Starting phenix.real_space_refine on Mon Nov 18 18:45:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xta_33444/11_2024/7xta_33444_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xta_33444/11_2024/7xta_33444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xta_33444/11_2024/7xta_33444.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xta_33444/11_2024/7xta_33444.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xta_33444/11_2024/7xta_33444_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xta_33444/11_2024/7xta_33444_neut_trim.cif" } resolution = 3.2 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= 0.003 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 70 5.16 5 C 5607 2.51 5 N 1476 2.21 5 O 1618 1.98 5 H 8707 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17478 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3538 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 5026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5026 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "E" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3472 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "G" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 794 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain: "R" Number of atoms: 4635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 4635 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 1 Chain: "R" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.72, per 1000 atoms: 0.50 Number of scatterers: 17478 At special positions: 0 Unit cell: (115.668, 128.52, 110.313, 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) S 70 16.00 O 1618 8.00 N 1476 7.00 C 5607 6.00 H 8707 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.73 Conformation dependent library (CDL) restraints added in 1.4 seconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 12 sheets defined 40.0% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.649A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.068A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 232 " --> pdb=" O ASP A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 232' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.861A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.205A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 281 No H-bonds generated for 'chain 'A' and resid 280 through 281' Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.868A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 9 through 25 removed outlier: 4.063A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.641A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'G' and resid 14 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.570A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 19 through 46 Processing helix chain 'R' and resid 46 through 51 Processing helix chain 'R' and resid 53 through 72 removed outlier: 4.329A pdb=" N PHE R 57 " --> pdb=" O LYS R 53 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 83 removed outlier: 3.664A pdb=" N VAL R 81 " --> pdb=" O ALA R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 123 removed outlier: 4.297A pdb=" N PHE R 91 " --> pdb=" O TYR R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 132 Processing helix chain 'R' and resid 133 through 153 removed outlier: 3.542A pdb=" N ILE R 137 " --> pdb=" O THR R 133 " (cutoff:3.500A) Proline residue: R 148 - end of helix removed outlier: 3.912A pdb=" N ILE R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 158 removed outlier: 3.654A pdb=" N GLN R 158 " --> pdb=" O LEU R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 174 removed outlier: 3.848A pdb=" N PHE R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 200 Processing helix chain 'R' and resid 200 through 222 Processing helix chain 'R' and resid 255 through 281 Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 282 through 284 No H-bonds generated for 'chain 'R' and resid 282 through 284' Processing helix chain 'R' and resid 289 through 312 removed outlier: 3.770A pdb=" N ASN R 303 " --> pdb=" O LEU R 299 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER R 304 " --> pdb=" O GLY R 300 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY R 305 " --> pdb=" O TYR R 301 " (cutoff:3.500A) Proline residue: R 308 - end of helix Processing helix chain 'R' and resid 317 through 328 removed outlier: 3.942A pdb=" N ALA R 321 " --> pdb=" O SER R 317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.880A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.903A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.726A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.656A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.964A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.969A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.511A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.594A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 7.156A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.128A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1194 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: 6.21 Time building geometry restraints manager: 5.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8668 1.03 - 1.23: 40 1.23 - 1.42: 3793 1.42 - 1.62: 5066 1.62 - 1.81: 99 Bond restraints: 17666 Sorted by residual: bond pdb=" CZ2 SRO R 401 " pdb=" CH2 SRO R 401 " ideal model delta sigma weight residual 1.386 1.521 -0.135 2.00e-02 2.50e+03 4.59e+01 bond pdb=" CG SRO R 401 " pdb=" CD2 SRO R 401 " ideal model delta sigma weight residual 1.438 1.508 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" CD1 SRO R 401 " pdb=" NE1 SRO R 401 " ideal model delta sigma weight residual 1.377 1.315 0.062 2.00e-02 2.50e+03 9.71e+00 bond pdb=" CE2 SRO R 401 " pdb=" CZ2 SRO R 401 " ideal model delta sigma weight residual 1.393 1.352 0.041 2.00e-02 2.50e+03 4.17e+00 bond pdb=" CD2 SRO R 401 " pdb=" CE3 SRO R 401 " ideal model delta sigma weight residual 1.404 1.366 0.038 2.00e-02 2.50e+03 3.66e+00 ... (remaining 17661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 31668 2.09 - 4.17: 120 4.17 - 6.26: 16 6.26 - 8.34: 2 8.34 - 10.43: 1 Bond angle restraints: 31807 Sorted by residual: angle pdb=" CD1 SRO R 401 " pdb=" NE1 SRO R 401 " pdb=" CE2 SRO R 401 " ideal model delta sigma weight residual 109.10 119.53 -10.43 3.00e+00 1.11e-01 1.21e+01 angle pdb=" CG SRO R 401 " pdb=" CD1 SRO R 401 " pdb=" NE1 SRO R 401 " ideal model delta sigma weight residual 110.16 102.15 8.01 3.00e+00 1.11e-01 7.12e+00 angle pdb=" CB LYS R 171 " pdb=" CG LYS R 171 " pdb=" CD LYS R 171 " ideal model delta sigma weight residual 111.30 116.87 -5.57 2.30e+00 1.89e-01 5.86e+00 angle pdb=" C LEU R 80 " pdb=" N VAL R 81 " pdb=" CA VAL R 81 " ideal model delta sigma weight residual 123.16 120.63 2.53 1.06e+00 8.90e-01 5.71e+00 angle pdb=" CA HIS R 223 " pdb=" C HIS R 223 " pdb=" N GLN R 224 " ideal model delta sigma weight residual 117.21 120.56 -3.35 1.42e+00 4.96e-01 5.56e+00 ... (remaining 31802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 7598 17.10 - 34.21: 542 34.21 - 51.31: 142 51.31 - 68.42: 45 68.42 - 85.52: 9 Dihedral angle restraints: 8336 sinusoidal: 4444 harmonic: 3892 Sorted by residual: dihedral pdb=" CA HIS R 221 " pdb=" C HIS R 221 " pdb=" N ALA R 222 " pdb=" CA ALA R 222 " ideal model delta harmonic sigma weight residual 180.00 160.90 19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 162.09 17.91 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 164.34 15.66 0 5.00e+00 4.00e-02 9.81e+00 ... (remaining 8333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 995 0.034 - 0.069: 256 0.069 - 0.103: 75 0.103 - 0.138: 49 0.138 - 0.172: 2 Chirality restraints: 1377 Sorted by residual: chirality pdb=" CA MET R 73 " pdb=" N MET R 73 " pdb=" C MET R 73 " pdb=" CB MET R 73 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA VAL R 288 " pdb=" N VAL R 288 " pdb=" C VAL R 288 " pdb=" CB VAL R 288 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 1374 not shown) Planarity restraints: 2597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.062 5.00e-02 4.00e+02 9.28e-02 1.38e+01 pdb=" N PRO B 236 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO B 39 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 119 " -0.013 2.00e-02 2.50e+03 9.48e-03 2.70e+00 pdb=" CG TYR R 119 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR R 119 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR R 119 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR R 119 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR R 119 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR R 119 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR R 119 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR R 119 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR R 119 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TYR R 119 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR R 119 " -0.002 2.00e-02 2.50e+03 ... (remaining 2594 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 808 2.18 - 2.78: 34729 2.78 - 3.39: 48052 3.39 - 3.99: 61642 3.99 - 4.60: 96141 Nonbonded interactions: 241372 Sorted by model distance: nonbonded pdb=" OD1 ASP B 290 " pdb=" HE ARG B 314 " model vdw 1.573 2.450 nonbonded pdb="HE21 GLN B 220 " pdb=" OD2 ASP B 258 " model vdw 1.576 2.450 nonbonded pdb=" O ALA A 41 " pdb=" HZ2 LYS A 46 " model vdw 1.603 2.450 nonbonded pdb=" OD1 ASP B 153 " pdb=" H GLN B 156 " model vdw 1.610 2.450 nonbonded pdb=" HH TYR A 290 " pdb=" O SER A 293 " model vdw 1.637 2.450 ... (remaining 241367 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.290 Extract box with map and model: 0.670 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 38.520 Find NCS groups from input model: 0.140 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 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 : 0.003 0.135 8959 Z= 0.205 Angle : 0.539 10.426 12135 Z= 0.307 Chirality : 0.039 0.172 1377 Planarity : 0.004 0.093 1523 Dihedral : 12.648 79.887 3207 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.64 (0.26), residues: 1097 helix: 2.24 (0.28), residues: 381 sheet: 1.15 (0.31), residues: 271 loop : 0.09 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 332 HIS 0.001 0.000 HIS E 35 PHE 0.023 0.001 PHE B 235 TYR 0.027 0.001 TYR R 119 ARG 0.008 0.001 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 11 is missing expected H atoms. Skipping. Evaluate side-chains 354 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7741 (ttm-80) cc_final: 0.7476 (ttm-80) REVERT: A 275 GLU cc_start: 0.7477 (tp30) cc_final: 0.7232 (tp30) REVERT: A 309 ASP cc_start: 0.7354 (m-30) cc_final: 0.6902 (m-30) REVERT: B 111 TYR cc_start: 0.8528 (m-80) cc_final: 0.7499 (m-80) REVERT: B 134 ARG cc_start: 0.7374 (ptp-170) cc_final: 0.6976 (ptp-170) REVERT: B 149 CYS cc_start: 0.7454 (m) cc_final: 0.7227 (m) REVERT: B 170 ASP cc_start: 0.8135 (t70) cc_final: 0.7713 (t0) REVERT: B 256 ARG cc_start: 0.8582 (mtp85) cc_final: 0.8153 (mtm180) REVERT: B 298 ASP cc_start: 0.7563 (t70) cc_final: 0.7249 (t0) REVERT: B 317 CYS cc_start: 0.7113 (p) cc_final: 0.6908 (p) REVERT: B 321 THR cc_start: 0.7243 (p) cc_final: 0.6959 (p) REVERT: B 323 ASP cc_start: 0.7115 (p0) cc_final: 0.6763 (p0) REVERT: E 67 ARG cc_start: 0.7191 (ttm170) cc_final: 0.6857 (ttm170) REVERT: G 14 LYS cc_start: 0.8030 (pttm) cc_final: 0.7818 (pttm) REVERT: G 58 GLU cc_start: 0.7418 (mp0) cc_final: 0.7105 (mp0) REVERT: R 53 LYS cc_start: 0.6841 (mmtp) cc_final: 0.6636 (mmtp) REVERT: R 79 GLU cc_start: 0.7659 (tt0) cc_final: 0.7448 (tt0) REVERT: R 112 CYS cc_start: 0.7292 (m) cc_final: 0.6707 (m) REVERT: R 139 LEU cc_start: 0.7271 (tp) cc_final: 0.6972 (tp) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.5742 time to fit residues: 264.5371 Evaluate side-chains 319 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN R 221 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8959 Z= 0.354 Angle : 0.568 5.455 12135 Z= 0.314 Chirality : 0.042 0.155 1377 Planarity : 0.004 0.046 1523 Dihedral : 4.317 20.351 1207 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.04 % Allowed : 9.68 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.27 (0.26), residues: 1097 helix: 2.01 (0.27), residues: 383 sheet: 0.83 (0.30), residues: 286 loop : -0.16 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 211 HIS 0.008 0.001 HIS R 109 PHE 0.018 0.002 PHE B 234 TYR 0.016 0.002 TYR E 60 ARG 0.007 0.001 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 11 is missing expected H atoms. Skipping. Evaluate side-chains 344 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 334 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7695 (m-30) cc_final: 0.7408 (m-30) REVERT: A 21 ARG cc_start: 0.7763 (ttm-80) cc_final: 0.7507 (ttm-80) REVERT: A 204 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7910 (mm-40) REVERT: A 205 ARG cc_start: 0.7399 (mmt-90) cc_final: 0.7126 (mmt-90) REVERT: A 252 SER cc_start: 0.8464 (t) cc_final: 0.8130 (p) REVERT: A 275 GLU cc_start: 0.7684 (tp30) cc_final: 0.7332 (tp30) REVERT: A 309 ASP cc_start: 0.7341 (m-30) cc_final: 0.6933 (m-30) REVERT: B 13 GLN cc_start: 0.8370 (tm-30) cc_final: 0.8089 (tm-30) REVERT: B 87 THR cc_start: 0.8414 (m) cc_final: 0.8105 (p) REVERT: B 111 TYR cc_start: 0.8667 (m-80) cc_final: 0.8301 (m-80) REVERT: B 134 ARG cc_start: 0.7449 (ptp-170) cc_final: 0.7160 (ptp-170) REVERT: B 189 SER cc_start: 0.8628 (p) cc_final: 0.8340 (t) REVERT: B 220 GLN cc_start: 0.7539 (mt0) cc_final: 0.6992 (mt0) REVERT: B 256 ARG cc_start: 0.8484 (mtp85) cc_final: 0.8081 (mtm180) REVERT: B 258 ASP cc_start: 0.7614 (t0) cc_final: 0.7157 (t0) REVERT: B 321 THR cc_start: 0.7482 (p) cc_final: 0.7247 (p) REVERT: E 68 PHE cc_start: 0.7871 (m-10) cc_final: 0.7649 (m-10) REVERT: G 14 LYS cc_start: 0.8067 (pttm) cc_final: 0.7663 (pttm) REVERT: R 53 LYS cc_start: 0.6857 (mmtp) cc_final: 0.6633 (mmtp) REVERT: R 72 VAL cc_start: 0.8242 (t) cc_final: 0.7893 (t) REVERT: R 112 CYS cc_start: 0.7377 (m) cc_final: 0.6849 (m) REVERT: R 139 LEU cc_start: 0.7303 (tp) cc_final: 0.7020 (tp) REVERT: R 185 PHE cc_start: 0.7835 (t80) cc_final: 0.7466 (t80) REVERT: R 301 TYR cc_start: 0.7861 (m-10) cc_final: 0.7222 (m-10) outliers start: 10 outliers final: 8 residues processed: 337 average time/residue: 0.5857 time to fit residues: 254.0472 Evaluate side-chains 330 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 322 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 183 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8959 Z= 0.340 Angle : 0.544 5.392 12135 Z= 0.300 Chirality : 0.041 0.147 1377 Planarity : 0.004 0.066 1523 Dihedral : 4.382 20.543 1207 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.98 % Allowed : 11.97 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.92 (0.26), residues: 1097 helix: 1.85 (0.27), residues: 383 sheet: 0.42 (0.29), residues: 291 loop : -0.33 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 211 HIS 0.005 0.001 HIS A 213 PHE 0.013 0.002 PHE B 199 TYR 0.013 0.002 TYR E 60 ARG 0.005 0.001 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 11 is missing expected H atoms. Skipping. Evaluate side-chains 356 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 337 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7655 (m-30) cc_final: 0.7386 (m-30) REVERT: A 21 ARG cc_start: 0.7738 (ttm-80) cc_final: 0.7489 (ttm-80) REVERT: A 25 GLU cc_start: 0.7157 (tt0) cc_final: 0.6955 (tt0) REVERT: A 190 THR cc_start: 0.8841 (m) cc_final: 0.8503 (p) REVERT: A 204 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7978 (mm-40) REVERT: A 252 SER cc_start: 0.8560 (t) cc_final: 0.8195 (p) REVERT: A 275 GLU cc_start: 0.7740 (tp30) cc_final: 0.7359 (tp30) REVERT: A 309 ASP cc_start: 0.7321 (m-30) cc_final: 0.6890 (m-30) REVERT: B 13 GLN cc_start: 0.8379 (tm-30) cc_final: 0.8153 (tm-30) REVERT: B 76 ASP cc_start: 0.6890 (m-30) cc_final: 0.6639 (m-30) REVERT: B 111 TYR cc_start: 0.8660 (m-80) cc_final: 0.8354 (m-80) REVERT: B 134 ARG cc_start: 0.7459 (ptp-170) cc_final: 0.7125 (ptp-170) REVERT: B 163 ASP cc_start: 0.6775 (t0) cc_final: 0.6569 (t0) REVERT: B 189 SER cc_start: 0.8636 (p) cc_final: 0.8336 (t) REVERT: B 256 ARG cc_start: 0.8473 (mtp85) cc_final: 0.8132 (mtm180) REVERT: B 321 THR cc_start: 0.7431 (p) cc_final: 0.7126 (p) REVERT: B 323 ASP cc_start: 0.7498 (p0) cc_final: 0.7191 (p0) REVERT: E 220 GLU cc_start: 0.7167 (pt0) cc_final: 0.6743 (pt0) REVERT: E 234 GLU cc_start: 0.7266 (pt0) cc_final: 0.6980 (pp20) REVERT: G 14 LYS cc_start: 0.8104 (pttm) cc_final: 0.7753 (pttm) REVERT: R 53 LYS cc_start: 0.6905 (mmtp) cc_final: 0.6688 (mmtp) REVERT: R 72 VAL cc_start: 0.8200 (t) cc_final: 0.7712 (t) REVERT: R 112 CYS cc_start: 0.7486 (m) cc_final: 0.6891 (m) REVERT: R 185 PHE cc_start: 0.7879 (t80) cc_final: 0.7521 (t80) REVERT: R 301 TYR cc_start: 0.7840 (m-10) cc_final: 0.7156 (m-10) outliers start: 19 outliers final: 16 residues processed: 341 average time/residue: 0.5886 time to fit residues: 259.5122 Evaluate side-chains 345 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 329 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 287 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8959 Z= 0.336 Angle : 0.540 4.899 12135 Z= 0.298 Chirality : 0.041 0.145 1377 Planarity : 0.004 0.061 1523 Dihedral : 4.432 20.919 1207 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.19 % Allowed : 13.53 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.74 (0.26), residues: 1097 helix: 1.80 (0.27), residues: 384 sheet: 0.16 (0.29), residues: 290 loop : -0.42 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 211 HIS 0.005 0.001 HIS A 213 PHE 0.017 0.002 PHE E 68 TYR 0.014 0.002 TYR E 190 ARG 0.006 0.001 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 11 is missing expected H atoms. Skipping. Evaluate side-chains 351 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 330 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7662 (m-30) cc_final: 0.7385 (m-30) REVERT: A 21 ARG cc_start: 0.7751 (ttm-80) cc_final: 0.7495 (ttm-80) REVERT: A 25 GLU cc_start: 0.7159 (tt0) cc_final: 0.6955 (tt0) REVERT: A 46 LYS cc_start: 0.8401 (mtmm) cc_final: 0.7873 (mtmt) REVERT: A 204 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7973 (mm-40) REVERT: A 252 SER cc_start: 0.8549 (t) cc_final: 0.8183 (p) REVERT: A 275 GLU cc_start: 0.7752 (tp30) cc_final: 0.7420 (tp30) REVERT: A 332 VAL cc_start: 0.8270 (t) cc_final: 0.8007 (m) REVERT: B 13 GLN cc_start: 0.8375 (tm-30) cc_final: 0.8145 (tm-30) REVERT: B 76 ASP cc_start: 0.6924 (m-30) cc_final: 0.6614 (m-30) REVERT: B 110 ASN cc_start: 0.8306 (m-40) cc_final: 0.8070 (m110) REVERT: B 134 ARG cc_start: 0.7430 (ptp-170) cc_final: 0.7185 (ptp-170) REVERT: B 189 SER cc_start: 0.8683 (p) cc_final: 0.8362 (t) REVERT: B 256 ARG cc_start: 0.8433 (mtp85) cc_final: 0.8065 (mtm180) REVERT: B 321 THR cc_start: 0.7406 (p) cc_final: 0.7097 (p) REVERT: B 323 ASP cc_start: 0.7501 (p0) cc_final: 0.7188 (p0) REVERT: E 220 GLU cc_start: 0.7111 (pt0) cc_final: 0.6685 (pt0) REVERT: E 234 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6965 (pp20) REVERT: G 14 LYS cc_start: 0.8067 (pttm) cc_final: 0.7714 (pttm) REVERT: G 58 GLU cc_start: 0.7467 (mp0) cc_final: 0.7223 (mp0) REVERT: R 53 LYS cc_start: 0.6928 (mmtp) cc_final: 0.6704 (mmtp) REVERT: R 72 VAL cc_start: 0.8268 (t) cc_final: 0.7816 (t) REVERT: R 132 MET cc_start: 0.5622 (mmp) cc_final: 0.4984 (mmp) REVERT: R 185 PHE cc_start: 0.7935 (t80) cc_final: 0.7577 (t80) REVERT: R 264 MET cc_start: 0.7983 (mmm) cc_final: 0.7732 (mmm) REVERT: R 301 TYR cc_start: 0.7870 (m-10) cc_final: 0.7271 (m-10) outliers start: 21 outliers final: 19 residues processed: 336 average time/residue: 0.6021 time to fit residues: 261.3741 Evaluate side-chains 340 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 320 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 183 GLN Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 287 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8959 Z= 0.420 Angle : 0.559 4.771 12135 Z= 0.312 Chirality : 0.042 0.151 1377 Planarity : 0.004 0.066 1523 Dihedral : 4.555 21.379 1207 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.29 % Allowed : 13.84 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.48 (0.26), residues: 1097 helix: 1.66 (0.27), residues: 384 sheet: -0.04 (0.29), residues: 292 loop : -0.58 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 176 HIS 0.006 0.001 HIS A 213 PHE 0.015 0.002 PHE B 151 TYR 0.014 0.002 TYR E 190 ARG 0.008 0.001 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 11 is missing expected H atoms. Skipping. Evaluate side-chains 353 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 331 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7638 (m-30) cc_final: 0.7378 (m-30) REVERT: A 21 ARG cc_start: 0.7760 (ttm-80) cc_final: 0.7514 (ttm-80) REVERT: A 25 GLU cc_start: 0.7193 (tt0) cc_final: 0.6950 (tt0) REVERT: A 28 GLU cc_start: 0.7529 (tt0) cc_final: 0.7304 (tt0) REVERT: A 204 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7958 (mm-40) REVERT: A 252 SER cc_start: 0.8537 (t) cc_final: 0.8162 (p) REVERT: A 275 GLU cc_start: 0.7785 (tp30) cc_final: 0.7443 (tp30) REVERT: A 332 VAL cc_start: 0.8273 (t) cc_final: 0.7990 (m) REVERT: B 13 GLN cc_start: 0.8427 (tm-30) cc_final: 0.8201 (tm-30) REVERT: B 76 ASP cc_start: 0.6997 (m-30) cc_final: 0.6614 (m-30) REVERT: B 110 ASN cc_start: 0.8306 (m-40) cc_final: 0.8086 (m110) REVERT: B 189 SER cc_start: 0.8676 (p) cc_final: 0.8366 (t) REVERT: B 219 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7758 (ttm170) REVERT: B 256 ARG cc_start: 0.8489 (mtp85) cc_final: 0.8094 (mtm180) REVERT: B 321 THR cc_start: 0.7394 (p) cc_final: 0.7081 (p) REVERT: B 323 ASP cc_start: 0.7510 (p0) cc_final: 0.7176 (p0) REVERT: E 158 SER cc_start: 0.8603 (t) cc_final: 0.8274 (p) REVERT: E 220 GLU cc_start: 0.7176 (pt0) cc_final: 0.6759 (pt0) REVERT: E 234 GLU cc_start: 0.7244 (pt0) cc_final: 0.6976 (pp20) REVERT: G 14 LYS cc_start: 0.8055 (pttm) cc_final: 0.7710 (pttm) REVERT: G 58 GLU cc_start: 0.7506 (mp0) cc_final: 0.7101 (mp0) REVERT: R 185 PHE cc_start: 0.7951 (t80) cc_final: 0.7612 (t80) REVERT: R 205 LEU cc_start: 0.7692 (tp) cc_final: 0.7459 (tt) REVERT: R 301 TYR cc_start: 0.7907 (m-10) cc_final: 0.7498 (m-10) REVERT: R 306 LEU cc_start: 0.7765 (mt) cc_final: 0.7358 (tp) outliers start: 22 outliers final: 18 residues processed: 339 average time/residue: 0.5970 time to fit residues: 265.6017 Evaluate side-chains 344 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 326 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 183 GLN Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 287 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8959 Z= 0.181 Angle : 0.494 4.559 12135 Z= 0.269 Chirality : 0.040 0.135 1377 Planarity : 0.004 0.066 1523 Dihedral : 4.302 20.629 1207 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.77 % Allowed : 15.92 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.73 (0.26), residues: 1097 helix: 1.94 (0.27), residues: 385 sheet: 0.01 (0.29), residues: 288 loop : -0.46 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 85 HIS 0.007 0.001 HIS R 109 PHE 0.010 0.001 PHE E 110 TYR 0.011 0.001 TYR E 190 ARG 0.007 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 11 is missing expected H atoms. Skipping. Evaluate side-chains 339 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 322 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7642 (m-30) cc_final: 0.7367 (m-30) REVERT: A 21 ARG cc_start: 0.7751 (ttm-80) cc_final: 0.7521 (ttm-80) REVERT: A 190 THR cc_start: 0.8621 (m) cc_final: 0.8375 (p) REVERT: A 204 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7927 (mm-40) REVERT: A 252 SER cc_start: 0.8531 (t) cc_final: 0.8202 (p) REVERT: A 275 GLU cc_start: 0.7721 (tp30) cc_final: 0.7401 (tp30) REVERT: A 332 VAL cc_start: 0.8227 (t) cc_final: 0.7958 (m) REVERT: B 13 GLN cc_start: 0.8340 (tm-30) cc_final: 0.8109 (tm-30) REVERT: B 76 ASP cc_start: 0.6975 (m-30) cc_final: 0.6570 (m-30) REVERT: B 110 ASN cc_start: 0.8280 (m-40) cc_final: 0.8052 (m110) REVERT: B 189 SER cc_start: 0.8667 (p) cc_final: 0.8350 (t) REVERT: B 219 ARG cc_start: 0.7960 (ttm-80) cc_final: 0.7727 (ttm170) REVERT: B 256 ARG cc_start: 0.8442 (mtp85) cc_final: 0.8021 (mtm180) REVERT: B 301 LYS cc_start: 0.8615 (mmtt) cc_final: 0.8409 (mmtt) REVERT: B 321 THR cc_start: 0.7364 (p) cc_final: 0.7036 (p) REVERT: B 323 ASP cc_start: 0.7488 (p0) cc_final: 0.7167 (p0) REVERT: E 158 SER cc_start: 0.8657 (t) cc_final: 0.8299 (p) REVERT: E 220 GLU cc_start: 0.7152 (pt0) cc_final: 0.6751 (pt0) REVERT: E 234 GLU cc_start: 0.7205 (pt0) cc_final: 0.6930 (pp20) REVERT: G 14 LYS cc_start: 0.8031 (pttm) cc_final: 0.7700 (pttm) REVERT: R 185 PHE cc_start: 0.7953 (t80) cc_final: 0.7604 (t80) REVERT: R 205 LEU cc_start: 0.7609 (tp) cc_final: 0.7373 (tt) REVERT: R 301 TYR cc_start: 0.7812 (m-10) cc_final: 0.7333 (m-10) REVERT: R 306 LEU cc_start: 0.7807 (mt) cc_final: 0.7486 (tp) outliers start: 17 outliers final: 16 residues processed: 330 average time/residue: 0.6048 time to fit residues: 260.7771 Evaluate side-chains 331 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 315 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 287 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8959 Z= 0.206 Angle : 0.494 4.913 12135 Z= 0.269 Chirality : 0.040 0.135 1377 Planarity : 0.004 0.069 1523 Dihedral : 4.238 20.318 1207 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.87 % Allowed : 15.92 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.81 (0.26), residues: 1097 helix: 1.97 (0.27), residues: 387 sheet: 0.05 (0.29), residues: 286 loop : -0.37 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 85 HIS 0.004 0.001 HIS R 109 PHE 0.009 0.001 PHE B 234 TYR 0.010 0.001 TYR E 190 ARG 0.008 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 11 is missing expected H atoms. Skipping. Evaluate side-chains 345 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 327 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7660 (m-30) cc_final: 0.7379 (m-30) REVERT: A 21 ARG cc_start: 0.7769 (ttm-80) cc_final: 0.7520 (ttm-80) REVERT: A 190 THR cc_start: 0.8603 (m) cc_final: 0.8381 (p) REVERT: A 204 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7928 (mm-40) REVERT: A 252 SER cc_start: 0.8530 (t) cc_final: 0.8198 (p) REVERT: A 255 ASN cc_start: 0.8556 (m-40) cc_final: 0.8343 (m-40) REVERT: A 275 GLU cc_start: 0.7725 (tp30) cc_final: 0.7377 (tp30) REVERT: A 297 GLU cc_start: 0.7631 (mp0) cc_final: 0.7224 (mp0) REVERT: A 332 VAL cc_start: 0.8214 (t) cc_final: 0.7958 (m) REVERT: B 76 ASP cc_start: 0.6976 (m-30) cc_final: 0.6550 (m-30) REVERT: B 110 ASN cc_start: 0.8271 (m-40) cc_final: 0.8057 (m110) REVERT: B 189 SER cc_start: 0.8664 (p) cc_final: 0.8357 (t) REVERT: B 219 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7718 (ttm170) REVERT: B 321 THR cc_start: 0.7346 (p) cc_final: 0.7014 (p) REVERT: B 323 ASP cc_start: 0.7466 (p0) cc_final: 0.7162 (p0) REVERT: E 158 SER cc_start: 0.8640 (t) cc_final: 0.8440 (m) REVERT: E 220 GLU cc_start: 0.7130 (pt0) cc_final: 0.6812 (pt0) REVERT: E 234 GLU cc_start: 0.7207 (pt0) cc_final: 0.6937 (pp20) REVERT: G 14 LYS cc_start: 0.8029 (pttm) cc_final: 0.7792 (pttm) REVERT: R 95 ARG cc_start: 0.6348 (ttp80) cc_final: 0.6035 (ttp80) REVERT: R 185 PHE cc_start: 0.7935 (t80) cc_final: 0.7588 (t80) REVERT: R 205 LEU cc_start: 0.7622 (tp) cc_final: 0.7389 (tt) REVERT: R 301 TYR cc_start: 0.7799 (m-10) cc_final: 0.7341 (m-10) REVERT: R 306 LEU cc_start: 0.7801 (mt) cc_final: 0.7503 (tp) outliers start: 18 outliers final: 16 residues processed: 334 average time/residue: 0.5809 time to fit residues: 254.8065 Evaluate side-chains 338 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 322 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 183 GLN Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 287 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.0050 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 304 GLN R 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8959 Z= 0.230 Angle : 0.498 4.790 12135 Z= 0.272 Chirality : 0.040 0.146 1377 Planarity : 0.004 0.071 1523 Dihedral : 4.216 20.167 1207 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.08 % Allowed : 16.34 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.81 (0.26), residues: 1097 helix: 1.97 (0.27), residues: 387 sheet: 0.03 (0.29), residues: 286 loop : -0.38 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 85 HIS 0.004 0.001 HIS A 213 PHE 0.010 0.001 PHE A 199 TYR 0.010 0.001 TYR E 190 ARG 0.009 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 11 is missing expected H atoms. Skipping. Evaluate side-chains 344 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 324 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7662 (m-30) cc_final: 0.7380 (m-30) REVERT: A 21 ARG cc_start: 0.7775 (ttm-80) cc_final: 0.7525 (ttm-80) REVERT: A 190 THR cc_start: 0.8599 (m) cc_final: 0.8366 (p) REVERT: A 204 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7938 (mm-40) REVERT: A 252 SER cc_start: 0.8551 (t) cc_final: 0.8203 (p) REVERT: A 255 ASN cc_start: 0.8562 (m-40) cc_final: 0.8352 (m-40) REVERT: A 275 GLU cc_start: 0.7728 (tp30) cc_final: 0.7372 (tp30) REVERT: A 297 GLU cc_start: 0.7638 (mp0) cc_final: 0.7218 (mp0) REVERT: A 321 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8580 (p) REVERT: A 332 VAL cc_start: 0.8208 (t) cc_final: 0.7955 (m) REVERT: B 76 ASP cc_start: 0.7000 (m-30) cc_final: 0.6573 (m-30) REVERT: B 110 ASN cc_start: 0.8267 (m-40) cc_final: 0.8052 (m110) REVERT: B 189 SER cc_start: 0.8710 (p) cc_final: 0.8359 (t) REVERT: B 205 ASP cc_start: 0.7601 (p0) cc_final: 0.7371 (p0) REVERT: B 219 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.7725 (ttm170) REVERT: B 321 THR cc_start: 0.7347 (p) cc_final: 0.6997 (p) REVERT: B 323 ASP cc_start: 0.7424 (p0) cc_final: 0.7046 (p0) REVERT: E 158 SER cc_start: 0.8641 (t) cc_final: 0.8439 (m) REVERT: E 220 GLU cc_start: 0.7136 (pt0) cc_final: 0.6816 (pt0) REVERT: E 234 GLU cc_start: 0.7212 (pt0) cc_final: 0.6943 (pp20) REVERT: G 14 LYS cc_start: 0.8037 (pttm) cc_final: 0.7805 (pttm) REVERT: R 95 ARG cc_start: 0.6303 (ttp80) cc_final: 0.6015 (ttp80) REVERT: R 185 PHE cc_start: 0.7939 (t80) cc_final: 0.7592 (t80) REVERT: R 205 LEU cc_start: 0.7614 (tp) cc_final: 0.7377 (tt) REVERT: R 301 TYR cc_start: 0.7814 (m-10) cc_final: 0.7403 (m-10) REVERT: R 306 LEU cc_start: 0.7816 (mt) cc_final: 0.7492 (tp) outliers start: 20 outliers final: 17 residues processed: 332 average time/residue: 0.5742 time to fit residues: 248.9407 Evaluate side-chains 339 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 321 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 183 GLN Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 287 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8959 Z= 0.282 Angle : 0.522 4.976 12135 Z= 0.285 Chirality : 0.040 0.148 1377 Planarity : 0.004 0.078 1523 Dihedral : 4.279 20.222 1207 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.98 % Allowed : 16.44 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.69 (0.26), residues: 1097 helix: 1.86 (0.27), residues: 388 sheet: 0.00 (0.29), residues: 286 loop : -0.46 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 85 HIS 0.005 0.001 HIS A 213 PHE 0.010 0.001 PHE B 151 TYR 0.011 0.001 TYR E 95 ARG 0.010 0.001 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 11 is missing expected H atoms. Skipping. Evaluate side-chains 343 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 324 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7660 (m-30) cc_final: 0.7388 (m-30) REVERT: A 21 ARG cc_start: 0.7773 (ttm-80) cc_final: 0.7530 (ttm-80) REVERT: A 28 GLU cc_start: 0.7513 (tt0) cc_final: 0.7309 (tt0) REVERT: A 204 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7956 (mm-40) REVERT: A 252 SER cc_start: 0.8545 (t) cc_final: 0.8193 (p) REVERT: A 255 ASN cc_start: 0.8558 (m-40) cc_final: 0.8332 (m-40) REVERT: A 275 GLU cc_start: 0.7766 (tp30) cc_final: 0.7393 (tp30) REVERT: A 321 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8559 (p) REVERT: A 332 VAL cc_start: 0.8207 (t) cc_final: 0.7957 (m) REVERT: B 76 ASP cc_start: 0.7003 (m-30) cc_final: 0.6576 (m-30) REVERT: B 110 ASN cc_start: 0.8273 (m-40) cc_final: 0.8060 (m110) REVERT: B 189 SER cc_start: 0.8690 (p) cc_final: 0.8346 (t) REVERT: B 219 ARG cc_start: 0.7978 (ttm-80) cc_final: 0.7750 (ttm170) REVERT: B 256 ARG cc_start: 0.8466 (mtp85) cc_final: 0.8027 (mtm180) REVERT: B 258 ASP cc_start: 0.7575 (t0) cc_final: 0.7256 (t70) REVERT: B 321 THR cc_start: 0.7368 (p) cc_final: 0.7011 (p) REVERT: B 323 ASP cc_start: 0.7427 (p0) cc_final: 0.7049 (p0) REVERT: B 332 TRP cc_start: 0.8132 (m-10) cc_final: 0.6926 (m-10) REVERT: E 220 GLU cc_start: 0.7169 (pt0) cc_final: 0.6847 (pt0) REVERT: E 234 GLU cc_start: 0.7216 (pt0) cc_final: 0.6952 (pp20) REVERT: R 95 ARG cc_start: 0.6285 (ttp80) cc_final: 0.6005 (ttp80) REVERT: R 163 ILE cc_start: 0.8154 (pt) cc_final: 0.7887 (mm) REVERT: R 185 PHE cc_start: 0.7935 (t80) cc_final: 0.7592 (t80) REVERT: R 205 LEU cc_start: 0.7654 (tp) cc_final: 0.7425 (tt) REVERT: R 301 TYR cc_start: 0.7858 (m-10) cc_final: 0.7434 (m-10) REVERT: R 306 LEU cc_start: 0.7829 (mt) cc_final: 0.7498 (tp) outliers start: 19 outliers final: 17 residues processed: 332 average time/residue: 0.5694 time to fit residues: 246.0730 Evaluate side-chains 340 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 322 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 183 GLN Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 287 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8959 Z= 0.244 Angle : 0.518 5.778 12135 Z= 0.282 Chirality : 0.040 0.153 1377 Planarity : 0.004 0.074 1523 Dihedral : 4.254 20.074 1207 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.77 % Allowed : 16.86 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.76 (0.26), residues: 1097 helix: 1.94 (0.27), residues: 386 sheet: 0.00 (0.29), residues: 286 loop : -0.41 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 85 HIS 0.004 0.001 HIS A 213 PHE 0.010 0.001 PHE A 199 TYR 0.011 0.001 TYR E 190 ARG 0.010 0.001 ARG G 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 11 is missing expected H atoms. Skipping. Evaluate side-chains 348 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 331 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7659 (m-30) cc_final: 0.7378 (m-30) REVERT: A 21 ARG cc_start: 0.7773 (ttm-80) cc_final: 0.7524 (ttm-80) REVERT: A 190 THR cc_start: 0.8583 (m) cc_final: 0.8355 (p) REVERT: A 204 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7953 (mm-40) REVERT: A 252 SER cc_start: 0.8544 (t) cc_final: 0.8184 (p) REVERT: A 255 ASN cc_start: 0.8568 (m-40) cc_final: 0.8352 (m-40) REVERT: A 275 GLU cc_start: 0.7769 (tp30) cc_final: 0.7384 (tp30) REVERT: A 297 GLU cc_start: 0.7657 (mp0) cc_final: 0.7224 (mp0) REVERT: A 321 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8564 (p) REVERT: A 332 VAL cc_start: 0.8181 (t) cc_final: 0.7934 (m) REVERT: B 76 ASP cc_start: 0.6994 (m-30) cc_final: 0.6569 (m-30) REVERT: B 110 ASN cc_start: 0.8264 (m-40) cc_final: 0.8051 (m110) REVERT: B 189 SER cc_start: 0.8681 (p) cc_final: 0.8347 (t) REVERT: B 205 ASP cc_start: 0.7608 (p0) cc_final: 0.7365 (p0) REVERT: B 219 ARG cc_start: 0.7978 (ttm-80) cc_final: 0.7751 (ttm170) REVERT: B 256 ARG cc_start: 0.8451 (mtp85) cc_final: 0.8016 (mtm180) REVERT: B 258 ASP cc_start: 0.7574 (t0) cc_final: 0.7255 (t70) REVERT: B 321 THR cc_start: 0.7341 (p) cc_final: 0.6991 (p) REVERT: B 323 ASP cc_start: 0.7425 (p0) cc_final: 0.7048 (p0) REVERT: E 186 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7590 (pt0) REVERT: E 220 GLU cc_start: 0.7164 (pt0) cc_final: 0.6826 (pt0) REVERT: E 234 GLU cc_start: 0.7218 (pt0) cc_final: 0.6951 (pp20) REVERT: R 79 GLU cc_start: 0.7552 (tp30) cc_final: 0.7241 (tp30) REVERT: R 95 ARG cc_start: 0.6281 (ttp80) cc_final: 0.5996 (ttp80) REVERT: R 163 ILE cc_start: 0.8112 (pt) cc_final: 0.7857 (mm) REVERT: R 185 PHE cc_start: 0.7935 (t80) cc_final: 0.7588 (t80) REVERT: R 205 LEU cc_start: 0.7628 (tp) cc_final: 0.7394 (tt) REVERT: R 301 TYR cc_start: 0.7838 (m-10) cc_final: 0.7418 (m-10) REVERT: R 306 LEU cc_start: 0.7848 (mt) cc_final: 0.7526 (tp) outliers start: 17 outliers final: 15 residues processed: 338 average time/residue: 0.5921 time to fit residues: 258.0733 Evaluate side-chains 347 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 330 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 183 GLN Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 287 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** B 119 ASN ** 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 = 0.3742 r_free = 0.3742 target = 0.131661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.113383 restraints weight = 37818.768| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.46 r_work: 0.3363 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8959 Z= 0.225 Angle : 0.514 5.656 12135 Z= 0.279 Chirality : 0.040 0.149 1377 Planarity : 0.004 0.076 1523 Dihedral : 4.218 19.833 1207 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.87 % Allowed : 17.48 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.80 (0.26), residues: 1097 helix: 1.97 (0.27), residues: 386 sheet: 0.02 (0.29), residues: 286 loop : -0.38 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 85 HIS 0.004 0.001 HIS A 213 PHE 0.010 0.001 PHE A 189 TYR 0.011 0.001 TYR E 190 ARG 0.010 0.001 ARG G 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5833.86 seconds wall clock time: 104 minutes 24.87 seconds (6264.87 seconds total)