Starting phenix.real_space_refine on Mon Jul 28 16:01:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v68_31738/07_2025/7v68_31738.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v68_31738/07_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_31738/07_2025/7v68_31738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v68_31738/07_2025/7v68_31738.map" model { file = "/net/cci-nas-00/data/ceres_data/7v68_31738/07_2025/7v68_31738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v68_31738/07_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-5711/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: 5.78, per 1000 atoms: 0.67 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: 2.51 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: 1.15 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: 2.65 Time building geometry restraints manager: 2.84 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.490 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.461 8766 Z= 0.285 Angle : 0.834 23.900 11923 Z= 0.437 Chirality : 0.049 0.702 1386 Planarity : 0.018 0.636 1484 Dihedral : 12.843 112.936 3027 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.08 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.17351 ( 414) hydrogen bonds : angle 6.95374 ( 1182) SS BOND : bond 0.00306 ( 3) SS BOND : angle 1.37550 ( 6) covalent geometry : bond 0.00715 ( 8763) covalent geometry : angle 0.83408 (11917) *********************** 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 : 0.851 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: 0.2241 time to fit residues: 94.0421 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 : 0.942 ------------------------------------------------------------------------------- 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 = 0.156162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.136872 restraints weight = 14261.413| |-----------------------------------------------------------------------------| 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: 0.7024 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 8766 Z= 0.163 Angle : 0.673 9.283 11923 Z= 0.348 Chirality : 0.046 0.282 1386 Planarity : 0.005 0.058 1484 Dihedral : 5.352 51.001 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 Details of bonding type rmsd hydrogen bonds : bond 0.04169 ( 414) hydrogen bonds : angle 5.54250 ( 1182) SS BOND : bond 0.00374 ( 3) SS BOND : angle 1.09929 ( 6) covalent geometry : bond 0.00364 ( 8763) covalent geometry : angle 0.67274 (11917) *********************** 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 : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7736 (tm-30) REVERT: A 35 LYS cc_start: 0.7973 (mtmm) cc_final: 0.7459 (mtmm) REVERT: A 197 LYS cc_start: 0.7991 (mmtt) cc_final: 0.7770 (mmtt) REVERT: A 198 MET cc_start: 0.7099 (ttm) cc_final: 0.6821 (ttm) REVERT: A 251 ASP cc_start: 0.7377 (t70) cc_final: 0.6764 (t0) REVERT: A 270 LYS cc_start: 0.7985 (mtmm) cc_final: 0.7540 (mtmm) REVERT: A 271 LYS cc_start: 0.6735 (ptpp) cc_final: 0.6297 (ptpp) REVERT: A 274 PHE cc_start: 0.6770 (t80) cc_final: 0.6296 (t80) REVERT: A 330 LYS cc_start: 0.8265 (mppt) cc_final: 0.8060 (mppt) REVERT: A 347 ASN cc_start: 0.7532 (m-40) cc_final: 0.7016 (m-40) REVERT: B 45 MET cc_start: 0.8140 (mtm) cc_final: 0.7914 (mtp) REVERT: B 63 TRP cc_start: 0.8039 (m100) cc_final: 0.7664 (m100) REVERT: B 65 THR cc_start: 0.7913 (m) cc_final: 0.7647 (p) REVERT: B 114 CYS cc_start: 0.6976 (t) cc_final: 0.6417 (p) REVERT: B 170 ASP cc_start: 0.7629 (t0) cc_final: 0.7378 (t0) REVERT: B 175 GLN cc_start: 0.7848 (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: 0.7437 (mmt) cc_final: 0.7216 (mmm) REVERT: B 220 GLN cc_start: 0.6652 (mt0) cc_final: 0.6433 (mt0) REVERT: B 233 CYS cc_start: 0.8016 (t) cc_final: 0.7810 (t) REVERT: B 253 PHE cc_start: 0.7937 (m-10) cc_final: 0.7561 (m-80) REVERT: B 259 GLN cc_start: 0.7722 (pt0) cc_final: 0.7369 (pt0) REVERT: B 275 SER cc_start: 0.8112 (m) cc_final: 0.7834 (p) REVERT: B 335 PHE cc_start: 0.7989 (m-80) cc_final: 0.7782 (m-80) REVERT: C 15 LEU cc_start: 0.8107 (mt) cc_final: 0.7718 (mt) REVERT: S 78 THR cc_start: 0.8071 (p) cc_final: 0.7822 (p) REVERT: S 176 LEU cc_start: 0.8539 (mm) cc_final: 0.8293 (mm) REVERT: S 182 ASN cc_start: 0.6997 (m110) cc_final: 0.6631 (m110) REVERT: R 52 LEU cc_start: 0.7265 (mt) cc_final: 0.7021 (mt) REVERT: R 54 MET cc_start: 0.6564 (ptp) cc_final: 0.6271 (ptp) REVERT: R 84 PHE cc_start: 0.6560 (m-80) cc_final: 0.6113 (m-80) REVERT: R 86 MET cc_start: 0.4759 (mmp) cc_final: 0.4381 (mmp) REVERT: R 89 TYR cc_start: 0.6851 (t80) cc_final: 0.6369 (t80) REVERT: R 93 ILE cc_start: 0.6161 (mt) cc_final: 0.5783 (mt) REVERT: R 111 LEU cc_start: 0.7655 (tt) cc_final: 0.7409 (tp) REVERT: R 121 MET cc_start: 0.8044 (mtt) cc_final: 0.7599 (mtt) REVERT: R 173 PHE cc_start: 0.6924 (t80) cc_final: 0.6625 (t80) REVERT: R 187 ILE cc_start: 0.7350 (tp) cc_final: 0.7099 (tp) REVERT: R 449 ASN cc_start: 0.7462 (m-40) cc_final: 0.7007 (m-40) outliers start: 17 outliers final: 14 residues processed: 314 average time/residue: 0.2856 time to fit residues: 121.2752 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 : 1.473 ------------------------------------------------------------------------------- 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: 0.7980 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 0.0000 chunk 46 optimal weight: 0.5980 chunk 85 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.156268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.137091 restraints weight = 14362.198| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 3.01 r_work: 0.3710 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8766 Z= 0.143 Angle : 0.630 8.288 11923 Z= 0.325 Chirality : 0.044 0.233 1386 Planarity : 0.004 0.050 1484 Dihedral : 5.349 48.709 1226 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.80 % Allowed : 17.45 % 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: -0.25 (0.25), residues: 1104 helix: 1.49 (0.25), residues: 396 sheet: -0.93 (0.30), residues: 267 loop : -1.15 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.007 0.001 HIS A 188 PHE 0.013 0.001 PHE B 235 TYR 0.020 0.002 TYR B 264 ARG 0.005 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 414) hydrogen bonds : angle 5.34460 ( 1182) SS BOND : bond 0.00432 ( 3) SS BOND : angle 1.03888 ( 6) covalent geometry : bond 0.00321 ( 8763) covalent geometry : angle 0.62963 (11917) *********************** 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: 25 poor density : 307 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.7962 (mtmm) cc_final: 0.7423 (mtmm) REVERT: A 197 LYS cc_start: 0.8014 (mmtt) cc_final: 0.7707 (mmtt) REVERT: A 251 ASP cc_start: 0.7334 (t70) cc_final: 0.6752 (t0) REVERT: A 270 LYS cc_start: 0.8038 (mtmm) cc_final: 0.7616 (mtmm) REVERT: A 274 PHE cc_start: 0.6741 (t80) cc_final: 0.6250 (t80) REVERT: A 330 LYS cc_start: 0.8278 (mppt) cc_final: 0.8031 (mppt) REVERT: A 345 LYS cc_start: 0.8544 (tptt) cc_final: 0.8258 (tptt) REVERT: A 347 ASN cc_start: 0.7502 (m-40) cc_final: 0.7030 (m-40) REVERT: B 45 MET cc_start: 0.8175 (mtm) cc_final: 0.7925 (mtp) REVERT: B 65 THR cc_start: 0.7895 (m) cc_final: 0.7612 (p) REVERT: B 170 ASP cc_start: 0.7541 (t0) cc_final: 0.7336 (t0) REVERT: B 175 GLN cc_start: 0.7829 (pp30) cc_final: 0.7579 (pp30) REVERT: B 176 GLN cc_start: 0.8321 (pt0) cc_final: 0.7753 (pt0) REVERT: B 188 MET cc_start: 0.7460 (mmt) cc_final: 0.7241 (mmm) REVERT: B 220 GLN cc_start: 0.6662 (mt0) cc_final: 0.6453 (mt0) REVERT: B 233 CYS cc_start: 0.8001 (t) cc_final: 0.7788 (t) REVERT: B 259 GLN cc_start: 0.7836 (pt0) cc_final: 0.7563 (pt0) REVERT: B 275 SER cc_start: 0.8149 (m) cc_final: 0.7782 (p) REVERT: B 323 ASP cc_start: 0.7930 (p0) cc_final: 0.7716 (p0) REVERT: C 15 LEU cc_start: 0.8108 (mt) cc_final: 0.7715 (mt) REVERT: S 72 ARG cc_start: 0.7592 (ptm160) cc_final: 0.7155 (ptm160) REVERT: S 78 THR cc_start: 0.8035 (p) cc_final: 0.7791 (p) REVERT: S 165 PHE cc_start: 0.8242 (m-10) cc_final: 0.7691 (m-80) REVERT: S 176 LEU cc_start: 0.8517 (mm) cc_final: 0.8079 (mm) REVERT: S 182 ASN cc_start: 0.6893 (m110) cc_final: 0.6509 (m110) REVERT: R 52 LEU cc_start: 0.7285 (mt) cc_final: 0.7043 (mt) REVERT: R 54 MET cc_start: 0.6299 (ptp) cc_final: 0.6042 (ptp) REVERT: R 74 LEU cc_start: 0.8313 (tp) cc_final: 0.8042 (tt) REVERT: R 84 PHE cc_start: 0.6550 (m-80) cc_final: 0.6065 (m-80) REVERT: R 86 MET cc_start: 0.4770 (mmp) cc_final: 0.4329 (mmp) REVERT: R 89 TYR cc_start: 0.6760 (t80) cc_final: 0.6365 (t80) REVERT: R 111 LEU cc_start: 0.7675 (tt) cc_final: 0.7451 (tp) REVERT: R 121 MET cc_start: 0.7962 (mtt) cc_final: 0.7577 (mtt) REVERT: R 173 PHE cc_start: 0.6877 (t80) cc_final: 0.6581 (t80) REVERT: R 187 ILE cc_start: 0.7414 (tp) cc_final: 0.7205 (tp) REVERT: R 449 ASN cc_start: 0.7409 (m-40) cc_final: 0.7137 (m-40) outliers start: 25 outliers final: 19 residues processed: 315 average time/residue: 0.2805 time to fit residues: 120.3743 Evaluate side-chains 310 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 291 time to evaluate : 1.521 ------------------------------------------------------------------------------- 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 327 VAL 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: 0.8980 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 0.1980 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.155354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.136163 restraints weight = 14159.469| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 3.00 r_work: 0.3699 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8766 Z= 0.157 Angle : 0.613 7.874 11923 Z= 0.318 Chirality : 0.044 0.209 1386 Planarity : 0.004 0.046 1484 Dihedral : 5.089 44.275 1226 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.03 % Allowed : 19.57 % Favored : 76.40 % 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: -0.22 (0.25), residues: 1104 helix: 1.62 (0.26), residues: 396 sheet: -1.01 (0.30), residues: 277 loop : -1.15 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 82 HIS 0.006 0.001 HIS A 188 PHE 0.015 0.001 PHE B 235 TYR 0.022 0.002 TYR B 264 ARG 0.004 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03685 ( 414) hydrogen bonds : angle 5.21773 ( 1182) SS BOND : bond 0.00739 ( 3) SS BOND : angle 1.14995 ( 6) covalent geometry : bond 0.00348 ( 8763) covalent geometry : angle 0.61240 (11917) *********************** 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 340 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 304 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7715 (tm-30) REVERT: A 35 LYS cc_start: 0.8165 (mtmm) cc_final: 0.7611 (mtmm) REVERT: A 197 LYS cc_start: 0.8254 (mmtt) cc_final: 0.7792 (mmmt) REVERT: A 198 MET cc_start: 0.7212 (ttm) cc_final: 0.6884 (ttm) REVERT: A 251 ASP cc_start: 0.7396 (t70) cc_final: 0.6723 (t0) REVERT: A 270 LYS cc_start: 0.8005 (mtmm) cc_final: 0.7788 (mtmm) REVERT: A 274 PHE cc_start: 0.6749 (t80) cc_final: 0.6217 (t80) REVERT: A 345 LYS cc_start: 0.8552 (tptt) cc_final: 0.8273 (tptt) REVERT: A 347 ASN cc_start: 0.7520 (m-40) cc_final: 0.7048 (m-40) REVERT: A 353 LEU cc_start: 0.8305 (tp) cc_final: 0.8069 (tt) REVERT: B 45 MET cc_start: 0.8182 (mtm) cc_final: 0.7948 (mtp) REVERT: B 65 THR cc_start: 0.7925 (m) cc_final: 0.7608 (p) REVERT: B 83 ASP cc_start: 0.7902 (t0) cc_final: 0.7575 (t0) REVERT: B 132 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.7311 (p0) REVERT: B 175 GLN cc_start: 0.7825 (pp30) cc_final: 0.7598 (pp30) REVERT: B 188 MET cc_start: 0.7420 (mmt) cc_final: 0.7145 (mmm) REVERT: B 253 PHE cc_start: 0.7969 (m-10) cc_final: 0.7595 (m-80) REVERT: C 15 LEU cc_start: 0.8140 (mt) cc_final: 0.7731 (mt) REVERT: S 72 ARG cc_start: 0.7675 (ptm160) cc_final: 0.7232 (ptm160) REVERT: S 78 THR cc_start: 0.8067 (p) cc_final: 0.7805 (p) REVERT: S 176 LEU cc_start: 0.8553 (mm) cc_final: 0.8195 (mm) REVERT: S 182 ASN cc_start: 0.7132 (m110) cc_final: 0.6750 (m-40) REVERT: S 218 MET cc_start: 0.6808 (ptm) cc_final: 0.6499 (ttm) REVERT: R 52 LEU cc_start: 0.7294 (mt) cc_final: 0.7055 (mt) REVERT: R 54 MET cc_start: 0.6398 (ptp) cc_final: 0.6050 (ptp) REVERT: R 74 LEU cc_start: 0.8169 (tp) cc_final: 0.7932 (tt) REVERT: R 84 PHE cc_start: 0.6539 (m-80) cc_final: 0.6039 (m-80) REVERT: R 86 MET cc_start: 0.5374 (mmp) cc_final: 0.4704 (mmp) REVERT: R 89 TYR cc_start: 0.6772 (t80) cc_final: 0.6442 (t80) REVERT: R 109 LEU cc_start: 0.7625 (mm) cc_final: 0.7257 (pp) REVERT: R 111 LEU cc_start: 0.7680 (tt) cc_final: 0.7442 (tp) REVERT: R 121 MET cc_start: 0.7932 (mtt) cc_final: 0.7537 (mtt) REVERT: R 173 PHE cc_start: 0.6886 (t80) cc_final: 0.6589 (t80) REVERT: R 395 GLU cc_start: 0.6992 (tp30) cc_final: 0.6697 (tp30) REVERT: R 441 LEU cc_start: 0.5501 (OUTLIER) cc_final: 0.5227 (pp) REVERT: R 449 ASN cc_start: 0.7426 (m-40) cc_final: 0.7168 (m-40) outliers start: 36 outliers final: 28 residues processed: 312 average time/residue: 0.2114 time to fit residues: 88.7067 Evaluate side-chains 323 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 293 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 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 79 LEU 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: 0.9980 chunk 39 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS B 259 GLN B 313 ASN S 39 GLN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 157 ASN S 167 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.153917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.134902 restraints weight = 14277.068| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 3.00 r_work: 0.3684 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8766 Z= 0.183 Angle : 0.625 7.964 11923 Z= 0.326 Chirality : 0.044 0.201 1386 Planarity : 0.004 0.043 1484 Dihedral : 5.129 42.794 1226 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.03 % Allowed : 21.03 % Favored : 73.94 % 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 (0.26), residues: 396 sheet: -1.07 (0.30), residues: 286 loop : -1.13 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 82 HIS 0.015 0.001 HIS A 213 PHE 0.015 0.002 PHE B 235 TYR 0.020 0.002 TYR B 264 ARG 0.005 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 414) hydrogen bonds : angle 5.21583 ( 1182) SS BOND : bond 0.00225 ( 3) SS BOND : angle 0.65498 ( 6) covalent geometry : bond 0.00404 ( 8763) covalent geometry : angle 0.62464 (11917) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 292 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7690 (tm-30) REVERT: A 35 LYS cc_start: 0.8139 (mtmm) cc_final: 0.7637 (mtmm) REVERT: A 197 LYS cc_start: 0.8187 (mmtt) cc_final: 0.7883 (mmmt) REVERT: A 198 MET cc_start: 0.7223 (ttm) cc_final: 0.6902 (ttm) REVERT: A 251 ASP cc_start: 0.7351 (t70) cc_final: 0.6687 (t0) REVERT: A 274 PHE cc_start: 0.6742 (t80) cc_final: 0.6196 (t80) REVERT: A 345 LYS cc_start: 0.8553 (tptt) cc_final: 0.8287 (tptt) REVERT: A 347 ASN cc_start: 0.7534 (m-40) cc_final: 0.7234 (m-40) REVERT: B 45 MET cc_start: 0.8271 (mtm) cc_final: 0.7992 (mtp) REVERT: B 65 THR cc_start: 0.7947 (m) cc_final: 0.7622 (p) REVERT: B 114 CYS cc_start: 0.6864 (t) cc_final: 0.6382 (t) REVERT: B 175 GLN cc_start: 0.7906 (pp30) cc_final: 0.7612 (pp30) REVERT: B 188 MET cc_start: 0.7439 (mmt) cc_final: 0.7158 (mmm) REVERT: B 304 ARG cc_start: 0.8345 (ttp80) cc_final: 0.8085 (ttp80) REVERT: C 11 GLN cc_start: 0.8148 (tm130) cc_final: 0.7611 (tm130) REVERT: C 15 LEU cc_start: 0.8192 (mt) cc_final: 0.7556 (mt) REVERT: S 176 LEU cc_start: 0.8553 (mm) cc_final: 0.8182 (mm) REVERT: S 180 MET cc_start: 0.5738 (ttp) cc_final: 0.5305 (ttm) REVERT: S 182 ASN cc_start: 0.7258 (m110) cc_final: 0.6842 (m-40) REVERT: R 54 MET cc_start: 0.6415 (ptp) cc_final: 0.6060 (ptp) REVERT: R 84 PHE cc_start: 0.6377 (m-80) cc_final: 0.5916 (m-80) REVERT: R 111 LEU cc_start: 0.7691 (tt) cc_final: 0.7447 (tp) REVERT: R 121 MET cc_start: 0.7935 (mtt) cc_final: 0.7559 (mtt) REVERT: R 173 PHE cc_start: 0.6913 (t80) cc_final: 0.6603 (t80) REVERT: R 214 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6747 (tt) outliers start: 45 outliers final: 36 residues processed: 305 average time/residue: 0.2230 time to fit residues: 92.0135 Evaluate side-chains 329 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 292 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 271 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 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 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 122 ASN Chi-restraints excluded: chain R residue 214 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 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: 0.5980 chunk 32 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 40 optimal weight: 0.2980 chunk 97 optimal weight: 0.0020 chunk 61 optimal weight: 0.0980 chunk 94 optimal weight: 0.1980 chunk 76 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 overall best weight: 0.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN C 11 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** R 417 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.155827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.136579 restraints weight = 14054.680| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 3.01 r_work: 0.3716 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8766 Z= 0.130 Angle : 0.646 15.533 11923 Z= 0.328 Chirality : 0.044 0.214 1386 Planarity : 0.004 0.040 1484 Dihedral : 5.089 42.398 1226 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.14 % Allowed : 23.49 % Favored : 72.37 % 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: -0.17 (0.25), residues: 1104 helix: 1.61 (0.25), residues: 396 sheet: -1.02 (0.30), residues: 285 loop : -1.04 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 82 HIS 0.004 0.001 HIS A 244 PHE 0.022 0.002 PHE R 403 TYR 0.021 0.002 TYR B 264 ARG 0.005 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 414) hydrogen bonds : angle 5.14734 ( 1182) SS BOND : bond 0.00189 ( 3) SS BOND : angle 1.22591 ( 6) covalent geometry : bond 0.00288 ( 8763) covalent geometry : angle 0.64552 (11917) *********************** 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 335 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 298 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7681 (tm-30) REVERT: A 35 LYS cc_start: 0.8145 (mtmm) cc_final: 0.7602 (mtmm) REVERT: A 197 LYS cc_start: 0.8153 (mmtt) cc_final: 0.7832 (mmmt) REVERT: A 198 MET cc_start: 0.7179 (ttm) cc_final: 0.6867 (ttm) REVERT: A 251 ASP cc_start: 0.7286 (t70) cc_final: 0.6628 (t0) REVERT: A 345 LYS cc_start: 0.8544 (tptt) cc_final: 0.8263 (tptt) REVERT: A 347 ASN cc_start: 0.7520 (m-40) cc_final: 0.7027 (m-40) REVERT: B 45 MET cc_start: 0.8181 (mtm) cc_final: 0.7933 (mtp) REVERT: B 65 THR cc_start: 0.7867 (m) cc_final: 0.7597 (p) REVERT: B 83 ASP cc_start: 0.7852 (t0) cc_final: 0.7500 (t0) REVERT: B 175 GLN cc_start: 0.7873 (pp30) cc_final: 0.7552 (pp30) REVERT: B 188 MET cc_start: 0.7410 (mmt) cc_final: 0.7137 (mmm) REVERT: B 234 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7620 (m-80) REVERT: B 253 PHE cc_start: 0.7865 (m-10) cc_final: 0.7515 (m-80) REVERT: B 304 ARG cc_start: 0.8229 (ttp80) cc_final: 0.7976 (ttp80) REVERT: C 11 GLN cc_start: 0.8156 (tm-30) cc_final: 0.7636 (tm-30) REVERT: C 15 LEU cc_start: 0.8184 (mt) cc_final: 0.7528 (mt) REVERT: S 155 HIS cc_start: 0.7780 (t-170) cc_final: 0.7443 (t-170) REVERT: S 176 LEU cc_start: 0.8514 (mm) cc_final: 0.8119 (mm) REVERT: S 180 MET cc_start: 0.5547 (ttp) cc_final: 0.5135 (ttm) REVERT: S 182 ASN cc_start: 0.7219 (m110) cc_final: 0.6786 (m-40) REVERT: R 54 MET cc_start: 0.6454 (ptp) cc_final: 0.6052 (ptp) REVERT: R 84 PHE cc_start: 0.6304 (m-80) cc_final: 0.5810 (m-80) REVERT: R 86 MET cc_start: 0.4689 (mmt) cc_final: 0.3937 (mmt) REVERT: R 109 LEU cc_start: 0.7608 (mm) cc_final: 0.7242 (pp) REVERT: R 111 LEU cc_start: 0.7659 (tt) cc_final: 0.7418 (tp) REVERT: R 121 MET cc_start: 0.7881 (mtt) cc_final: 0.7511 (mtt) REVERT: R 140 TYR cc_start: 0.8062 (t80) cc_final: 0.7661 (t80) REVERT: R 151 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6818 (pp) REVERT: R 173 PHE cc_start: 0.6790 (t80) cc_final: 0.6496 (t80) outliers start: 37 outliers final: 29 residues processed: 309 average time/residue: 0.2202 time to fit residues: 91.4521 Evaluate side-chains 319 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 288 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 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 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 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 119 SER Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 437 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 60 optimal weight: 0.2980 chunk 107 optimal weight: 0.0370 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN R 68 ASN ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.155336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.136166 restraints weight = 14329.558| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.04 r_work: 0.3703 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8766 Z= 0.148 Angle : 0.664 12.895 11923 Z= 0.335 Chirality : 0.045 0.211 1386 Planarity : 0.004 0.039 1484 Dihedral : 5.111 43.168 1226 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.14 % Allowed : 24.94 % Favored : 70.92 % 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: -0.22 (0.25), residues: 1104 helix: 1.53 (0.25), residues: 402 sheet: -1.07 (0.30), residues: 278 loop : -1.05 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.004 0.001 HIS B 311 PHE 0.018 0.002 PHE R 403 TYR 0.021 0.002 TYR S 216 ARG 0.004 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 414) hydrogen bonds : angle 5.16142 ( 1182) SS BOND : bond 0.00927 ( 3) SS BOND : angle 1.45233 ( 6) covalent geometry : bond 0.00334 ( 8763) covalent geometry : angle 0.66365 (11917) *********************** 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 323 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 286 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7696 (tm-30) REVERT: A 35 LYS cc_start: 0.8135 (mtmm) cc_final: 0.7576 (mtmm) REVERT: A 197 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7884 (mmtt) REVERT: A 198 MET cc_start: 0.7249 (ttm) cc_final: 0.6918 (ttm) REVERT: A 251 ASP cc_start: 0.7273 (t70) cc_final: 0.6629 (t0) REVERT: A 345 LYS cc_start: 0.8553 (tptt) cc_final: 0.8266 (tptt) REVERT: A 347 ASN cc_start: 0.7543 (m-40) cc_final: 0.7044 (m-40) REVERT: B 8 ARG cc_start: 0.6688 (ppt170) cc_final: 0.6468 (ppt170) REVERT: B 45 MET cc_start: 0.8231 (mtm) cc_final: 0.7991 (mtp) REVERT: B 65 THR cc_start: 0.7875 (m) cc_final: 0.7605 (p) REVERT: B 83 ASP cc_start: 0.7862 (t0) cc_final: 0.7507 (t0) REVERT: B 175 GLN cc_start: 0.7893 (pp30) cc_final: 0.7579 (pp30) REVERT: B 188 MET cc_start: 0.7441 (mmt) cc_final: 0.7158 (mmm) REVERT: B 220 GLN cc_start: 0.6535 (mt0) cc_final: 0.6067 (mt0) REVERT: B 234 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7640 (m-80) REVERT: B 251 ARG cc_start: 0.7452 (ttm-80) cc_final: 0.6629 (tpp80) REVERT: B 253 PHE cc_start: 0.7885 (m-10) cc_final: 0.7434 (m-80) REVERT: B 289 TYR cc_start: 0.8408 (m-80) cc_final: 0.8090 (m-80) REVERT: B 304 ARG cc_start: 0.8207 (ttp80) cc_final: 0.7949 (ttp80) REVERT: C 11 GLN cc_start: 0.8154 (tm-30) cc_final: 0.7642 (tm-30) REVERT: C 15 LEU cc_start: 0.8206 (mt) cc_final: 0.7550 (mt) REVERT: S 34 MET cc_start: 0.7351 (mmm) cc_final: 0.6823 (mmm) REVERT: S 79 LEU cc_start: 0.6887 (pp) cc_final: 0.6300 (pp) REVERT: S 155 HIS cc_start: 0.7802 (t-170) cc_final: 0.7489 (t-170) REVERT: S 176 LEU cc_start: 0.8528 (mm) cc_final: 0.8126 (mm) REVERT: S 180 MET cc_start: 0.5585 (ttp) cc_final: 0.5220 (tpp) REVERT: S 182 ASN cc_start: 0.7218 (m110) cc_final: 0.6792 (m-40) REVERT: R 54 MET cc_start: 0.6444 (ptp) cc_final: 0.6061 (ptp) REVERT: R 84 PHE cc_start: 0.6332 (m-80) cc_final: 0.5835 (m-80) REVERT: R 89 TYR cc_start: 0.6800 (t80) cc_final: 0.6534 (t80) REVERT: R 121 MET cc_start: 0.7912 (mtt) cc_final: 0.7541 (mtt) REVERT: R 140 TYR cc_start: 0.8081 (t80) cc_final: 0.7722 (t80) REVERT: R 173 PHE cc_start: 0.6849 (t80) cc_final: 0.6546 (t80) outliers start: 37 outliers final: 30 residues processed: 295 average time/residue: 0.2228 time to fit residues: 88.1310 Evaluate side-chains 315 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 284 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 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 119 SER Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 217 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 19 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 99 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 0.0980 chunk 88 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.155107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.135789 restraints weight = 14411.692| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 3.05 r_work: 0.3701 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8766 Z= 0.148 Angle : 0.663 12.882 11923 Z= 0.335 Chirality : 0.045 0.210 1386 Planarity : 0.004 0.039 1484 Dihedral : 5.124 43.168 1226 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.47 % Allowed : 26.51 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.22 (0.25), residues: 1104 helix: 1.53 (0.25), residues: 402 sheet: -1.07 (0.30), residues: 278 loop : -1.05 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.004 0.001 HIS B 311 PHE 0.018 0.002 PHE R 403 TYR 0.020 0.002 TYR S 216 ARG 0.004 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 414) hydrogen bonds : angle 5.16148 ( 1182) SS BOND : bond 0.00917 ( 3) SS BOND : angle 1.44881 ( 6) covalent geometry : bond 0.00335 ( 8763) covalent geometry : angle 0.66285 (11917) *********************** 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 315 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 284 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7719 (tm-30) REVERT: A 35 LYS cc_start: 0.8128 (mtmm) cc_final: 0.7571 (mtmm) REVERT: A 197 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7876 (mmtt) REVERT: A 198 MET cc_start: 0.7242 (ttm) cc_final: 0.6912 (ttm) REVERT: A 251 ASP cc_start: 0.7270 (t70) cc_final: 0.6626 (t0) REVERT: A 345 LYS cc_start: 0.8542 (tptt) cc_final: 0.8253 (tptt) REVERT: A 347 ASN cc_start: 0.7547 (m-40) cc_final: 0.7044 (m-40) REVERT: B 8 ARG cc_start: 0.6670 (ppt170) cc_final: 0.6460 (ppt170) REVERT: B 45 MET cc_start: 0.8244 (mtm) cc_final: 0.8004 (mtp) REVERT: B 65 THR cc_start: 0.7873 (m) cc_final: 0.7603 (p) REVERT: B 83 ASP cc_start: 0.7835 (t0) cc_final: 0.7488 (t0) REVERT: B 175 GLN cc_start: 0.7900 (pp30) cc_final: 0.7578 (pp30) REVERT: B 188 MET cc_start: 0.7427 (mmt) cc_final: 0.7147 (mmm) REVERT: B 220 GLN cc_start: 0.6545 (mt0) cc_final: 0.6107 (mt0) REVERT: B 234 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7647 (m-80) REVERT: B 251 ARG cc_start: 0.7432 (ttm-80) cc_final: 0.6620 (tpp80) REVERT: B 253 PHE cc_start: 0.7878 (m-10) cc_final: 0.7429 (m-80) REVERT: B 289 TYR cc_start: 0.8404 (m-80) cc_final: 0.8090 (m-80) REVERT: B 304 ARG cc_start: 0.8192 (ttp80) cc_final: 0.7945 (ttp80) REVERT: C 11 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7646 (tm-30) REVERT: C 15 LEU cc_start: 0.8202 (mt) cc_final: 0.7550 (mt) REVERT: S 34 MET cc_start: 0.7360 (mmm) cc_final: 0.6824 (mmm) REVERT: S 79 LEU cc_start: 0.6888 (pp) cc_final: 0.6310 (pp) REVERT: S 155 HIS cc_start: 0.7791 (t-170) cc_final: 0.7488 (t-170) REVERT: S 176 LEU cc_start: 0.8532 (mm) cc_final: 0.8119 (mm) REVERT: S 180 MET cc_start: 0.5600 (ttp) cc_final: 0.5222 (tpp) REVERT: S 182 ASN cc_start: 0.7210 (m110) cc_final: 0.6788 (m-40) REVERT: R 54 MET cc_start: 0.6439 (ptp) cc_final: 0.6052 (ptp) REVERT: R 84 PHE cc_start: 0.6373 (m-80) cc_final: 0.5868 (m-80) REVERT: R 89 TYR cc_start: 0.6800 (t80) cc_final: 0.6515 (t80) REVERT: R 121 MET cc_start: 0.7932 (mtt) cc_final: 0.7548 (mtt) REVERT: R 140 TYR cc_start: 0.8072 (t80) cc_final: 0.7711 (t80) REVERT: R 173 PHE cc_start: 0.6868 (t80) cc_final: 0.6560 (t80) outliers start: 31 outliers final: 30 residues processed: 291 average time/residue: 0.2156 time to fit residues: 84.0125 Evaluate side-chains 315 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 284 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 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 119 SER Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 217 HIS 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: 0.9990 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 0.0770 chunk 93 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 42 optimal weight: 0.0010 chunk 95 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 overall best weight: 0.4344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.155107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.135802 restraints weight = 14410.402| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 3.04 r_work: 0.3702 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8766 Z= 0.150 Angle : 0.658 12.790 11923 Z= 0.332 Chirality : 0.044 0.203 1386 Planarity : 0.004 0.039 1484 Dihedral : 5.257 43.170 1226 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.47 % Allowed : 26.62 % Favored : 69.91 % 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: -0.22 (0.25), residues: 1104 helix: 1.53 (0.25), residues: 402 sheet: -1.07 (0.30), residues: 278 loop : -1.05 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.015 0.001 PHE R 403 TYR 0.017 0.002 TYR S 216 ARG 0.003 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 414) hydrogen bonds : angle 5.16207 ( 1182) SS BOND : bond 0.00853 ( 3) SS BOND : angle 1.42231 ( 6) covalent geometry : bond 0.00340 ( 8763) covalent geometry : angle 0.65785 (11917) *********************** 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 315 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 284 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7707 (tm-30) REVERT: A 35 LYS cc_start: 0.8127 (mtmm) cc_final: 0.7571 (mtmm) REVERT: A 197 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7879 (mmtt) REVERT: A 198 MET cc_start: 0.7243 (ttm) cc_final: 0.6913 (ttm) REVERT: A 251 ASP cc_start: 0.7272 (t70) cc_final: 0.6627 (t0) REVERT: A 345 LYS cc_start: 0.8540 (tptt) cc_final: 0.8251 (tptt) REVERT: A 347 ASN cc_start: 0.7542 (m-40) cc_final: 0.7041 (m-40) REVERT: B 8 ARG cc_start: 0.6679 (ppt170) cc_final: 0.6465 (ppt170) REVERT: B 45 MET cc_start: 0.8248 (mtm) cc_final: 0.8010 (mtp) REVERT: B 65 THR cc_start: 0.7870 (m) cc_final: 0.7601 (p) REVERT: B 83 ASP cc_start: 0.7846 (t0) cc_final: 0.7496 (t0) REVERT: B 175 GLN cc_start: 0.7897 (pp30) cc_final: 0.7570 (pp30) REVERT: B 188 MET cc_start: 0.7421 (mmt) cc_final: 0.7143 (mmm) REVERT: B 220 GLN cc_start: 0.6554 (mt0) cc_final: 0.6114 (mt0) REVERT: B 234 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7647 (m-80) REVERT: B 251 ARG cc_start: 0.7433 (ttm-80) cc_final: 0.6622 (tpp80) REVERT: B 253 PHE cc_start: 0.7879 (m-10) cc_final: 0.7432 (m-80) REVERT: B 289 TYR cc_start: 0.8406 (m-80) cc_final: 0.8092 (m-80) REVERT: B 304 ARG cc_start: 0.8201 (ttp80) cc_final: 0.7952 (ttp80) REVERT: C 11 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7647 (tm-30) REVERT: C 15 LEU cc_start: 0.8202 (mt) cc_final: 0.7546 (mt) REVERT: S 34 MET cc_start: 0.7352 (mmm) cc_final: 0.6818 (mmm) REVERT: S 79 LEU cc_start: 0.6890 (pp) cc_final: 0.6308 (pp) REVERT: S 155 HIS cc_start: 0.7799 (t-170) cc_final: 0.7496 (t-170) REVERT: S 176 LEU cc_start: 0.8532 (mm) cc_final: 0.8137 (mm) REVERT: S 180 MET cc_start: 0.5605 (ttp) cc_final: 0.5229 (tpp) REVERT: S 182 ASN cc_start: 0.7211 (m110) cc_final: 0.6791 (m-40) REVERT: R 54 MET cc_start: 0.6429 (ptp) cc_final: 0.6046 (ptp) REVERT: R 84 PHE cc_start: 0.6353 (m-80) cc_final: 0.5850 (m-80) REVERT: R 89 TYR cc_start: 0.6795 (t80) cc_final: 0.6508 (t80) REVERT: R 121 MET cc_start: 0.7930 (mtt) cc_final: 0.7549 (mtt) REVERT: R 140 TYR cc_start: 0.8075 (t80) cc_final: 0.7717 (t80) REVERT: R 173 PHE cc_start: 0.6838 (t80) cc_final: 0.6540 (t80) REVERT: R 184 GLN cc_start: 0.7452 (pm20) cc_final: 0.7201 (pm20) outliers start: 31 outliers final: 30 residues processed: 291 average time/residue: 0.2738 time to fit residues: 107.4649 Evaluate side-chains 315 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 284 time to evaluate : 1.372 ------------------------------------------------------------------------------- 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 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 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 119 SER Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 217 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 70 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN ** 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 = 0.4037 r_free = 0.4037 target = 0.154228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.135130 restraints weight = 14356.055| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 3.02 r_work: 0.3691 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8766 Z= 0.181 Angle : 0.715 12.599 11923 Z= 0.357 Chirality : 0.046 0.231 1386 Planarity : 0.004 0.039 1484 Dihedral : 5.119 43.330 1226 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.14 % Allowed : 26.17 % Favored : 69.69 % 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: -0.28 (0.25), residues: 1104 helix: 1.47 (0.25), residues: 402 sheet: -1.08 (0.30), residues: 278 loop : -1.08 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 211 HIS 0.005 0.001 HIS B 311 PHE 0.037 0.002 PHE R 128 TYR 0.020 0.002 TYR S 216 ARG 0.004 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 414) hydrogen bonds : angle 5.19089 ( 1182) SS BOND : bond 0.00360 ( 3) SS BOND : angle 1.51320 ( 6) covalent geometry : bond 0.00404 ( 8763) covalent geometry : angle 0.71436 (11917) ********************** 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 327 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 290 time to evaluate : 2.427 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7713 (tm-30) REVERT: A 35 LYS cc_start: 0.8142 (mtmm) cc_final: 0.7592 (mtmm) REVERT: A 197 LYS cc_start: 0.8187 (mmtt) cc_final: 0.7951 (mtpp) REVERT: A 198 MET cc_start: 0.7271 (ttm) cc_final: 0.6933 (ttm) REVERT: A 210 LYS cc_start: 0.8455 (tppp) cc_final: 0.8184 (mmmm) REVERT: A 251 ASP cc_start: 0.7281 (t70) cc_final: 0.6637 (t0) REVERT: A 345 LYS cc_start: 0.8547 (tptt) cc_final: 0.8261 (tptt) REVERT: A 347 ASN cc_start: 0.7556 (m-40) cc_final: 0.7059 (m-40) REVERT: B 8 ARG cc_start: 0.6708 (ppt170) cc_final: 0.6495 (ppt170) REVERT: B 45 MET cc_start: 0.8215 (mtm) cc_final: 0.7974 (mtp) REVERT: B 65 THR cc_start: 0.7916 (m) cc_final: 0.7608 (p) REVERT: B 83 ASP cc_start: 0.7859 (t0) cc_final: 0.7515 (t0) REVERT: B 171 ILE cc_start: 0.7841 (mm) cc_final: 0.7128 (mt) REVERT: B 175 GLN cc_start: 0.7903 (pp30) cc_final: 0.7573 (pp30) REVERT: B 188 MET cc_start: 0.7445 (mmt) cc_final: 0.7028 (mmm) REVERT: B 211 TRP cc_start: 0.8070 (OUTLIER) cc_final: 0.7761 (m-10) REVERT: B 220 GLN cc_start: 0.6539 (mt0) cc_final: 0.6070 (mt0) REVERT: B 234 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7651 (m-80) REVERT: B 251 ARG cc_start: 0.7435 (ttm-80) cc_final: 0.6623 (tpp80) REVERT: B 253 PHE cc_start: 0.7941 (m-10) cc_final: 0.7498 (m-80) REVERT: B 289 TYR cc_start: 0.8405 (m-80) cc_final: 0.8102 (m-80) REVERT: B 292 PHE cc_start: 0.6943 (OUTLIER) cc_final: 0.6533 (m-80) REVERT: B 304 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7977 (ttp80) REVERT: C 11 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7648 (tm-30) REVERT: C 15 LEU cc_start: 0.8214 (mt) cc_final: 0.7560 (mt) REVERT: C 27 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7421 (mtm180) REVERT: S 34 MET cc_start: 0.7357 (mmm) cc_final: 0.6818 (mmm) REVERT: S 79 LEU cc_start: 0.6855 (pp) cc_final: 0.6456 (pp) REVERT: S 176 LEU cc_start: 0.8530 (mm) cc_final: 0.8125 (mm) REVERT: S 180 MET cc_start: 0.5648 (ttp) cc_final: 0.5202 (ttm) REVERT: S 182 ASN cc_start: 0.7236 (m110) cc_final: 0.6785 (m-40) REVERT: S 190 ARG cc_start: 0.6729 (ptt-90) cc_final: 0.6426 (ptt-90) REVERT: R 54 MET cc_start: 0.6480 (ptp) cc_final: 0.6100 (ptp) REVERT: R 84 PHE cc_start: 0.6385 (m-80) cc_final: 0.5873 (m-80) REVERT: R 121 MET cc_start: 0.7938 (mtt) cc_final: 0.7552 (mtt) REVERT: R 140 TYR cc_start: 0.8084 (t80) cc_final: 0.7728 (t80) REVERT: R 173 PHE cc_start: 0.6899 (t80) cc_final: 0.6585 (t80) REVERT: R 183 ASN cc_start: 0.6650 (OUTLIER) cc_final: 0.6447 (p0) outliers start: 37 outliers final: 30 residues processed: 302 average time/residue: 0.3896 time to fit residues: 162.4621 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 : 1.557 ------------------------------------------------------------------------------- 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 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 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 217 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 5 optimal weight: 0.0970 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.154123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.135023 restraints weight = 14397.055| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 3.03 r_work: 0.3685 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8766 Z= 0.181 Angle : 0.715 12.599 11923 Z= 0.357 Chirality : 0.046 0.231 1386 Planarity : 0.004 0.039 1484 Dihedral : 5.119 43.330 1226 Min Nonbonded Distance : 1.504 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.91 % Allowed : 26.51 % Favored : 69.57 % 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: -0.28 (0.25), residues: 1104 helix: 1.47 (0.25), residues: 402 sheet: -1.08 (0.30), residues: 278 loop : -1.08 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 211 HIS 0.005 0.001 HIS B 311 PHE 0.037 0.002 PHE R 128 TYR 0.020 0.002 TYR S 216 ARG 0.004 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 414) hydrogen bonds : angle 5.19089 ( 1182) SS BOND : bond 0.00360 ( 3) SS BOND : angle 1.51319 ( 6) covalent geometry : bond 0.00404 ( 8763) covalent geometry : angle 0.71437 (11917) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4940.39 seconds wall clock time: 91 minutes 19.96 seconds (5479.96 seconds total)