Starting phenix.real_space_refine on Sun Dec 29 12:06:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v68_31738/12_2024/7v68_31738.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v68_31738/12_2024/7v68_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_31738/12_2024/7v68_31738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v68_31738/12_2024/7v68_31738.map" model { file = "/net/cci-nas-00/data/ceres_data/7v68_31738/12_2024/7v68_31738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v68_31738/12_2024/7v68_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.12, per 1000 atoms: 0.60 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: 2.47 Conformation dependent library (CDL) restraints added in 1.0 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: 1.09 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: 2.54 Time building geometry restraints manager: 2.69 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: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.560 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.461 8763 Z= 0.481 Angle : 0.834 23.900 11917 Z= 0.437 Chirality : 0.049 0.702 1386 Planarity : 0.018 0.636 1484 Dihedral : 12.843 112.936 3027 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.08 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.25), residues: 1104 helix: 1.30 (0.26), residues: 395 sheet: -0.91 (0.31), residues: 261 loop : -1.31 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP R 435 HIS 0.009 0.001 HIS R 217 PHE 0.036 0.002 PHE B 253 TYR 0.026 0.002 TYR B 264 ARG 0.010 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.879 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: 0.2125 time to fit residues: 89.0487 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 : 0.912 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8763 Z= 0.237 Angle : 0.673 9.282 11917 Z= 0.347 Chirality : 0.046 0.282 1386 Planarity : 0.005 0.058 1484 Dihedral : 5.345 50.994 1226 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.90 % Allowed : 14.09 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.25), residues: 1104 helix: 1.38 (0.25), residues: 397 sheet: -0.88 (0.30), residues: 268 loop : -1.23 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 435 HIS 0.012 0.001 HIS A 188 PHE 0.019 0.002 PHE A 191 TYR 0.021 0.002 TYR S 216 ARG 0.006 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 310 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7492 (tm-30) REVERT: A 35 LYS cc_start: 0.7791 (mtmm) cc_final: 0.7279 (mtmm) REVERT: A 197 LYS cc_start: 0.7832 (mmtt) cc_final: 0.7600 (mmtt) REVERT: A 198 MET cc_start: 0.6400 (ttm) cc_final: 0.6193 (ttm) REVERT: A 251 ASP cc_start: 0.7287 (t70) cc_final: 0.6647 (t0) REVERT: A 270 LYS cc_start: 0.7890 (mtmm) cc_final: 0.7452 (mtmm) REVERT: A 271 LYS cc_start: 0.6667 (ptpp) cc_final: 0.6270 (ptpp) REVERT: A 274 PHE cc_start: 0.6645 (t80) cc_final: 0.6190 (t80) REVERT: A 330 LYS cc_start: 0.8148 (mppt) cc_final: 0.7940 (mppt) REVERT: A 347 ASN cc_start: 0.7346 (m-40) cc_final: 0.6795 (m-40) REVERT: B 63 TRP cc_start: 0.7948 (m100) cc_final: 0.7607 (m100) REVERT: B 65 THR cc_start: 0.7850 (m) cc_final: 0.7583 (p) REVERT: B 114 CYS cc_start: 0.6359 (t) cc_final: 0.5993 (p) REVERT: B 163 ASP cc_start: 0.7334 (p0) cc_final: 0.7128 (p0) REVERT: B 175 GLN cc_start: 0.7639 (pp30) cc_final: 0.7406 (pp30) REVERT: B 176 GLN cc_start: 0.8088 (pt0) cc_final: 0.7504 (pt0) REVERT: B 233 CYS cc_start: 0.7433 (t) cc_final: 0.7203 (t) REVERT: B 253 PHE cc_start: 0.7772 (m-10) cc_final: 0.7408 (m-80) REVERT: B 259 GLN cc_start: 0.7470 (pt0) cc_final: 0.7070 (pt0) REVERT: B 275 SER cc_start: 0.7927 (m) cc_final: 0.7634 (p) REVERT: B 277 SER cc_start: 0.8041 (t) cc_final: 0.7833 (t) REVERT: C 15 LEU cc_start: 0.8025 (mt) cc_final: 0.7640 (mt) REVERT: S 78 THR cc_start: 0.7931 (p) cc_final: 0.7633 (p) REVERT: S 176 LEU cc_start: 0.8300 (mm) cc_final: 0.8064 (mm) REVERT: S 182 ASN cc_start: 0.6579 (m110) cc_final: 0.6275 (m110) REVERT: R 52 LEU cc_start: 0.7224 (mt) cc_final: 0.6983 (mt) REVERT: R 54 MET cc_start: 0.6264 (ptp) cc_final: 0.5994 (ptp) REVERT: R 84 PHE cc_start: 0.6236 (m-80) cc_final: 0.5828 (m-80) REVERT: R 86 MET cc_start: 0.4184 (mmp) cc_final: 0.3923 (mmp) REVERT: R 89 TYR cc_start: 0.6391 (t80) cc_final: 0.6072 (t80) REVERT: R 93 ILE cc_start: 0.6004 (mt) cc_final: 0.5604 (mt) REVERT: R 111 LEU cc_start: 0.7644 (tt) cc_final: 0.7413 (tp) REVERT: R 121 MET cc_start: 0.7148 (mtt) cc_final: 0.6724 (mtt) REVERT: R 173 PHE cc_start: 0.6645 (t80) cc_final: 0.6385 (t80) REVERT: R 187 ILE cc_start: 0.7101 (tp) cc_final: 0.6884 (tp) REVERT: R 449 ASN cc_start: 0.7362 (m-40) cc_final: 0.6892 (m-40) outliers start: 17 outliers final: 14 residues processed: 314 average time/residue: 0.2211 time to fit residues: 93.4597 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 : 1.008 ------------------------------------------------------------------------------- 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 55 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 0.0270 chunk 67 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 79 optimal weight: 7.9990 overall best weight: 0.8844 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8763 Z= 0.270 Angle : 0.650 8.297 11917 Z= 0.337 Chirality : 0.045 0.235 1386 Planarity : 0.004 0.051 1484 Dihedral : 5.482 49.682 1226 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.36 % Allowed : 16.89 % 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: -0.36 (0.25), residues: 1104 helix: 1.48 (0.25), residues: 395 sheet: -1.07 (0.29), residues: 278 loop : -1.21 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.019 0.002 HIS A 213 PHE 0.018 0.002 PHE B 235 TYR 0.017 0.002 TYR B 264 ARG 0.006 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 301 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7487 (tm-30) REVERT: A 35 LYS cc_start: 0.8019 (mtmm) cc_final: 0.7453 (mtmm) REVERT: A 197 LYS cc_start: 0.7894 (mmtt) cc_final: 0.7682 (mmtt) REVERT: A 198 MET cc_start: 0.6505 (ttm) cc_final: 0.6222 (ttm) REVERT: A 251 ASP cc_start: 0.7277 (t70) cc_final: 0.6635 (t0) REVERT: A 270 LYS cc_start: 0.7904 (mtmm) cc_final: 0.7701 (mtmm) REVERT: A 274 PHE cc_start: 0.6613 (t80) cc_final: 0.6112 (t80) REVERT: A 330 LYS cc_start: 0.8179 (mppt) cc_final: 0.7907 (mppt) REVERT: A 345 LYS cc_start: 0.8280 (tptt) cc_final: 0.7928 (tptt) REVERT: A 347 ASN cc_start: 0.7344 (m-40) cc_final: 0.6834 (m-40) REVERT: A 353 LEU cc_start: 0.8319 (tp) cc_final: 0.8062 (tt) REVERT: B 65 THR cc_start: 0.7888 (m) cc_final: 0.7551 (p) REVERT: B 175 GLN cc_start: 0.7636 (pp30) cc_final: 0.7393 (pp30) REVERT: B 176 GLN cc_start: 0.8181 (pt0) cc_final: 0.7507 (pt0) REVERT: B 188 MET cc_start: 0.6837 (mmm) cc_final: 0.6589 (mmm) REVERT: B 249 THR cc_start: 0.8267 (p) cc_final: 0.8019 (p) REVERT: B 251 ARG cc_start: 0.7053 (tpp80) cc_final: 0.6365 (tpp80) REVERT: B 259 GLN cc_start: 0.7801 (pt0) cc_final: 0.7532 (pt0) REVERT: B 275 SER cc_start: 0.7967 (m) cc_final: 0.7632 (p) REVERT: B 277 SER cc_start: 0.8094 (t) cc_final: 0.7843 (t) REVERT: C 15 LEU cc_start: 0.8058 (mt) cc_final: 0.7670 (mt) REVERT: S 78 THR cc_start: 0.7956 (p) cc_final: 0.7637 (p) REVERT: S 176 LEU cc_start: 0.8404 (mm) cc_final: 0.8000 (mm) REVERT: S 182 ASN cc_start: 0.6774 (m110) cc_final: 0.6441 (m-40) REVERT: R 54 MET cc_start: 0.6082 (ptp) cc_final: 0.5817 (ptp) REVERT: R 84 PHE cc_start: 0.6255 (m-80) cc_final: 0.5821 (m-80) REVERT: R 86 MET cc_start: 0.4790 (mmp) cc_final: 0.4267 (mmp) REVERT: R 111 LEU cc_start: 0.7635 (tt) cc_final: 0.7424 (tp) REVERT: R 121 MET cc_start: 0.7063 (mtt) cc_final: 0.6697 (mtt) REVERT: R 173 PHE cc_start: 0.6692 (t80) cc_final: 0.6408 (t80) REVERT: R 214 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6492 (tt) REVERT: R 449 ASN cc_start: 0.7351 (m-40) cc_final: 0.7086 (m-40) outliers start: 30 outliers final: 23 residues processed: 310 average time/residue: 0.2302 time to fit residues: 95.4930 Evaluate side-chains 308 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 284 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 260 THR Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 46 GLU 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 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 97 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 239 ASN S 39 GLN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 157 ASN S 167 GLN ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8763 Z= 0.231 Angle : 0.656 14.913 11917 Z= 0.334 Chirality : 0.045 0.248 1386 Planarity : 0.004 0.045 1484 Dihedral : 5.184 44.415 1226 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.25 % Allowed : 19.57 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.32 (0.25), residues: 1104 helix: 1.51 (0.25), residues: 396 sheet: -1.09 (0.29), residues: 278 loop : -1.16 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 211 HIS 0.007 0.001 HIS A 188 PHE 0.013 0.002 PHE S 200 TYR 0.024 0.002 TYR B 264 ARG 0.004 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 296 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7481 (tm-30) REVERT: A 35 LYS cc_start: 0.8019 (mtmm) cc_final: 0.7452 (mtmm) REVERT: A 197 LYS cc_start: 0.8014 (mmtt) cc_final: 0.7634 (mmtt) REVERT: A 198 MET cc_start: 0.6516 (ttm) cc_final: 0.6235 (ttm) REVERT: A 244 HIS cc_start: 0.7569 (m90) cc_final: 0.7257 (m90) REVERT: A 251 ASP cc_start: 0.7259 (t70) cc_final: 0.6640 (t0) REVERT: A 270 LYS cc_start: 0.7901 (mtmm) cc_final: 0.7688 (mtmm) REVERT: A 274 PHE cc_start: 0.6583 (t80) cc_final: 0.6082 (t80) REVERT: A 345 LYS cc_start: 0.8283 (tptt) cc_final: 0.7955 (tptt) REVERT: A 347 ASN cc_start: 0.7343 (m-40) cc_final: 0.6842 (m-40) REVERT: B 65 THR cc_start: 0.7855 (m) cc_final: 0.7524 (p) REVERT: B 83 ASP cc_start: 0.7644 (t0) cc_final: 0.7361 (t0) REVERT: B 132 ASN cc_start: 0.7723 (OUTLIER) cc_final: 0.7428 (p0) REVERT: B 175 GLN cc_start: 0.7619 (pp30) cc_final: 0.7411 (pp30) REVERT: B 249 THR cc_start: 0.8302 (p) cc_final: 0.7968 (p) REVERT: B 253 PHE cc_start: 0.7780 (m-10) cc_final: 0.7375 (m-80) REVERT: B 259 GLN cc_start: 0.7613 (pt0) cc_final: 0.7362 (pt0) REVERT: B 275 SER cc_start: 0.7935 (m) cc_final: 0.7622 (p) REVERT: B 277 SER cc_start: 0.8067 (t) cc_final: 0.7820 (t) REVERT: C 15 LEU cc_start: 0.8052 (mt) cc_final: 0.7668 (mt) REVERT: S 78 THR cc_start: 0.7901 (p) cc_final: 0.7645 (p) REVERT: S 79 LEU cc_start: 0.7082 (pp) cc_final: 0.6872 (pp) REVERT: S 155 HIS cc_start: 0.7706 (t-170) cc_final: 0.7431 (t-170) REVERT: S 176 LEU cc_start: 0.8394 (mm) cc_final: 0.7952 (mm) REVERT: S 180 MET cc_start: 0.4881 (ttp) cc_final: 0.4566 (ttm) REVERT: S 182 ASN cc_start: 0.6731 (m110) cc_final: 0.6379 (m-40) REVERT: R 54 MET cc_start: 0.6125 (ptp) cc_final: 0.5783 (ptp) REVERT: R 84 PHE cc_start: 0.6221 (m-80) cc_final: 0.5758 (m-80) REVERT: R 86 MET cc_start: 0.4939 (mmp) cc_final: 0.4348 (mmp) REVERT: R 89 TYR cc_start: 0.6180 (t80) cc_final: 0.5926 (t80) REVERT: R 111 LEU cc_start: 0.7677 (tt) cc_final: 0.7441 (tp) REVERT: R 121 MET cc_start: 0.7054 (mtt) cc_final: 0.6751 (mtt) REVERT: R 151 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6737 (pp) REVERT: R 173 PHE cc_start: 0.6663 (t80) cc_final: 0.6384 (t80) REVERT: R 441 LEU cc_start: 0.5350 (OUTLIER) cc_final: 0.5093 (pp) REVERT: R 449 ASN cc_start: 0.7358 (m-40) cc_final: 0.7084 (m-40) outliers start: 38 outliers final: 27 residues processed: 307 average time/residue: 0.2204 time to fit residues: 91.2644 Evaluate side-chains 322 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 292 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 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 179 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 46 GLU Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 123 LEU 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 441 LEU Chi-restraints excluded: chain R residue 463 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.2980 chunk 1 optimal weight: 0.8980 chunk 78 optimal weight: 0.0970 chunk 43 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 241 ASN B 132 ASN B 239 ASN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 157 ASN S 167 GLN R 417 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8763 Z= 0.210 Angle : 0.626 11.450 11917 Z= 0.321 Chirality : 0.044 0.193 1386 Planarity : 0.004 0.042 1484 Dihedral : 5.113 42.168 1226 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.14 % Allowed : 21.14 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.25), residues: 1104 helix: 1.59 (0.25), residues: 395 sheet: -1.07 (0.30), residues: 278 loop : -1.13 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 82 HIS 0.005 0.001 HIS B 311 PHE 0.018 0.002 PHE R 403 TYR 0.019 0.002 TYR B 264 ARG 0.005 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 284 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7479 (tm-30) REVERT: A 35 LYS cc_start: 0.8007 (mtmm) cc_final: 0.7446 (mtmm) REVERT: A 197 LYS cc_start: 0.8058 (mmtt) cc_final: 0.7774 (mmmt) REVERT: A 198 MET cc_start: 0.6506 (ttm) cc_final: 0.6237 (ttm) REVERT: A 251 ASP cc_start: 0.7265 (t70) cc_final: 0.6577 (t0) REVERT: A 274 PHE cc_start: 0.6585 (t80) cc_final: 0.6071 (t80) REVERT: A 345 LYS cc_start: 0.8287 (tptt) cc_final: 0.7960 (tptt) REVERT: A 347 ASN cc_start: 0.7374 (m-40) cc_final: 0.6860 (m-40) REVERT: B 65 THR cc_start: 0.7791 (m) cc_final: 0.7476 (p) REVERT: B 83 ASP cc_start: 0.7572 (t0) cc_final: 0.7290 (t0) REVERT: B 163 ASP cc_start: 0.7136 (p0) cc_final: 0.6881 (p0) REVERT: B 175 GLN cc_start: 0.7631 (pp30) cc_final: 0.7350 (pp30) REVERT: B 211 TRP cc_start: 0.7879 (OUTLIER) cc_final: 0.7092 (m100) REVERT: B 249 THR cc_start: 0.8280 (p) cc_final: 0.8031 (p) REVERT: B 259 GLN cc_start: 0.7685 (pt0) cc_final: 0.7431 (pt0) REVERT: C 11 GLN cc_start: 0.8128 (tm130) cc_final: 0.7560 (tm130) REVERT: C 15 LEU cc_start: 0.8078 (mt) cc_final: 0.7447 (mt) REVERT: S 176 LEU cc_start: 0.8326 (mm) cc_final: 0.7922 (mm) REVERT: S 180 MET cc_start: 0.4828 (ttp) cc_final: 0.4522 (ttm) REVERT: S 182 ASN cc_start: 0.6719 (m110) cc_final: 0.6325 (m-40) REVERT: R 54 MET cc_start: 0.6158 (ptp) cc_final: 0.5813 (ptp) REVERT: R 84 PHE cc_start: 0.6007 (m-80) cc_final: 0.5562 (m-80) REVERT: R 86 MET cc_start: 0.4557 (mmp) cc_final: 0.3782 (mmp) REVERT: R 109 LEU cc_start: 0.7295 (mm) cc_final: 0.7000 (pp) REVERT: R 111 LEU cc_start: 0.7661 (tt) cc_final: 0.7450 (tp) REVERT: R 121 MET cc_start: 0.7021 (mtt) cc_final: 0.6698 (mtt) REVERT: R 140 TYR cc_start: 0.7992 (t80) cc_final: 0.7632 (t80) REVERT: R 151 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6542 (pp) REVERT: R 173 PHE cc_start: 0.6578 (t80) cc_final: 0.6316 (t80) REVERT: R 449 ASN cc_start: 0.7365 (m-40) cc_final: 0.7132 (m-40) outliers start: 37 outliers final: 27 residues processed: 297 average time/residue: 0.2238 time to fit residues: 89.3037 Evaluate side-chains 312 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 283 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 314 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 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 217 HIS Chi-restraints excluded: chain R residue 407 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.2980 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS B 313 ASN C 11 GLN S 39 GLN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8763 Z= 0.208 Angle : 0.629 10.197 11917 Z= 0.322 Chirality : 0.044 0.202 1386 Planarity : 0.004 0.039 1484 Dihedral : 5.092 43.295 1226 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.14 % Allowed : 24.16 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1104 helix: 1.62 (0.25), residues: 402 sheet: -0.97 (0.30), residues: 276 loop : -1.08 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP B 82 HIS 0.005 0.001 HIS B 311 PHE 0.012 0.001 PHE B 235 TYR 0.017 0.002 TYR S 103 ARG 0.006 0.000 ARG B 52 *********************** 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 338 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 301 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7317 (tm-30) REVERT: A 35 LYS cc_start: 0.7993 (mtmm) cc_final: 0.7471 (mtmm) REVERT: A 197 LYS cc_start: 0.7963 (mmtt) cc_final: 0.7687 (mmmt) REVERT: A 198 MET cc_start: 0.6538 (ttm) cc_final: 0.6260 (ttm) REVERT: A 243 MET cc_start: 0.7665 (mmm) cc_final: 0.7269 (mmm) REVERT: A 251 ASP cc_start: 0.7229 (t70) cc_final: 0.6548 (t0) REVERT: A 274 PHE cc_start: 0.6587 (t80) cc_final: 0.6035 (t80) REVERT: A 304 GLN cc_start: 0.7368 (tp40) cc_final: 0.7033 (tp40) REVERT: A 345 LYS cc_start: 0.8293 (tptt) cc_final: 0.7957 (tptt) REVERT: A 347 ASN cc_start: 0.7388 (m-40) cc_final: 0.6883 (m-40) REVERT: B 65 THR cc_start: 0.7784 (m) cc_final: 0.7474 (p) REVERT: B 70 LEU cc_start: 0.7659 (mt) cc_final: 0.7288 (mp) REVERT: B 83 ASP cc_start: 0.7539 (t0) cc_final: 0.7276 (t0) REVERT: B 132 ASN cc_start: 0.7674 (p0) cc_final: 0.7390 (p0) REVERT: B 175 GLN cc_start: 0.7638 (pp30) cc_final: 0.7361 (pp30) REVERT: B 211 TRP cc_start: 0.7857 (OUTLIER) cc_final: 0.7009 (m100) REVERT: B 212 ASP cc_start: 0.7585 (t0) cc_final: 0.7027 (p0) REVERT: B 234 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7382 (m-80) REVERT: B 249 THR cc_start: 0.8356 (p) cc_final: 0.8085 (p) REVERT: B 253 PHE cc_start: 0.7749 (m-10) cc_final: 0.7382 (m-80) REVERT: B 259 GLN cc_start: 0.7721 (pt0) cc_final: 0.7500 (pt0) REVERT: C 11 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7612 (tm-30) REVERT: C 15 LEU cc_start: 0.8110 (mt) cc_final: 0.7442 (mt) REVERT: S 23 SER cc_start: 0.8204 (t) cc_final: 0.7974 (p) REVERT: S 60 TYR cc_start: 0.7669 (m-80) cc_final: 0.7305 (m-80) REVERT: S 165 PHE cc_start: 0.8223 (m-10) cc_final: 0.7985 (m-80) REVERT: S 176 LEU cc_start: 0.8285 (mm) cc_final: 0.7909 (mm) REVERT: S 182 ASN cc_start: 0.6808 (m110) cc_final: 0.6473 (m-40) REVERT: R 54 MET cc_start: 0.6168 (ptp) cc_final: 0.5810 (ptp) REVERT: R 84 PHE cc_start: 0.5983 (m-80) cc_final: 0.5582 (m-80) REVERT: R 86 MET cc_start: 0.4591 (mmp) cc_final: 0.3922 (mmp) REVERT: R 121 MET cc_start: 0.7016 (mtt) cc_final: 0.6690 (mtt) REVERT: R 140 TYR cc_start: 0.7974 (t80) cc_final: 0.7674 (t80) REVERT: R 173 PHE cc_start: 0.6583 (t80) cc_final: 0.6316 (t80) outliers start: 37 outliers final: 29 residues processed: 315 average time/residue: 0.2302 time to fit residues: 97.4087 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 : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 187 VAL 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 286 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 437 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 0.0870 chunk 65 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS B 142 HIS ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 417 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8763 Z= 0.212 Angle : 0.656 9.785 11917 Z= 0.333 Chirality : 0.045 0.236 1386 Planarity : 0.004 0.039 1484 Dihedral : 5.102 43.594 1226 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.03 % Allowed : 26.06 % 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: -0.18 (0.25), residues: 1104 helix: 1.57 (0.25), residues: 403 sheet: -0.98 (0.31), residues: 271 loop : -1.09 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 82 HIS 0.004 0.001 HIS B 311 PHE 0.014 0.001 PHE S 108 TYR 0.021 0.002 TYR S 216 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 288 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7315 (tm-30) REVERT: A 35 LYS cc_start: 0.7984 (mtmm) cc_final: 0.7456 (mtmm) REVERT: A 198 MET cc_start: 0.6533 (ttm) cc_final: 0.6255 (ttm) REVERT: A 243 MET cc_start: 0.7727 (mmm) cc_final: 0.7263 (mmm) REVERT: A 251 ASP cc_start: 0.7201 (t70) cc_final: 0.6527 (t0) REVERT: A 274 PHE cc_start: 0.6586 (t80) cc_final: 0.6029 (t80) REVERT: A 304 GLN cc_start: 0.7326 (tp40) cc_final: 0.6965 (tp40) REVERT: A 345 LYS cc_start: 0.8296 (tptt) cc_final: 0.7892 (tptt) REVERT: A 347 ASN cc_start: 0.7392 (m-40) cc_final: 0.6885 (m-40) REVERT: B 65 THR cc_start: 0.7765 (m) cc_final: 0.7494 (p) REVERT: B 70 LEU cc_start: 0.7623 (mt) cc_final: 0.7279 (mp) REVERT: B 83 ASP cc_start: 0.7515 (t0) cc_final: 0.7239 (t0) REVERT: B 132 ASN cc_start: 0.7647 (p0) cc_final: 0.7320 (p0) REVERT: B 175 GLN cc_start: 0.7642 (pp30) cc_final: 0.7344 (pp30) REVERT: B 211 TRP cc_start: 0.7841 (OUTLIER) cc_final: 0.6954 (m100) REVERT: B 220 GLN cc_start: 0.6031 (mt0) cc_final: 0.5676 (mt0) REVERT: B 234 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: B 249 THR cc_start: 0.8338 (p) cc_final: 0.8089 (p) REVERT: B 253 PHE cc_start: 0.7683 (m-10) cc_final: 0.7339 (m-80) REVERT: B 259 GLN cc_start: 0.7683 (pt0) cc_final: 0.7481 (pt0) REVERT: B 292 PHE cc_start: 0.6639 (OUTLIER) cc_final: 0.6304 (m-80) REVERT: B 313 ASN cc_start: 0.8321 (m-40) cc_final: 0.7688 (m-40) REVERT: C 11 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7617 (tm-30) REVERT: C 15 LEU cc_start: 0.8116 (mt) cc_final: 0.7459 (mt) REVERT: S 23 SER cc_start: 0.8152 (t) cc_final: 0.7925 (p) REVERT: S 155 HIS cc_start: 0.7673 (t-170) cc_final: 0.7317 (t-170) REVERT: S 176 LEU cc_start: 0.8304 (mm) cc_final: 0.7938 (mm) REVERT: S 182 ASN cc_start: 0.6830 (m110) cc_final: 0.6408 (m-40) REVERT: R 54 MET cc_start: 0.6181 (ptp) cc_final: 0.5813 (ptp) REVERT: R 84 PHE cc_start: 0.5969 (m-80) cc_final: 0.5558 (m-80) REVERT: R 86 MET cc_start: 0.4583 (mmp) cc_final: 0.3781 (mmp) REVERT: R 121 MET cc_start: 0.7003 (mtt) cc_final: 0.6658 (mtt) REVERT: R 140 TYR cc_start: 0.7974 (t80) cc_final: 0.7720 (t80) REVERT: R 173 PHE cc_start: 0.6575 (t80) cc_final: 0.6302 (t80) REVERT: R 183 ASN cc_start: 0.6426 (OUTLIER) cc_final: 0.6204 (p0) outliers start: 36 outliers final: 25 residues processed: 300 average time/residue: 0.2271 time to fit residues: 92.1083 Evaluate side-chains 316 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 287 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 314 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 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 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 151 LEU Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 437 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 0.0070 chunk 95 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 213 HIS ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8763 Z= 0.215 Angle : 0.663 11.035 11917 Z= 0.335 Chirality : 0.045 0.220 1386 Planarity : 0.004 0.039 1484 Dihedral : 5.076 43.806 1226 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.03 % Allowed : 26.29 % 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: -0.18 (0.26), residues: 1104 helix: 1.58 (0.26), residues: 403 sheet: -1.00 (0.31), residues: 271 loop : -1.10 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 82 HIS 0.005 0.001 HIS A 188 PHE 0.026 0.002 PHE R 128 TYR 0.019 0.001 TYR S 216 ARG 0.004 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 292 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.7996 (mtmm) cc_final: 0.7406 (mtmm) REVERT: A 198 MET cc_start: 0.6548 (ttm) cc_final: 0.6251 (ttm) REVERT: A 243 MET cc_start: 0.7730 (mmm) cc_final: 0.7252 (mmm) REVERT: A 251 ASP cc_start: 0.7194 (t70) cc_final: 0.6531 (t0) REVERT: A 274 PHE cc_start: 0.6589 (t80) cc_final: 0.6027 (t80) REVERT: A 345 LYS cc_start: 0.8256 (tptt) cc_final: 0.7852 (tptt) REVERT: A 347 ASN cc_start: 0.7397 (m-40) cc_final: 0.6882 (m-40) REVERT: B 65 THR cc_start: 0.7759 (m) cc_final: 0.7488 (p) REVERT: B 70 LEU cc_start: 0.7618 (mt) cc_final: 0.7278 (mp) REVERT: B 83 ASP cc_start: 0.7523 (t0) cc_final: 0.7239 (t0) REVERT: B 132 ASN cc_start: 0.7661 (p0) cc_final: 0.7318 (p0) REVERT: B 175 GLN cc_start: 0.7633 (pp30) cc_final: 0.7312 (pp30) REVERT: B 211 TRP cc_start: 0.7846 (OUTLIER) cc_final: 0.6948 (m100) REVERT: B 220 GLN cc_start: 0.6015 (mt0) cc_final: 0.5672 (mt0) REVERT: B 234 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7396 (m-80) REVERT: B 249 THR cc_start: 0.8332 (p) cc_final: 0.8090 (p) REVERT: B 253 PHE cc_start: 0.7661 (m-10) cc_final: 0.7279 (m-80) REVERT: B 259 GLN cc_start: 0.7691 (pt0) cc_final: 0.7488 (pt0) REVERT: B 292 PHE cc_start: 0.6626 (OUTLIER) cc_final: 0.6291 (m-80) REVERT: B 313 ASN cc_start: 0.8422 (m-40) cc_final: 0.7848 (m-40) REVERT: C 11 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7617 (tm-30) REVERT: C 15 LEU cc_start: 0.8116 (mt) cc_final: 0.7456 (mt) REVERT: S 23 SER cc_start: 0.8151 (t) cc_final: 0.7946 (p) REVERT: S 155 HIS cc_start: 0.7680 (t-170) cc_final: 0.7342 (t-170) REVERT: S 176 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7912 (mm) REVERT: S 182 ASN cc_start: 0.6842 (m110) cc_final: 0.6432 (m-40) REVERT: S 190 ARG cc_start: 0.6601 (ptt-90) cc_final: 0.6215 (ptt-90) REVERT: R 54 MET cc_start: 0.6184 (ptp) cc_final: 0.5826 (ptp) REVERT: R 74 LEU cc_start: 0.7908 (tt) cc_final: 0.7705 (tp) REVERT: R 84 PHE cc_start: 0.5964 (m-80) cc_final: 0.5541 (m-80) REVERT: R 86 MET cc_start: 0.4584 (mmp) cc_final: 0.3674 (mmp) REVERT: R 121 MET cc_start: 0.7011 (mtt) cc_final: 0.6693 (mtt) REVERT: R 123 LEU cc_start: 0.7828 (tp) cc_final: 0.7586 (mt) REVERT: R 140 TYR cc_start: 0.7960 (t80) cc_final: 0.7744 (t80) REVERT: R 173 PHE cc_start: 0.6578 (t80) cc_final: 0.6309 (t80) REVERT: R 183 ASN cc_start: 0.6423 (OUTLIER) cc_final: 0.6198 (p0) outliers start: 36 outliers final: 27 residues processed: 303 average time/residue: 0.2249 time to fit residues: 90.8794 Evaluate side-chains 323 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 291 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 271 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 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 327 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 176 LEU Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 437 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.4980 chunk 100 optimal weight: 0.6980 chunk 58 optimal weight: 0.0770 chunk 42 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 88 optimal weight: 0.4980 chunk 92 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8763 Z= 0.215 Angle : 0.663 11.035 11917 Z= 0.335 Chirality : 0.045 0.220 1386 Planarity : 0.004 0.039 1484 Dihedral : 5.076 43.806 1226 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.69 % Allowed : 27.29 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.18 (0.26), residues: 1104 helix: 1.58 (0.26), residues: 403 sheet: -1.00 (0.31), residues: 271 loop : -1.10 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 82 HIS 0.005 0.001 HIS A 188 PHE 0.026 0.002 PHE R 128 TYR 0.019 0.001 TYR S 216 ARG 0.004 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 291 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.7990 (mtmm) cc_final: 0.7405 (mtmm) REVERT: A 198 MET cc_start: 0.6546 (ttm) cc_final: 0.6253 (ttm) REVERT: A 243 MET cc_start: 0.7728 (mmm) cc_final: 0.7252 (mmm) REVERT: A 251 ASP cc_start: 0.7187 (t70) cc_final: 0.6530 (t0) REVERT: A 274 PHE cc_start: 0.6589 (t80) cc_final: 0.6027 (t80) REVERT: A 345 LYS cc_start: 0.8256 (tptt) cc_final: 0.7852 (tptt) REVERT: A 347 ASN cc_start: 0.7393 (m-40) cc_final: 0.6883 (m-40) REVERT: B 65 THR cc_start: 0.7755 (m) cc_final: 0.7488 (p) REVERT: B 70 LEU cc_start: 0.7628 (mt) cc_final: 0.7277 (mp) REVERT: B 83 ASP cc_start: 0.7530 (t0) cc_final: 0.7240 (t0) REVERT: B 132 ASN cc_start: 0.7653 (p0) cc_final: 0.7318 (p0) REVERT: B 175 GLN cc_start: 0.7634 (pp30) cc_final: 0.7312 (pp30) REVERT: B 211 TRP cc_start: 0.7847 (OUTLIER) cc_final: 0.6949 (m100) REVERT: B 220 GLN cc_start: 0.6019 (mt0) cc_final: 0.5671 (mt0) REVERT: B 234 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7396 (m-80) REVERT: B 249 THR cc_start: 0.8332 (p) cc_final: 0.8090 (p) REVERT: B 253 PHE cc_start: 0.7659 (m-10) cc_final: 0.7279 (m-80) REVERT: B 259 GLN cc_start: 0.7691 (pt0) cc_final: 0.7488 (pt0) REVERT: B 292 PHE cc_start: 0.6623 (OUTLIER) cc_final: 0.6292 (m-80) REVERT: B 313 ASN cc_start: 0.8425 (m-40) cc_final: 0.7847 (m-40) REVERT: C 11 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7617 (tm-30) REVERT: C 15 LEU cc_start: 0.8114 (mt) cc_final: 0.7457 (mt) REVERT: S 23 SER cc_start: 0.8150 (t) cc_final: 0.7946 (p) REVERT: S 155 HIS cc_start: 0.7691 (t-170) cc_final: 0.7342 (t-170) REVERT: S 176 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7910 (mm) REVERT: S 182 ASN cc_start: 0.6841 (m110) cc_final: 0.6432 (m-40) REVERT: S 190 ARG cc_start: 0.6604 (ptt-90) cc_final: 0.6215 (ptt-90) REVERT: R 54 MET cc_start: 0.6182 (ptp) cc_final: 0.5826 (ptp) REVERT: R 74 LEU cc_start: 0.7908 (tt) cc_final: 0.7705 (tp) REVERT: R 84 PHE cc_start: 0.5962 (m-80) cc_final: 0.5541 (m-80) REVERT: R 86 MET cc_start: 0.4586 (mmp) cc_final: 0.3673 (mmp) REVERT: R 121 MET cc_start: 0.7011 (mtt) cc_final: 0.6693 (mtt) REVERT: R 123 LEU cc_start: 0.7831 (tp) cc_final: 0.7586 (mt) REVERT: R 140 TYR cc_start: 0.7958 (t80) cc_final: 0.7745 (t80) REVERT: R 173 PHE cc_start: 0.6580 (t80) cc_final: 0.6309 (t80) REVERT: R 183 ASN cc_start: 0.6420 (OUTLIER) cc_final: 0.6198 (p0) outliers start: 33 outliers final: 27 residues processed: 301 average time/residue: 0.2370 time to fit residues: 95.8645 Evaluate side-chains 322 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 290 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 271 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 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 327 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 176 LEU Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 437 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8763 Z= 0.254 Angle : 0.692 10.888 11917 Z= 0.349 Chirality : 0.046 0.223 1386 Planarity : 0.004 0.039 1484 Dihedral : 5.116 44.261 1226 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.80 % Allowed : 27.29 % Favored : 68.90 % 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 (0.26), residues: 1104 helix: 1.58 (0.26), residues: 403 sheet: -0.99 (0.31), residues: 270 loop : -1.08 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 82 HIS 0.005 0.001 HIS B 311 PHE 0.013 0.002 PHE S 200 TYR 0.020 0.002 TYR S 216 ARG 0.004 0.000 ARG B 304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 288 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8004 (mtmm) cc_final: 0.7405 (mtmm) REVERT: A 198 MET cc_start: 0.6546 (ttm) cc_final: 0.6245 (ttm) REVERT: A 210 LYS cc_start: 0.8138 (tppp) cc_final: 0.7927 (ttmm) REVERT: A 243 MET cc_start: 0.7777 (mmm) cc_final: 0.7281 (mmm) REVERT: A 251 ASP cc_start: 0.7181 (t70) cc_final: 0.6531 (t0) REVERT: A 274 PHE cc_start: 0.6603 (t80) cc_final: 0.6047 (t80) REVERT: A 304 GLN cc_start: 0.7289 (tp40) cc_final: 0.6942 (tp40) REVERT: A 345 LYS cc_start: 0.8261 (tptt) cc_final: 0.7853 (tptt) REVERT: A 347 ASN cc_start: 0.7428 (m-40) cc_final: 0.6927 (m-40) REVERT: B 65 THR cc_start: 0.7790 (m) cc_final: 0.7471 (p) REVERT: B 83 ASP cc_start: 0.7596 (t0) cc_final: 0.7228 (t0) REVERT: B 101 MET cc_start: 0.7580 (mtp) cc_final: 0.7259 (mtm) REVERT: B 132 ASN cc_start: 0.7615 (p0) cc_final: 0.7293 (p0) REVERT: B 175 GLN cc_start: 0.7654 (pp30) cc_final: 0.7304 (pp30) REVERT: B 220 GLN cc_start: 0.6004 (mt0) cc_final: 0.5669 (mt0) REVERT: B 234 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7405 (m-80) REVERT: B 249 THR cc_start: 0.8312 (p) cc_final: 0.8073 (p) REVERT: B 259 GLN cc_start: 0.7603 (pt0) cc_final: 0.7362 (pt0) REVERT: B 292 PHE cc_start: 0.6672 (OUTLIER) cc_final: 0.6339 (m-80) REVERT: C 11 GLN cc_start: 0.8139 (tm-30) cc_final: 0.7627 (tm-30) REVERT: C 15 LEU cc_start: 0.8137 (mt) cc_final: 0.7471 (mt) REVERT: S 176 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7915 (mm) REVERT: S 190 ARG cc_start: 0.6618 (ptt-90) cc_final: 0.6275 (ptt-90) REVERT: R 54 MET cc_start: 0.6206 (ptp) cc_final: 0.5842 (ptp) REVERT: R 84 PHE cc_start: 0.5943 (m-80) cc_final: 0.5526 (m-80) REVERT: R 86 MET cc_start: 0.4930 (mmp) cc_final: 0.3852 (mmp) REVERT: R 121 MET cc_start: 0.7033 (mtt) cc_final: 0.6689 (mtt) REVERT: R 123 LEU cc_start: 0.7848 (tp) cc_final: 0.7642 (tp) REVERT: R 140 TYR cc_start: 0.7978 (t80) cc_final: 0.7758 (t80) REVERT: R 173 PHE cc_start: 0.6647 (t80) cc_final: 0.6359 (t80) REVERT: R 421 LEU cc_start: 0.8264 (tp) cc_final: 0.7880 (tt) outliers start: 34 outliers final: 29 residues processed: 298 average time/residue: 0.2266 time to fit residues: 90.7733 Evaluate side-chains 319 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 287 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 158 VAL 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 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 167 GLN Chi-restraints excluded: chain S residue 176 LEU Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 437 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 88 optimal weight: 0.1980 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.154010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.134959 restraints weight = 14316.058| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.98 r_work: 0.3681 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8763 Z= 0.258 Angle : 0.702 11.006 11917 Z= 0.354 Chirality : 0.047 0.259 1386 Planarity : 0.004 0.039 1484 Dihedral : 5.126 44.212 1226 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.69 % Allowed : 27.74 % Favored : 68.57 % 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: -0.18 (0.26), residues: 1104 helix: 1.58 (0.26), residues: 403 sheet: -0.99 (0.31), residues: 270 loop : -1.10 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 82 HIS 0.007 0.001 HIS A 213 PHE 0.017 0.002 PHE S 200 TYR 0.021 0.002 TYR S 216 ARG 0.006 0.000 ARG S 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2466.62 seconds wall clock time: 45 minutes 52.82 seconds (2752.82 seconds total)