Starting phenix.real_space_refine on Fri Nov 15 06:52:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9a_35263/11_2024/8i9a_35263.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9a_35263/11_2024/8i9a_35263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9a_35263/11_2024/8i9a_35263.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9a_35263/11_2024/8i9a_35263.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9a_35263/11_2024/8i9a_35263.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9a_35263/11_2024/8i9a_35263.cif" } resolution = 3.57 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= 0.000 sd= 0.019 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: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 5353 2.51 5 N 1458 2.21 5 O 1547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8409 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1858 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 3 Chain: "B" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2415 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 103 Chain: "G" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 400 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1658 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2006 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 14, 'TRANS': 257} Chain breaks: 2 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 75 Chain: "D" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 17 Classifications: {'peptide': 2} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 1} Time building chain proxies: 5.54, per 1000 atoms: 0.66 Number of scatterers: 8409 At special positions: 0 Unit cell: (84.64, 119.6, 122.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 1547 8.00 N 1458 7.00 C 5353 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 172 " 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 Links applied TRANS " DAL D 9 " - " LEU D 8 " Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.0 seconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL D 9 " Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 39.0% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 15 through 40 removed outlier: 3.539A pdb=" N ALA A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 265 through 279 removed outlier: 3.516A pdb=" N ASN A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 removed outlier: 4.141A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.595A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.792A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.534A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 220 through 224 Processing helix chain 'C' and resid 20 through 50 Proline residue: C 39 - end of helix removed outlier: 3.545A pdb=" N VAL C 44 " --> pdb=" O GLY C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 74 removed outlier: 3.519A pdb=" N TRP C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE C 61 " --> pdb=" O ASN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 85 removed outlier: 4.201A pdb=" N SER C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 126 Proline residue: C 99 - end of helix removed outlier: 3.687A pdb=" N ASN C 105 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 134 Processing helix chain 'C' and resid 135 through 161 Proline residue: C 156 - end of helix Processing helix chain 'C' and resid 332 through 345 Processing helix chain 'C' and resid 345 through 363 removed outlier: 3.550A pdb=" N VAL C 360 " --> pdb=" O TYR C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 403 Proline residue: C 392 - end of helix removed outlier: 3.659A pdb=" N LEU C 401 " --> pdb=" O GLY C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 435 removed outlier: 3.924A pdb=" N HIS C 418 " --> pdb=" O MET C 414 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N CYS C 429 " --> pdb=" O SER C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'C' and resid 439 through 450 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.822A pdb=" N ASP A 223 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N PHE A 222 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.755A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.531A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.949A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.625A 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: 3.674A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.679A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.624A 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: 3.737A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.976A 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: 3.924A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.005A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.670A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.877A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 149 removed outlier: 6.131A pdb=" N VAL H 147 " --> pdb=" O GLU H 246 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 162 through 163 460 hydrogen bonds defined for protein. 1284 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: 2.88 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1559 1.33 - 1.45: 2235 1.45 - 1.57: 4728 1.57 - 1.69: 0 1.69 - 1.82: 68 Bond restraints: 8590 Sorted by residual: bond pdb=" C PRO G 60 " pdb=" O PRO G 60 " ideal model delta sigma weight residual 1.239 1.204 0.035 1.22e-02 6.72e+03 8.11e+00 bond pdb=" N ARG A 231 " pdb=" CA ARG A 231 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.30e-02 5.92e+03 7.11e+00 bond pdb=" N VAL C 388 " pdb=" CA VAL C 388 " ideal model delta sigma weight residual 1.461 1.491 -0.029 1.17e-02 7.31e+03 6.31e+00 bond pdb=" N GLU A 330 " pdb=" CA GLU A 330 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.25e-02 6.40e+03 5.81e+00 bond pdb=" CA PHE A 208 " pdb=" CB PHE A 208 " ideal model delta sigma weight residual 1.526 1.565 -0.039 1.68e-02 3.54e+03 5.34e+00 ... (remaining 8585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 11132 1.60 - 3.20: 471 3.20 - 4.80: 77 4.80 - 6.40: 13 6.40 - 8.00: 1 Bond angle restraints: 11694 Sorted by residual: angle pdb=" C PHE A 273 " pdb=" N LYS A 274 " pdb=" CA LYS A 274 " ideal model delta sigma weight residual 120.44 115.14 5.30 1.30e+00 5.92e-01 1.66e+01 angle pdb=" N ASP A 272 " pdb=" CA ASP A 272 " pdb=" C ASP A 272 " ideal model delta sigma weight residual 111.07 107.05 4.02 1.07e+00 8.73e-01 1.41e+01 angle pdb=" N LYS A 274 " pdb=" CA LYS A 274 " pdb=" C LYS A 274 " ideal model delta sigma weight residual 111.07 107.10 3.97 1.07e+00 8.73e-01 1.37e+01 angle pdb=" N GLU A 21 " pdb=" CA GLU A 21 " pdb=" C GLU A 21 " ideal model delta sigma weight residual 111.07 107.25 3.82 1.07e+00 8.73e-01 1.27e+01 angle pdb=" N PRO C 156 " pdb=" CA PRO C 156 " pdb=" C PRO C 156 " ideal model delta sigma weight residual 113.78 108.15 5.63 1.62e+00 3.81e-01 1.21e+01 ... (remaining 11689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4599 17.97 - 35.94: 353 35.94 - 53.90: 62 53.90 - 71.87: 20 71.87 - 89.84: 6 Dihedral angle restraints: 5040 sinusoidal: 1775 harmonic: 3265 Sorted by residual: dihedral pdb=" CA ASN A 279 " pdb=" C ASN A 279 " pdb=" N ARG A 280 " pdb=" CA ARG A 280 " ideal model delta harmonic sigma weight residual 180.00 -152.35 -27.65 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA PRO G 53 " pdb=" C PRO G 53 " pdb=" N VAL G 54 " pdb=" CA VAL G 54 " ideal model delta harmonic sigma weight residual 180.00 -158.45 -21.55 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 5037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1188 0.071 - 0.142: 155 0.142 - 0.213: 6 0.213 - 0.284: 0 0.284 - 0.355: 1 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CA ASN B 313 " pdb=" N ASN B 313 " pdb=" C ASN B 313 " pdb=" CB ASN B 313 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CB VAL C 388 " pdb=" CA VAL C 388 " pdb=" CG1 VAL C 388 " pdb=" CG2 VAL C 388 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ARG A 333 " pdb=" N ARG A 333 " pdb=" C ARG A 333 " pdb=" CB ARG A 333 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.63e-01 ... (remaining 1347 not shown) Planarity restraints: 1495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 325 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO A 326 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 326 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 326 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 340 " 0.010 2.00e-02 2.50e+03 1.21e-02 2.56e+00 pdb=" CG PHE A 340 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 340 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 340 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 340 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 340 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 340 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 347 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO C 348 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 348 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 348 " -0.022 5.00e-02 4.00e+02 ... (remaining 1492 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 41 2.55 - 3.14: 7128 3.14 - 3.72: 13063 3.72 - 4.31: 18059 4.31 - 4.90: 30403 Nonbonded interactions: 68694 Sorted by model distance: nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 1.959 3.040 nonbonded pdb=" N GLU G 47 " pdb=" OE1 GLU G 47 " model vdw 2.100 3.120 nonbonded pdb=" O MET C 138 " pdb=" OG SER C 141 " model vdw 2.246 3.040 nonbonded pdb=" NH1 ARG C 340 " pdb=" OXT ARG D 10 " model vdw 2.290 3.120 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.302 3.040 ... (remaining 68689 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 group one per residue 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: 3.180 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.890 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: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 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 : 0.004 0.041 8590 Z= 0.259 Angle : 0.758 8.005 11694 Z= 0.443 Chirality : 0.046 0.355 1350 Planarity : 0.005 0.052 1494 Dihedral : 14.157 89.840 2916 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.19 % Allowed : 12.53 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.11 (0.26), residues: 1103 helix: 0.57 (0.25), residues: 390 sheet: -0.38 (0.30), residues: 293 loop : -0.24 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.006 0.002 HIS H 167 PHE 0.028 0.002 PHE A 340 TYR 0.016 0.002 TYR C 393 ARG 0.007 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 205 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.6924 (mmm) cc_final: 0.6705 (mpp) REVERT: A 274 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.9039 (mttp) REVERT: A 391 TYR cc_start: 0.6059 (OUTLIER) cc_final: 0.5514 (m-80) REVERT: B 67 SER cc_start: 0.8448 (t) cc_final: 0.7879 (t) REVERT: H 184 SER cc_start: 0.9289 (p) cc_final: 0.8987 (m) REVERT: D 6 MET cc_start: 0.8072 (tpp) cc_final: 0.7682 (tpp) outliers start: 10 outliers final: 2 residues processed: 212 average time/residue: 0.2417 time to fit residues: 67.5629 Evaluate side-chains 177 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 173 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 434 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 278 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8590 Z= 0.269 Angle : 0.662 7.858 11694 Z= 0.353 Chirality : 0.045 0.185 1350 Planarity : 0.005 0.054 1494 Dihedral : 6.025 54.607 1216 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.03 % Allowed : 13.48 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.50 (0.26), residues: 1103 helix: 1.41 (0.26), residues: 395 sheet: -0.33 (0.30), residues: 290 loop : -0.05 (0.33), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 297 HIS 0.006 0.001 HIS C 394 PHE 0.022 0.002 PHE A 208 TYR 0.014 0.002 TYR A 318 ARG 0.005 0.001 ARG D 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: A 212 PHE cc_start: 0.8106 (p90) cc_final: 0.7892 (p90) REVERT: A 308 ILE cc_start: 0.5517 (mp) cc_final: 0.5284 (mm) REVERT: A 309 GLU cc_start: 0.8344 (pm20) cc_final: 0.8133 (pm20) REVERT: B 234 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.7767 (m-80) REVERT: H 184 SER cc_start: 0.9314 (p) cc_final: 0.9035 (m) REVERT: C 92 ARG cc_start: 0.7050 (tpt-90) cc_final: 0.5842 (tmm-80) REVERT: C 160 TYR cc_start: 0.6770 (t80) cc_final: 0.6456 (t80) REVERT: C 414 MET cc_start: 0.7698 (ppp) cc_final: 0.7476 (ppp) REVERT: C 418 HIS cc_start: 0.7568 (m90) cc_final: 0.7365 (m90) REVERT: C 434 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8447 (tt) outliers start: 17 outliers final: 10 residues processed: 204 average time/residue: 0.2319 time to fit residues: 63.7007 Evaluate side-chains 191 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 434 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 7.9990 chunk 31 optimal weight: 0.0670 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN H 167 HIS H 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8590 Z= 0.216 Angle : 0.614 7.336 11694 Z= 0.323 Chirality : 0.044 0.184 1350 Planarity : 0.005 0.057 1494 Dihedral : 5.460 58.551 1212 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.39 % Allowed : 15.87 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.65 (0.26), residues: 1103 helix: 1.61 (0.26), residues: 405 sheet: -0.33 (0.30), residues: 277 loop : -0.04 (0.33), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 88 HIS 0.007 0.001 HIS C 394 PHE 0.024 0.002 PHE C 34 TYR 0.015 0.001 TYR A 318 ARG 0.005 0.001 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.986 Fit side-chains REVERT: A 280 ARG cc_start: 0.8197 (ptm160) cc_final: 0.7754 (ttp-170) REVERT: B 168 LEU cc_start: 0.8822 (tp) cc_final: 0.8375 (tt) REVERT: B 234 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.7681 (m-80) REVERT: H 184 SER cc_start: 0.9412 (p) cc_final: 0.9119 (m) REVERT: C 34 PHE cc_start: 0.8616 (t80) cc_final: 0.8407 (t80) REVERT: C 92 ARG cc_start: 0.7028 (tpt-90) cc_final: 0.5811 (tmm-80) REVERT: C 107 PHE cc_start: 0.6189 (m-80) cc_final: 0.5925 (m-80) REVERT: C 160 TYR cc_start: 0.6752 (t80) cc_final: 0.6282 (t80) REVERT: C 355 CYS cc_start: 0.8456 (m) cc_final: 0.7971 (m) REVERT: C 418 HIS cc_start: 0.7572 (m90) cc_final: 0.7346 (m90) outliers start: 20 outliers final: 14 residues processed: 209 average time/residue: 0.2432 time to fit residues: 68.8917 Evaluate side-chains 184 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 174 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.0570 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN H 183 GLN ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8590 Z= 0.197 Angle : 0.596 8.898 11694 Z= 0.311 Chirality : 0.043 0.169 1350 Planarity : 0.004 0.058 1494 Dihedral : 5.008 59.754 1210 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.34 % Allowed : 15.75 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.82 (0.26), residues: 1103 helix: 1.82 (0.26), residues: 404 sheet: -0.30 (0.30), residues: 275 loop : 0.03 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 88 HIS 0.005 0.001 HIS C 394 PHE 0.032 0.002 PHE A 208 TYR 0.012 0.001 TYR H 190 ARG 0.003 0.000 ARG D 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.891 Fit side-chains REVERT: A 280 ARG cc_start: 0.8141 (ptm160) cc_final: 0.7724 (ttp-170) REVERT: A 312 PHE cc_start: 0.7393 (m-80) cc_final: 0.7144 (m-10) REVERT: B 168 LEU cc_start: 0.8767 (tp) cc_final: 0.8338 (tt) REVERT: B 198 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7570 (pp) REVERT: B 215 GLU cc_start: 0.7200 (tm-30) cc_final: 0.6657 (tt0) REVERT: B 234 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.7614 (m-80) REVERT: B 292 PHE cc_start: 0.8652 (m-10) cc_final: 0.8285 (m-10) REVERT: G 27 ARG cc_start: 0.8425 (ttm110) cc_final: 0.7744 (ttm110) REVERT: H 140 MET cc_start: 0.7950 (mmm) cc_final: 0.7642 (mmm) REVERT: H 184 SER cc_start: 0.9440 (p) cc_final: 0.9076 (m) REVERT: C 92 ARG cc_start: 0.6822 (tpt-90) cc_final: 0.5645 (tmm-80) REVERT: C 107 PHE cc_start: 0.6188 (m-80) cc_final: 0.5981 (m-80) REVERT: C 355 CYS cc_start: 0.8511 (m) cc_final: 0.8074 (m) REVERT: D 6 MET cc_start: 0.8230 (tpp) cc_final: 0.7922 (tpp) outliers start: 28 outliers final: 15 residues processed: 216 average time/residue: 0.2118 time to fit residues: 63.1333 Evaluate side-chains 195 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 172 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 90 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 GLN ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8590 Z= 0.222 Angle : 0.623 10.287 11694 Z= 0.321 Chirality : 0.045 0.364 1350 Planarity : 0.004 0.057 1494 Dihedral : 4.805 59.941 1208 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.22 % Allowed : 18.62 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1103 helix: 1.78 (0.26), residues: 403 sheet: -0.35 (0.30), residues: 277 loop : -0.05 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 88 HIS 0.007 0.001 HIS C 394 PHE 0.027 0.002 PHE A 340 TYR 0.012 0.001 TYR H 190 ARG 0.002 0.000 ARG D 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 205 SER cc_start: 0.8792 (t) cc_final: 0.8459 (p) REVERT: A 295 ASP cc_start: 0.8809 (p0) cc_final: 0.8451 (p0) REVERT: B 168 LEU cc_start: 0.8787 (tp) cc_final: 0.8342 (tt) REVERT: B 198 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7597 (pp) REVERT: B 215 GLU cc_start: 0.7348 (tm-30) cc_final: 0.6833 (tt0) REVERT: B 234 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.7641 (m-80) REVERT: H 184 SER cc_start: 0.9411 (p) cc_final: 0.9022 (m) REVERT: C 355 CYS cc_start: 0.8506 (m) cc_final: 0.8100 (m) outliers start: 27 outliers final: 18 residues processed: 200 average time/residue: 0.2053 time to fit residues: 56.8306 Evaluate side-chains 193 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 55 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 GLN ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8590 Z= 0.221 Angle : 0.617 9.915 11694 Z= 0.319 Chirality : 0.044 0.281 1350 Planarity : 0.004 0.058 1494 Dihedral : 4.734 59.923 1208 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.46 % Allowed : 19.09 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.75 (0.26), residues: 1103 helix: 1.79 (0.26), residues: 403 sheet: -0.35 (0.30), residues: 276 loop : -0.04 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 88 HIS 0.003 0.001 HIS B 225 PHE 0.030 0.001 PHE A 340 TYR 0.015 0.002 TYR A 318 ARG 0.005 0.000 ARG C 340 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 205 SER cc_start: 0.8787 (t) cc_final: 0.8433 (p) REVERT: B 168 LEU cc_start: 0.8867 (tp) cc_final: 0.8417 (tt) REVERT: B 198 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7557 (pp) REVERT: B 215 GLU cc_start: 0.7332 (tm-30) cc_final: 0.6877 (tt0) REVERT: B 234 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: B 292 PHE cc_start: 0.8639 (m-10) cc_final: 0.8278 (m-10) REVERT: H 184 SER cc_start: 0.9412 (p) cc_final: 0.9012 (m) outliers start: 29 outliers final: 20 residues processed: 196 average time/residue: 0.2070 time to fit residues: 55.7155 Evaluate side-chains 190 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 59 optimal weight: 0.0970 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8590 Z= 0.209 Angle : 0.634 11.035 11694 Z= 0.324 Chirality : 0.043 0.291 1350 Planarity : 0.004 0.057 1494 Dihedral : 4.690 58.803 1208 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.34 % Allowed : 19.09 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.71 (0.26), residues: 1103 helix: 1.82 (0.26), residues: 403 sheet: -0.52 (0.31), residues: 269 loop : -0.03 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 88 HIS 0.004 0.001 HIS C 394 PHE 0.019 0.002 PHE C 151 TYR 0.014 0.001 TYR A 318 ARG 0.004 0.000 ARG C 161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 1.001 Fit side-chains REVERT: A 205 SER cc_start: 0.8776 (t) cc_final: 0.8426 (p) REVERT: A 218 ASN cc_start: 0.8408 (p0) cc_final: 0.8159 (p0) REVERT: B 17 GLN cc_start: 0.7964 (pt0) cc_final: 0.7647 (mm-40) REVERT: B 168 LEU cc_start: 0.8867 (tp) cc_final: 0.8419 (tt) REVERT: B 198 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7571 (pp) REVERT: B 215 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6857 (tt0) REVERT: B 234 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.7635 (m-80) REVERT: B 292 PHE cc_start: 0.8584 (m-10) cc_final: 0.8242 (m-10) REVERT: H 184 SER cc_start: 0.9424 (p) cc_final: 0.9014 (m) REVERT: C 375 THR cc_start: 0.7940 (m) cc_final: 0.7618 (m) outliers start: 28 outliers final: 21 residues processed: 198 average time/residue: 0.2036 time to fit residues: 56.0269 Evaluate side-chains 195 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS H 183 GLN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8590 Z= 0.254 Angle : 0.639 10.294 11694 Z= 0.329 Chirality : 0.044 0.284 1350 Planarity : 0.004 0.058 1494 Dihedral : 4.771 58.735 1208 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.46 % Allowed : 18.97 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.66 (0.26), residues: 1103 helix: 1.78 (0.26), residues: 403 sheet: -0.51 (0.31), residues: 278 loop : -0.06 (0.33), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 88 HIS 0.003 0.001 HIS A 362 PHE 0.024 0.002 PHE A 340 TYR 0.016 0.002 TYR C 160 ARG 0.003 0.000 ARG C 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.919 Fit side-chains REVERT: A 218 ASN cc_start: 0.8433 (p0) cc_final: 0.8179 (p0) REVERT: B 17 GLN cc_start: 0.7907 (pt0) cc_final: 0.7636 (mm-40) REVERT: B 168 LEU cc_start: 0.8884 (tp) cc_final: 0.8415 (tt) REVERT: B 198 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7620 (pp) REVERT: B 215 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6927 (tt0) REVERT: B 234 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.7663 (m-80) REVERT: B 292 PHE cc_start: 0.8602 (m-10) cc_final: 0.8233 (m-10) REVERT: H 37 VAL cc_start: 0.7860 (t) cc_final: 0.6703 (p) REVERT: H 184 SER cc_start: 0.9440 (p) cc_final: 0.9009 (m) REVERT: C 375 THR cc_start: 0.7955 (m) cc_final: 0.7662 (m) REVERT: D 6 MET cc_start: 0.8251 (tpp) cc_final: 0.7650 (tpp) outliers start: 29 outliers final: 22 residues processed: 196 average time/residue: 0.2016 time to fit residues: 55.1561 Evaluate side-chains 192 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS H 183 GLN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8590 Z= 0.236 Angle : 0.648 11.325 11694 Z= 0.330 Chirality : 0.044 0.307 1350 Planarity : 0.004 0.055 1494 Dihedral : 4.740 58.377 1208 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.98 % Allowed : 20.29 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.71 (0.26), residues: 1103 helix: 1.90 (0.26), residues: 399 sheet: -0.41 (0.32), residues: 264 loop : -0.19 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 88 HIS 0.003 0.001 HIS B 142 PHE 0.016 0.002 PHE C 111 TYR 0.013 0.001 TYR B 111 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.991 Fit side-chains REVERT: A 218 ASN cc_start: 0.8447 (p0) cc_final: 0.8194 (p0) REVERT: B 17 GLN cc_start: 0.7975 (pt0) cc_final: 0.7679 (mm-40) REVERT: B 168 LEU cc_start: 0.8872 (tp) cc_final: 0.8405 (tt) REVERT: B 198 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7694 (pp) REVERT: B 215 GLU cc_start: 0.7290 (tm-30) cc_final: 0.6872 (tt0) REVERT: B 234 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.7715 (m-80) REVERT: B 292 PHE cc_start: 0.8581 (m-10) cc_final: 0.8196 (m-10) REVERT: H 37 VAL cc_start: 0.7834 (t) cc_final: 0.6667 (p) REVERT: H 184 SER cc_start: 0.9428 (p) cc_final: 0.8996 (m) REVERT: C 375 THR cc_start: 0.7906 (m) cc_final: 0.7662 (m) REVERT: D 6 MET cc_start: 0.8315 (tpp) cc_final: 0.7710 (tpp) outliers start: 25 outliers final: 22 residues processed: 195 average time/residue: 0.2095 time to fit residues: 56.5125 Evaluate side-chains 200 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.6980 chunk 72 optimal weight: 0.1980 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 GLN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8590 Z= 0.193 Angle : 0.640 11.910 11694 Z= 0.325 Chirality : 0.043 0.296 1350 Planarity : 0.004 0.055 1494 Dihedral : 4.600 57.980 1208 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.39 % Allowed : 21.12 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1103 helix: 1.96 (0.26), residues: 399 sheet: -0.41 (0.33), residues: 250 loop : -0.09 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 88 HIS 0.007 0.001 HIS B 225 PHE 0.019 0.002 PHE A 208 TYR 0.020 0.001 TYR C 160 ARG 0.004 0.000 ARG G 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8428 (p0) cc_final: 0.8187 (p0) REVERT: B 17 GLN cc_start: 0.8033 (pt0) cc_final: 0.7736 (mm-40) REVERT: B 168 LEU cc_start: 0.8839 (tp) cc_final: 0.8359 (tt) REVERT: B 198 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7617 (pp) REVERT: B 215 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6807 (tt0) REVERT: B 234 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.7566 (m-80) REVERT: B 292 PHE cc_start: 0.8511 (m-10) cc_final: 0.8165 (m-10) REVERT: H 184 SER cc_start: 0.9444 (p) cc_final: 0.9006 (m) REVERT: D 6 MET cc_start: 0.8343 (tpp) cc_final: 0.7728 (tpp) outliers start: 20 outliers final: 17 residues processed: 195 average time/residue: 0.2119 time to fit residues: 56.5065 Evaluate side-chains 196 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 GLN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.185650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.144002 restraints weight = 10760.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.140982 restraints weight = 8136.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.143884 restraints weight = 6450.927| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8590 Z= 0.320 Angle : 0.699 11.680 11694 Z= 0.358 Chirality : 0.045 0.302 1350 Planarity : 0.005 0.054 1494 Dihedral : 4.924 58.718 1208 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.98 % Allowed : 21.00 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.63 (0.26), residues: 1103 helix: 1.88 (0.26), residues: 395 sheet: -0.56 (0.32), residues: 265 loop : -0.17 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 88 HIS 0.007 0.002 HIS B 225 PHE 0.028 0.002 PHE A 208 TYR 0.018 0.002 TYR B 111 ARG 0.009 0.001 ARG A 265 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2091.31 seconds wall clock time: 38 minutes 57.00 seconds (2337.00 seconds total)