1226 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.91 % Allowed : 17.34 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1104 helix: 1.50 (0.25), residues: 396 sheet: -0.92 (0.30), residues: 267 loop : -1.15 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.009 0.001 HIS A 213 PHE 0.013 0.001 PHE B 235 TYR 0.018 0.002 TYR B 264 ARG 0.005 0.000 ARG B 251 *********************** 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 332 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 306 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.7956 (mtmm) cc_final: 0.7420 (mtmm) REVERT: A 197 LYS cc_start: 0.8053 (mmtt) cc_final: 0.7836 (mmtt) REVERT: A 251 ASP cc_start: 0.7330 (t70) cc_final: 0.6745 (t0) REVERT: A 270 LYS cc_start: 0.8046 (mtmm) cc_final: 0.7624 (mtmm) REVERT: A 274 PHE cc_start: 0.6733 (t80) cc_final: 0.6239 (t80) REVERT: A 330 LYS cc_start: 0.8278 (mppt) cc_final: 0.8027 (mppt) REVERT: A 345 LYS cc_start: 0.8543 (tptt) cc_final: 0.8255 (tptt) REVERT: A 347 ASN cc_start: 0.7500 (m-40) cc_final: 0.7029 (m-40) REVERT: B 45 MET cc_start: 0.8168 (mtm) cc_final: 0.7920 (mtp) REVERT: B 65 THR cc_start: 0.7894 (m) cc_final: 0.7615 (p) REVERT: B 156 GLN cc_start: 0.7021 (mt0) cc_final: 0.6819 (mt0) REVERT: B 163 ASP cc_start: 0.7716 (p0) cc_final: 0.7460 (p0) REVERT: B 170 ASP cc_start: 0.7529 (t0) cc_final: 0.7313 (t0) REVERT: B 175 GLN cc_start: 0.7824 (pp30) cc_final: 0.7572 (pp30) REVERT: B 176 GLN cc_start: 0.8314 (pt0) cc_final: 0.7744 (pt0) REVERT: B 188 MET cc_start: 0.7463 (mmt) cc_final: 0.7239 (mmm) REVERT: B 233 CYS cc_start: 0.7981 (t) cc_final: 0.7772 (t) REVERT: B 249 THR cc_start: 0.8321 (p) cc_final: 0.8095 (p) REVERT: B 259 GLN cc_start: 0.7832 (pt0) cc_final: 0.7568 (pt0) REVERT: B 275 SER cc_start: 0.8146 (m) cc_final: 0.7779 (p) REVERT: B 323 ASP cc_start: 0.7930 (p0) cc_final: 0.7725 (p0) REVERT: C 15 LEU cc_start: 0.8110 (mt) cc_final: 0.7723 (mt) REVERT: S 78 THR cc_start: 0.8057 (p) cc_final: 0.7823 (p) REVERT: S 176 LEU cc_start: 0.8512 (mm) cc_final: 0.8078 (mm) REVERT: S 182 ASN cc_start: 0.6877 (m110) cc_final: 0.6496 (m110) REVERT: R 52 LEU cc_start: 0.7278 (mt) cc_final: 0.7036 (mt) REVERT: R 54 MET cc_start: 0.6265 (ptp) cc_final: 0.6011 (ptp) REVERT: R 74 LEU cc_start: 0.8314 (tp) cc_final: 0.8039 (tt) REVERT: R 84 PHE cc_start: 0.6516 (m-80) cc_final: 0.6029 (m-80) REVERT: R 86 MET cc_start: 0.4728 (mmp) cc_final: 0.4290 (mmp) REVERT: R 89 TYR cc_start: 0.6745 (t80) cc_final: 0.6358 (t80) REVERT: R 111 LEU cc_start: 0.7648 (tt) cc_final: 0.7416 (tp) REVERT: R 121 MET cc_start: 0.7948 (mtt) cc_final: 0.7563 (mtt) REVERT: R 173 PHE cc_start: 0.6850 (t80) cc_final: 0.6559 (t80) REVERT: R 187 ILE cc_start: 0.7422 (tp) cc_final: 0.7216 (tp) REVERT: R 449 ASN cc_start: 0.7414 (m-40) cc_final: 0.7155 (m-40) outliers start: 26 outliers final: 21 residues processed: 314 average time/residue: 0.2237 time to fit residues: 93.6514 Evaluate side-chains 311 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 290 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 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 101 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 41 optimal weight: 0.0070 chunk 62 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- 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 ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 157 ASN S 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.155464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.136289 restraints weight = 14176.963| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 3.00 r_work: 0.3696 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8763 Z= 0.235 Angle : 0.615 7.914 11917 Z= 0.320 Chirality : 0.044 0.211 1386 Planarity : 0.004 0.046 1484 Dihedral : 5.112 44.674 1226 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.25 % Allowed : 19.24 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1104 helix: 1.61 (0.26), residues: 396 sheet: -1.00 (0.30), residues: 277 loop : -1.14 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 82 HIS 0.006 0.001 HIS A 188 PHE 0.015 0.001 PHE B 235 TYR 0.021 0.002 TYR B 264 ARG 0.004 0.000 ARG B 251 *********************** 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 345 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 307 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7732 (tm-30) REVERT: A 35 LYS cc_start: 0.8162 (mtmm) cc_final: 0.7610 (mtmm) REVERT: A 197 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7827 (mmtt) REVERT: A 198 MET cc_start: 0.7219 (ttm) cc_final: 0.6897 (ttm) REVERT: A 251 ASP cc_start: 0.7399 (t70) cc_final: 0.6717 (t0) REVERT: A 270 LYS cc_start: 0.8010 (mtmm) cc_final: 0.7795 (mtmm) REVERT: A 274 PHE cc_start: 0.6755 (t80) cc_final: 0.6223 (t80) REVERT: A 345 LYS cc_start: 0.8557 (tptt) cc_final: 0.8273 (tptt) REVERT: A 347 ASN cc_start: 0.7516 (m-40) cc_final: 0.7037 (m-40) REVERT: A 353 LEU cc_start: 0.8305 (tp) cc_final: 0.8051 (tt) REVERT: B 45 MET cc_start: 0.8211 (mtm) cc_final: 0.7967 (mtp) REVERT: B 65 THR cc_start: 0.7936 (m) cc_final: 0.7626 (p) REVERT: B 132 ASN cc_start: 0.7665 (OUTLIER) cc_final: 0.7353 (p0) REVERT: B 163 ASP cc_start: 0.7571 (p0) cc_final: 0.7284 (p0) REVERT: B 170 ASP cc_start: 0.7556 (t0) cc_final: 0.7356 (t0) REVERT: B 175 GLN cc_start: 0.7824 (pp30) cc_final: 0.7595 (pp30) REVERT: B 188 MET cc_start: 0.7442 (mmt) cc_final: 0.7161 (mmm) REVERT: B 249 THR cc_start: 0.8312 (p) cc_final: 0.8052 (p) REVERT: B 253 PHE cc_start: 0.7966 (m-10) cc_final: 0.7581 (m-80) REVERT: B 259 GLN cc_start: 0.8066 (pt0) cc_final: 0.7832 (pt0) REVERT: C 15 LEU cc_start: 0.8140 (mt) cc_final: 0.7738 (mt) REVERT: S 78 THR cc_start: 0.8062 (p) cc_final: 0.7817 (p) REVERT: S 176 LEU cc_start: 0.8551 (mm) cc_final: 0.8182 (mm) REVERT: S 182 ASN cc_start: 0.7123 (m110) cc_final: 0.6726 (m-40) REVERT: R 52 LEU cc_start: 0.7295 (mt) cc_final: 0.7055 (mt) REVERT: R 54 MET cc_start: 0.6388 (ptp) cc_final: 0.6047 (ptp) REVERT: R 74 LEU cc_start: 0.8178 (tp) cc_final: 0.7938 (tt) REVERT: R 84 PHE cc_start: 0.6517 (m-80) cc_final: 0.6019 (m-80) REVERT: R 86 MET cc_start: 0.5175 (mmp) cc_final: 0.4502 (mmp) REVERT: R 89 TYR cc_start: 0.6742 (t80) cc_final: 0.6406 (t80) REVERT: R 109 LEU cc_start: 0.7633 (mm) cc_final: 0.7268 (pp) REVERT: R 111 LEU cc_start: 0.7694 (tt) cc_final: 0.7459 (tp) REVERT: R 121 MET cc_start: 0.7938 (mtt) cc_final: 0.7533 (mtt) REVERT: R 173 PHE cc_start: 0.6900 (t80) cc_final: 0.6601 (t80) REVERT: R 441 LEU cc_start: 0.5522 (OUTLIER) cc_final: 0.5239 (pp) REVERT: R 449 ASN cc_start: 0.7427 (m-40) cc_final: 0.7173 (m-40) outliers start: 38 outliers final: 24 residues processed: 317 average time/residue: 0.2141 time to fit residues: 91.4765 Evaluate side-chains 318 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 292 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 247 MET 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 102 THR Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 243 THR 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 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 38 VAL Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 148 MET Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 217 HIS 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 49 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.155118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.136021 restraints weight = 14300.407| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 3.00 r_work: 0.3702 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8763 Z= 0.235 Angle : 0.617 7.899 11917 Z= 0.321 Chirality : 0.044 0.195 1386 Planarity : 0.004 0.043 1484 Dihedral : 5.093 43.221 1226 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.36 % Allowed : 20.92 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1104 helix: 1.66 (0.25), residues: 396 sheet: -1.00 (0.30), residues: 281 loop : -1.11 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 82 HIS 0.008 0.001 HIS A 213 PHE 0.014 0.001 PHE B 235 TYR 0.021 0.002 TYR B 264 ARG 0.003 0.000 ARG B 251 *********************** 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 328 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 289 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7714 (tm-30) REVERT: A 35 LYS cc_start: 0.8148 (mtmm) cc_final: 0.7586 (mtmm) REVERT: A 197 LYS cc_start: 0.8188 (mmtt) cc_final: 0.7883 (mmmt) REVERT: A 198 MET cc_start: 0.7197 (ttm) cc_final: 0.6880 (ttm) REVERT: A 251 ASP cc_start: 0.7355 (t70) cc_final: 0.6696 (t0) REVERT: A 274 PHE cc_start: 0.6740 (t80) cc_final: 0.6204 (t80) REVERT: A 345 LYS cc_start: 0.8543 (tptt) cc_final: 0.8252 (tptt) REVERT: A 347 ASN cc_start: 0.7531 (m-40) cc_final: 0.7045 (m-40) REVERT: B 45 MET cc_start: 0.8186 (mtm) cc_final: 0.7935 (mtp) REVERT: B 65 THR cc_start: 0.7915 (m) cc_final: 0.7609 (p) REVERT: B 163 ASP cc_start: 0.7579 (p0) cc_final: 0.7378 (p0) REVERT: B 175 GLN cc_start: 0.7862 (pp30) cc_final: 0.7602 (pp30) REVERT: B 188 MET cc_start: 0.7455 (mmt) cc_final: 0.7195 (mmm) REVERT: B 249 THR cc_start: 0.8352 (p) cc_final: 0.8124 (p) REVERT: B 251 ARG cc_start: 0.7352 (tpp80) cc_final: 0.6528 (tpp80) REVERT: B 259 GLN cc_start: 0.7930 (pt0) cc_final: 0.7676 (pt0) REVERT: B 304 ARG cc_start: 0.8305 (ttp80) cc_final: 0.8028 (ttp80) REVERT: C 11 GLN cc_start: 0.8130 (tm130) cc_final: 0.7596 (tm130) REVERT: C 15 LEU cc_start: 0.8179 (mt) cc_final: 0.7542 (mt) REVERT: S 176 LEU cc_start: 0.8551 (mm) cc_final: 0.8158 (mm) REVERT: S 180 MET cc_start: 0.5635 (ttp) cc_final: 0.5178 (ttm) REVERT: S 182 ASN cc_start: 0.7184 (m110) cc_final: 0.6770 (m-40) REVERT: S 218 MET cc_start: 0.6913 (ptm) cc_final: 0.6651 (ttm) REVERT: R 54 MET cc_start: 0.6407 (ptp) cc_final: 0.6080 (ptp) REVERT: R 84 PHE cc_start: 0.6506 (m-80) cc_final: 0.6000 (m-80) REVERT: R 86 MET cc_start: 0.4805 (mmp) cc_final: 0.3925 (mmp) REVERT: R 89 TYR cc_start: 0.6781 (t80) cc_final: 0.6448 (t80) REVERT: R 109 LEU cc_start: 0.7646 (mm) cc_final: 0.7284 (pp) REVERT: R 111 LEU cc_start: 0.7680 (tt) cc_final: 0.7406 (tp) REVERT: R 121 MET cc_start: 0.7910 (mtt) cc_final: 0.7523 (mtt) REVERT: R 173 PHE cc_start: 0.6877 (t80) cc_final: 0.6573 (t80) REVERT: R 403 PHE cc_start: 0.7000 (m-10) cc_final: 0.6791 (m-10) REVERT: R 449 ASN cc_start: 0.7425 (m-40) cc_final: 0.7224 (m-40) outliers start: 39 outliers final: 34 residues processed: 301 average time/residue: 0.2262 time to fit residues: 91.8559 Evaluate side-chains 314 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 280 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 247 MET Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 269 ASN 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 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 313 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 437 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 89 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 0.2980 chunk 97 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 76 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** S 39 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.155021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.136076 restraints weight = 14094.050| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.95 r_work: 0.3701 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8763 Z= 0.235 Angle : 0.618 7.877 11917 Z= 0.321 Chirality : 0.044 0.194 1386 Planarity : 0.004 0.043 1484 Dihedral : 5.522 54.019 1226 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.91 % Allowed : 22.82 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1104 helix: 1.66 (0.25), residues: 396 sheet: -1.00 (0.30), residues: 281 loop : -1.11 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 82 HIS 0.008 0.001 HIS A 213 PHE 0.013 0.001 PHE B 235 TYR 0.021 0.002 TYR B 264 ARG 0.003 0.000 ARG B 251 *********************** 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 315 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 280 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7717 (tm-30) REVERT: A 35 LYS cc_start: 0.8149 (mtmm) cc_final: 0.7591 (mtmm) REVERT: A 197 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7876 (mmmt) REVERT: A 198 MET cc_start: 0.7151 (ttm) cc_final: 0.6837 (ttm) REVERT: A 251 ASP cc_start: 0.7348 (t70) cc_final: 0.6680 (t0) REVERT: A 274 PHE cc_start: 0.6728 (t80) cc_final: 0.6188 (t80) REVERT: A 345 LYS cc_start: 0.8531 (tptt) cc_final: 0.8242 (tptt) REVERT: A 347 ASN cc_start: 0.7543 (m-40) cc_final: 0.7052 (m-40) REVERT: B 45 MET cc_start: 0.8176 (mtm) cc_final: 0.7929 (mtp) REVERT: B 65 THR cc_start: 0.7913 (m) cc_final: 0.7609 (p) REVERT: B 163 ASP cc_start: 0.7590 (p0) cc_final: 0.7385 (p0) REVERT: B 175 GLN cc_start: 0.7859 (pp30) cc_final: 0.7596 (pp30) REVERT: B 188 MET cc_start: 0.7440 (mmt) cc_final: 0.7187 (mmm) REVERT: B 249 THR cc_start: 0.8379 (p) cc_final: 0.8126 (p) REVERT: B 251 ARG cc_start: 0.7313 (tpp80) cc_final: 0.6546 (tpp80) REVERT: B 259 GLN cc_start: 0.7945 (pt0) cc_final: 0.7690 (pt0) REVERT: B 304 ARG cc_start: 0.8259 (ttp80) cc_final: 0.7997 (ttp80) REVERT: C 11 GLN cc_start: 0.8143 (tm130) cc_final: 0.7606 (tm130) REVERT: C 15 LEU cc_start: 0.8190 (mt) cc_final: 0.7554 (mt) REVERT: S 176 LEU cc_start: 0.8561 (mm) cc_final: 0.8159 (mm) REVERT: S 180 MET cc_start: 0.5649 (ttp) cc_final: 0.5165 (ttm) REVERT: S 182 ASN cc_start: 0.7185 (m110) cc_final: 0.6777 (m-40) REVERT: S 218 MET cc_start: 0.6889 (ptm) cc_final: 0.6633 (ttm) REVERT: R 54 MET cc_start: 0.6417 (ptp) cc_final: 0.6078 (ptp) REVERT: R 84 PHE cc_start: 0.6477 (m-80) cc_final: 0.5975 (m-80) REVERT: R 86 MET cc_start: 0.4761 (mmp) cc_final: 0.3893 (mmp) REVERT: R 89 TYR cc_start: 0.6748 (t80) cc_final: 0.6431 (t80) REVERT: R 109 LEU cc_start: 0.7652 (mm) cc_final: 0.7285 (pp) REVERT: R 111 LEU cc_start: 0.7638 (tt) cc_final: 0.7396 (tp) REVERT: R 121 MET cc_start: 0.7888 (mtt) cc_final: 0.7516 (mtt) REVERT: R 173 PHE cc_start: 0.6841 (t80) cc_final: 0.6549 (t80) REVERT: R 403 PHE cc_start: 0.7005 (m-10) cc_final: 0.6797 (m-10) REVERT: R 449 ASN cc_start: 0.7428 (m-40) cc_final: 0.7218 (m-40) outliers start: 35 outliers final: 33 residues processed: 286 average time/residue: 0.2249 time to fit residues: 85.9517 Evaluate side-chains 312 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 279 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 247 MET Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 269 ASN 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 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 313 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 119 SER 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 437 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 60 optimal weight: 0.0000 chunk 107 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 C 11 GLN S 39 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.155089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.135746 restraints weight = 14338.567| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 3.01 r_work: 0.3690 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8763 Z= 0.237 Angle : 0.672 15.119 11917 Z= 0.341 Chirality : 0.046 0.213 1386 Planarity : 0.004 0.042 1484 Dihedral : 5.114 43.129 1226 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.59 % Allowed : 23.71 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1104 helix: 1.64 (0.25), residues: 396 sheet: -1.08 (0.30), residues: 281 loop : -1.10 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 211 HIS 0.004 0.001 HIS B 183 PHE 0.012 0.001 PHE B 235 TYR 0.021 0.002 TYR B 264 ARG 0.005 0.000 ARG B 314 *********************** 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 330 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 289 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7715 (tm-30) REVERT: A 35 LYS cc_start: 0.8133 (mtmm) cc_final: 0.7591 (mtmm) REVERT: A 197 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7846 (mmmt) REVERT: A 198 MET cc_start: 0.7206 (ttm) cc_final: 0.6890 (ttm) REVERT: A 251 ASP cc_start: 0.7338 (t70) cc_final: 0.6693 (t0) REVERT: A 274 PHE cc_start: 0.6736 (t80) cc_final: 0.6186 (t80) REVERT: A 345 LYS cc_start: 0.8560 (tptt) cc_final: 0.8276 (tptt) REVERT: A 347 ASN cc_start: 0.7537 (m-40) cc_final: 0.7054 (m-40) REVERT: B 45 MET cc_start: 0.8216 (mtm) cc_final: 0.7949 (mtp) REVERT: B 65 THR cc_start: 0.7914 (m) cc_final: 0.7603 (p) REVERT: B 163 ASP cc_start: 0.7575 (p0) cc_final: 0.7324 (p0) REVERT: B 175 GLN cc_start: 0.7870 (pp30) cc_final: 0.7582 (pp30) REVERT: B 188 MET cc_start: 0.7469 (mmt) cc_final: 0.7204 (mmm) REVERT: B 249 THR cc_start: 0.8416 (p) cc_final: 0.8143 (p) REVERT: B 253 PHE cc_start: 0.7916 (m-10) cc_final: 0.7556 (m-80) REVERT: B 259 GLN cc_start: 0.7968 (pt0) cc_final: 0.7717 (pt0) REVERT: B 289 TYR cc_start: 0.8420 (m-80) cc_final: 0.8120 (m-80) REVERT: B 304 ARG cc_start: 0.8310 (ttp80) cc_final: 0.8052 (ttp80) REVERT: B 313 ASN cc_start: 0.8430 (m-40) cc_final: 0.8149 (m-40) REVERT: C 11 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7672 (tm-30) REVERT: C 15 LEU cc_start: 0.8215 (mt) cc_final: 0.7569 (mt) REVERT: S 34 MET cc_start: 0.7281 (mmm) cc_final: 0.6818 (mmm) REVERT: S 79 LEU cc_start: 0.6749 (pp) cc_final: 0.6422 (pp) REVERT: S 165 PHE cc_start: 0.8429 (m-10) cc_final: 0.8187 (m-80) REVERT: S 176 LEU cc_start: 0.8523 (mm) cc_final: 0.8132 (mm) REVERT: S 180 MET cc_start: 0.5621 (ttp) cc_final: 0.5170 (ttm) REVERT: S 182 ASN cc_start: 0.7224 (m110) cc_final: 0.6805 (m-40) REVERT: R 54 MET cc_start: 0.6465 (ptp) cc_final: 0.6064 (ptp) REVERT: R 84 PHE cc_start: 0.6347 (m-80) cc_final: 0.5890 (m-80) REVERT: R 109 LEU cc_start: 0.7665 (mm) cc_final: 0.7285 (pp) REVERT: R 111 LEU cc_start: 0.7711 (tt) cc_final: 0.7465 (tp) REVERT: R 121 MET cc_start: 0.7903 (mtt) cc_final: 0.7539 (mtt) REVERT: R 140 TYR cc_start: 0.8078 (t80) cc_final: 0.7540 (t80) REVERT: R 151 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6627 (pp) REVERT: R 173 PHE cc_start: 0.6888 (t80) cc_final: 0.6578 (t80) REVERT: R 183 ASN cc_start: 0.6731 (OUTLIER) cc_final: 0.6471 (p0) REVERT: R 403 PHE cc_start: 0.7026 (m-10) cc_final: 0.6801 (m-10) outliers start: 41 outliers final: 33 residues processed: 300 average time/residue: 0.2222 time to fit residues: 88.8644 Evaluate side-chains 320 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 285 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 247 MET Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 260 THR 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 96 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 211 TRP 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 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 437 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 19 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 59 optimal weight: 0.3980 chunk 88 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 167 GLN ** 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 = 0.4046 r_free = 0.4046 target = 0.154902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.135608 restraints weight = 14404.032| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 3.03 r_work: 0.3688 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8763 Z= 0.231 Angle : 0.679 13.408 11917 Z= 0.344 Chirality : 0.046 0.209 1386 Planarity : 0.004 0.041 1484 Dihedral : 5.113 43.159 1226 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.59 % Allowed : 24.27 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.25), residues: 1104 helix: 1.68 (0.25), residues: 396 sheet: -1.05 (0.30), residues: 271 loop : -1.14 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 211 HIS 0.005 0.001 HIS A 213 PHE 0.013 0.001 PHE B 241 TYR 0.021 0.002 TYR S 216 ARG 0.006 0.000 ARG B 251 *********************** 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: 41 poor density : 291 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7593 (tm-30) REVERT: A 35 LYS cc_start: 0.8134 (mtmm) cc_final: 0.7584 (mtmm) REVERT: A 197 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7905 (mmtt) REVERT: A 198 MET cc_start: 0.7246 (ttm) cc_final: 0.6907 (ttm) REVERT: A 251 ASP cc_start: 0.7319 (t70) cc_final: 0.6677 (t0) REVERT: A 345 LYS cc_start: 0.8569 (tptt) cc_final: 0.8236 (tptt) REVERT: A 347 ASN cc_start: 0.7532 (m-40) cc_final: 0.7043 (m-40) REVERT: B 8 ARG cc_start: 0.6722 (ppt170) cc_final: 0.6479 (ppt170) REVERT: B 45 MET cc_start: 0.8188 (mtm) cc_final: 0.7942 (mtp) REVERT: B 65 THR cc_start: 0.7880 (m) cc_final: 0.7612 (p) REVERT: B 70 LEU cc_start: 0.7885 (mt) cc_final: 0.7560 (mp) REVERT: B 83 ASP cc_start: 0.7917 (t0) cc_final: 0.7554 (t0) REVERT: B 163 ASP cc_start: 0.7567 (p0) cc_final: 0.7322 (p0) REVERT: B 171 ILE cc_start: 0.7803 (mm) cc_final: 0.7091 (mt) REVERT: B 175 GLN cc_start: 0.7879 (pp30) cc_final: 0.7579 (pp30) REVERT: B 188 MET cc_start: 0.7461 (mmt) cc_final: 0.7184 (mmm) REVERT: B 234 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7662 (m-80) REVERT: B 249 THR cc_start: 0.8410 (p) cc_final: 0.8153 (p) REVERT: B 253 PHE cc_start: 0.7915 (m-10) cc_final: 0.7543 (m-80) REVERT: B 259 GLN cc_start: 0.7957 (pt0) cc_final: 0.7732 (pt0) REVERT: B 289 TYR cc_start: 0.8409 (m-80) cc_final: 0.8119 (m-80) REVERT: B 304 ARG cc_start: 0.8243 (ttp80) cc_final: 0.7988 (ttp80) REVERT: C 11 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7663 (tm-30) REVERT: C 15 LEU cc_start: 0.8217 (mt) cc_final: 0.7567 (mt) REVERT: S 34 MET cc_start: 0.7337 (mmm) cc_final: 0.6830 (mmm) REVERT: S 79 LEU cc_start: 0.6664 (pp) cc_final: 0.6360 (pp) REVERT: S 176 LEU cc_start: 0.8519 (mm) cc_final: 0.8124 (mm) REVERT: S 180 MET cc_start: 0.5637 (ttp) cc_final: 0.5194 (ttm) REVERT: S 182 ASN cc_start: 0.7245 (m110) cc_final: 0.6804 (m-40) REVERT: R 54 MET cc_start: 0.6480 (ptp) cc_final: 0.6092 (ptp) REVERT: R 74 LEU cc_start: 0.8178 (tp) cc_final: 0.7938 (tt) REVERT: R 84 PHE cc_start: 0.6357 (m-80) cc_final: 0.5854 (m-80) REVERT: R 121 MET cc_start: 0.7911 (mtt) cc_final: 0.7543 (mtt) REVERT: R 140 TYR cc_start: 0.8077 (t80) cc_final: 0.7649 (t80) REVERT: R 173 PHE cc_start: 0.6889 (t80) cc_final: 0.6582 (t80) REVERT: R 183 ASN cc_start: 0.6710 (OUTLIER) cc_final: 0.6447 (p0) REVERT: R 403 PHE cc_start: 0.7017 (m-10) cc_final: 0.6794 (m-10) outliers start: 41 outliers final: 32 residues processed: 301 average time/residue: 0.2280 time to fit residues: 91.8841 Evaluate side-chains 321 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 287 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 260 THR 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 96 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 437 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.0470 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 93 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 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 = 0.4046 r_free = 0.4046 target = 0.154933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.135635 restraints weight = 14437.317| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.04 r_work: 0.3693 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8763 Z= 0.231 Angle : 0.679 13.408 11917 Z= 0.344 Chirality : 0.046 0.209 1386 Planarity : 0.004 0.041 1484 Dihedral : 5.113 43.159 1226 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.91 % Allowed : 25.50 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.25), residues: 1104 helix: 1.68 (0.25), residues: 396 sheet: -1.05 (0.30), residues: 271 loop : -1.14 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 211 HIS 0.005 0.001 HIS A 213 PHE 0.013 0.001 PHE B 241 TYR 0.021 0.002 TYR S 216 ARG 0.006 0.000 ARG B 251 *********************** 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 322 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 287 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7589 (tm-30) REVERT: A 35 LYS cc_start: 0.8122 (mtmm) cc_final: 0.7569 (mtmm) REVERT: A 197 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7903 (mmtt) REVERT: A 198 MET cc_start: 0.7211 (ttm) cc_final: 0.6873 (ttm) REVERT: A 251 ASP cc_start: 0.7306 (t70) cc_final: 0.6661 (t0) REVERT: A 345 LYS cc_start: 0.8552 (tptt) cc_final: 0.8220 (tptt) REVERT: A 347 ASN cc_start: 0.7541 (m-40) cc_final: 0.7048 (m-40) REVERT: B 8 ARG cc_start: 0.6699 (ppt170) cc_final: 0.6476 (ppt170) REVERT: B 45 MET cc_start: 0.8204 (mtm) cc_final: 0.7948 (mtp) REVERT: B 65 THR cc_start: 0.7872 (m) cc_final: 0.7606 (p) REVERT: B 70 LEU cc_start: 0.7885 (mt) cc_final: 0.7563 (mp) REVERT: B 83 ASP cc_start: 0.7908 (t0) cc_final: 0.7546 (t0) REVERT: B 163 ASP cc_start: 0.7570 (p0) cc_final: 0.7324 (p0) REVERT: B 171 ILE cc_start: 0.7804 (mm) cc_final: 0.7095 (mt) REVERT: B 175 GLN cc_start: 0.7877 (pp30) cc_final: 0.7579 (pp30) REVERT: B 188 MET cc_start: 0.7455 (mmt) cc_final: 0.7176 (mmm) REVERT: B 234 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7649 (m-80) REVERT: B 249 THR cc_start: 0.8407 (p) cc_final: 0.8153 (p) REVERT: B 253 PHE cc_start: 0.7907 (m-10) cc_final: 0.7537 (m-80) REVERT: B 259 GLN cc_start: 0.7971 (pt0) cc_final: 0.7742 (pt0) REVERT: B 289 TYR cc_start: 0.8406 (m-80) cc_final: 0.8118 (m-80) REVERT: B 304 ARG cc_start: 0.8239 (ttp80) cc_final: 0.7986 (ttp80) REVERT: C 11 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7661 (tm-30) REVERT: C 15 LEU cc_start: 0.8218 (mt) cc_final: 0.7566 (mt) REVERT: S 34 MET cc_start: 0.7314 (mmm) cc_final: 0.6810 (mmm) REVERT: S 79 LEU cc_start: 0.6657 (pp) cc_final: 0.6362 (pp) REVERT: S 176 LEU cc_start: 0.8526 (mm) cc_final: 0.8126 (mm) REVERT: S 180 MET cc_start: 0.5641 (ttp) cc_final: 0.5199 (ttm) REVERT: S 182 ASN cc_start: 0.7249 (m110) cc_final: 0.6812 (m-40) REVERT: R 54 MET cc_start: 0.6480 (ptp) cc_final: 0.6089 (ptp) REVERT: R 74 LEU cc_start: 0.8171 (tp) cc_final: 0.7932 (tt) REVERT: R 84 PHE cc_start: 0.6409 (m-80) cc_final: 0.5904 (m-80) REVERT: R 121 MET cc_start: 0.7921 (mtt) cc_final: 0.7543 (mtt) REVERT: R 140 TYR cc_start: 0.8079 (t80) cc_final: 0.7652 (t80) REVERT: R 173 PHE cc_start: 0.6874 (t80) cc_final: 0.6568 (t80) REVERT: R 183 ASN cc_start: 0.6714 (OUTLIER) cc_final: 0.6451 (p0) REVERT: R 403 PHE cc_start: 0.7001 (m-10) cc_final: 0.6782 (m-10) outliers start: 35 outliers final: 32 residues processed: 296 average time/residue: 0.2284 time to fit residues: 90.2867 Evaluate side-chains 321 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 287 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 260 THR 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 96 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 437 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 70 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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 = 0.4046 r_free = 0.4046 target = 0.154940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.135672 restraints weight = 14349.232| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.03 r_work: 0.3694 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8763 Z= 0.231 Angle : 0.679 13.408 11917 Z= 0.344 Chirality : 0.046 0.209 1386 Planarity : 0.004 0.041 1484 Dihedral : 5.113 43.159 1226 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.91 % Allowed : 25.50 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.25), residues: 1104 helix: 1.68 (0.25), residues: 396 sheet: -1.05 (0.30), residues: 271 loop : -1.14 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 211 HIS 0.005 0.001 HIS A 213 PHE 0.013 0.001 PHE B 241 TYR 0.021 0.002 TYR S 216 ARG 0.006 0.000 ARG B 251 ********************** 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 322 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 287 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7589 (tm-30) REVERT: A 35 LYS cc_start: 0.8116 (mtmm) cc_final: 0.7566 (mtmm) REVERT: A 197 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7907 (mmtt) REVERT: A 198 MET cc_start: 0.7215 (ttm) cc_final: 0.6875 (ttm) REVERT: A 251 ASP cc_start: 0.7310 (t70) cc_final: 0.6663 (t0) REVERT: A 345 LYS cc_start: 0.8547 (tptt) cc_final: 0.8215 (tptt) REVERT: A 347 ASN cc_start: 0.7542 (m-40) cc_final: 0.7051 (m-40) REVERT: B 8 ARG cc_start: 0.6699 (ppt170) cc_final: 0.6478 (ppt170) REVERT: B 45 MET cc_start: 0.8198 (mtm) cc_final: 0.7948 (mtp) REVERT: B 65 THR cc_start: 0.7877 (m) cc_final: 0.7613 (p) REVERT: B 70 LEU cc_start: 0.7885 (mt) cc_final: 0.7564 (mp) REVERT: B 83 ASP cc_start: 0.7910 (t0) cc_final: 0.7547 (t0) REVERT: B 163 ASP cc_start: 0.7568 (p0) cc_final: 0.7323 (p0) REVERT: B 171 ILE cc_start: 0.7800 (mm) cc_final: 0.7092 (mt) REVERT: B 175 GLN cc_start: 0.7885 (pp30) cc_final: 0.7584 (pp30) REVERT: B 188 MET cc_start: 0.7451 (mmt) cc_final: 0.7173 (mmm) REVERT: B 234 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7648 (m-80) REVERT: B 249 THR cc_start: 0.8408 (p) cc_final: 0.8154 (p) REVERT: B 253 PHE cc_start: 0.7906 (m-10) cc_final: 0.7538 (m-80) REVERT: B 259 GLN cc_start: 0.7974 (pt0) cc_final: 0.7747 (pt0) REVERT: B 289 TYR cc_start: 0.8409 (m-80) cc_final: 0.8122 (m-80) REVERT: B 304 ARG cc_start: 0.8246 (ttp80) cc_final: 0.7991 (ttp80) REVERT: C 11 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7656 (tm-30) REVERT: C 15 LEU cc_start: 0.8220 (mt) cc_final: 0.7567 (mt) REVERT: S 34 MET cc_start: 0.7317 (mmm) cc_final: 0.6815 (mmm) REVERT: S 79 LEU cc_start: 0.6657 (pp) cc_final: 0.6361 (pp) REVERT: S 176 LEU cc_start: 0.8526 (mm) cc_final: 0.8128 (mm) REVERT: S 180 MET cc_start: 0.5640 (ttp) cc_final: 0.5200 (ttm) REVERT: S 182 ASN cc_start: 0.7247 (m110) cc_final: 0.6812 (m-40) REVERT: R 54 MET cc_start: 0.6460 (ptp) cc_final: 0.6072 (ptp) REVERT: R 74 LEU cc_start: 0.8175 (tp) cc_final: 0.7936 (tt) REVERT: R 84 PHE cc_start: 0.6395 (m-80) cc_final: 0.5891 (m-80) REVERT: R 121 MET cc_start: 0.7915 (mtt) cc_final: 0.7538 (mtt) REVERT: R 140 TYR cc_start: 0.8083 (t80) cc_final: 0.7654 (t80) REVERT: R 173 PHE cc_start: 0.6857 (t80) cc_final: 0.6558 (t80) REVERT: R 183 ASN cc_start: 0.6700 (OUTLIER) cc_final: 0.6439 (p0) REVERT: R 403 PHE cc_start: 0.7001 (m-10) cc_final: 0.6784 (m-10) outliers start: 35 outliers final: 32 residues processed: 296 average time/residue: 0.2325 time to fit residues: 91.7232 Evaluate side-chains 321 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 287 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 260 THR 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 96 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 437 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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 = 0.4046 r_free = 0.4046 target = 0.154930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.135658 restraints weight = 14387.116| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.03 r_work: 0.3692 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8763 Z= 0.231 Angle : 0.679 13.408 11917 Z= 0.344 Chirality : 0.046 0.209 1386 Planarity : 0.004 0.041 1484 Dihedral : 5.113 43.159 1226 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.91 % Allowed : 25.62 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.25), residues: 1104 helix: 1.68 (0.25), residues: 396 sheet: -1.05 (0.30), residues: 271 loop : -1.14 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 211 HIS 0.005 0.001 HIS A 213 PHE 0.013 0.001 PHE B 241 TYR 0.021 0.002 TYR S 216 ARG 0.006 0.000 ARG B 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3946.00 seconds wall clock time: 71 minutes 0.95 seconds (4260.95 seconds total)