Starting phenix.real_space_refine on Fri Nov 15 07:12:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yn4_39414/11_2024/8yn4_39414.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yn4_39414/11_2024/8yn4_39414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yn4_39414/11_2024/8yn4_39414.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yn4_39414/11_2024/8yn4_39414.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yn4_39414/11_2024/8yn4_39414.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yn4_39414/11_2024/8yn4_39414.cif" } resolution = 2.97 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= 0.011 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 57 5.16 5 C 5509 2.51 5 N 1491 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8661 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1754 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 5, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2034 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 7, 'TRANS': 260} Chain breaks: 2 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "R" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'CLR': 1, 'HSM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.24, per 1000 atoms: 0.61 Number of scatterers: 8661 At special positions: 0 Unit cell: (109.14, 115.56, 110.21, 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 57 16.00 O 1604 8.00 N 1491 7.00 C 5509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 91 " - pdb=" SG CYS R 174 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.0 seconds 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 38.6% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 6 through 29 removed outlier: 3.991A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 95 through 101 removed outlier: 3.548A pdb=" N GLN A 98 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.024A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 183 through 204 removed outlier: 3.525A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 356 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.516A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.513A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.538A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 46 removed outlier: 3.509A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 53 No H-bonds generated for 'chain 'R' and resid 51 through 53' Processing helix chain 'R' and resid 54 through 71 Processing helix chain 'R' and resid 71 through 82 Processing helix chain 'R' and resid 87 through 122 removed outlier: 3.510A pdb=" N ASN R 92 " --> pdb=" O LYS R 88 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE R 93 " --> pdb=" O VAL R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 130 Processing helix chain 'R' and resid 131 through 156 removed outlier: 3.653A pdb=" N LEU R 152 " --> pdb=" O THR R 148 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N SER R 153 " --> pdb=" O LEU R 149 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE R 154 " --> pdb=" O SER R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 191 Processing helix chain 'R' and resid 191 through 216 Processing helix chain 'R' and resid 230 through 261 removed outlier: 3.550A pdb=" N PHE R 243 " --> pdb=" O VAL R 239 " (cutoff:3.500A) Proline residue: R 249 - end of helix Processing helix chain 'R' and resid 266 through 288 removed outlier: 3.676A pdb=" N GLY R 277 " --> pdb=" O VAL R 273 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR R 278 " --> pdb=" O LEU R 274 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER R 281 " --> pdb=" O GLY R 277 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA R 282 " --> pdb=" O TYR R 278 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU R 283 " --> pdb=" O ALA R 279 " (cutoff:3.500A) Proline residue: R 285 - end of helix Processing helix chain 'R' and resid 292 through 301 removed outlier: 3.737A pdb=" N GLN R 300 " --> pdb=" O ARG R 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 75 removed outlier: 6.154A pdb=" N LEU A 34 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N PHE A 84 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU A 36 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N ALA A 105 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 75 removed outlier: 6.154A pdb=" N LEU A 34 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N PHE A 84 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU A 36 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N ALA A 105 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.599A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.559A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.181A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.331A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.466A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.530A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.727A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.805A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.442A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.152A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1311 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: 2.69 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2825 1.35 - 1.46: 2153 1.46 - 1.58: 3777 1.58 - 1.70: 0 1.70 - 1.82: 81 Bond restraints: 8836 Sorted by residual: bond pdb=" CG HSM R 701 " pdb=" ND1 HSM R 701 " ideal model delta sigma weight residual 1.383 1.340 0.043 2.00e-02 2.50e+03 4.61e+00 bond pdb=" C5 CLR R 702 " pdb=" C6 CLR R 702 " ideal model delta sigma weight residual 1.332 1.300 0.032 2.00e-02 2.50e+03 2.55e+00 bond pdb=" C10 CLR R 702 " pdb=" C9 CLR R 702 " ideal model delta sigma weight residual 1.551 1.521 0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" CG HSM R 701 " pdb=" CD2 HSM R 701 " ideal model delta sigma weight residual 1.373 1.347 0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C13 CLR R 702 " pdb=" C17 CLR R 702 " ideal model delta sigma weight residual 1.550 1.529 0.021 2.00e-02 2.50e+03 1.10e+00 ... (remaining 8831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 11901 1.51 - 3.02: 85 3.02 - 4.52: 15 4.52 - 6.03: 8 6.03 - 7.54: 1 Bond angle restraints: 12010 Sorted by residual: angle pdb=" C13 CLR R 702 " pdb=" C17 CLR R 702 " pdb=" C20 CLR R 702 " ideal model delta sigma weight residual 119.60 112.06 7.54 3.00e+00 1.11e-01 6.32e+00 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 125.35 -3.81 1.91e+00 2.74e-01 3.97e+00 angle pdb=" C23 CLR R 702 " pdb=" C24 CLR R 702 " pdb=" C25 CLR R 702 " ideal model delta sigma weight residual 115.14 109.81 5.33 3.00e+00 1.11e-01 3.16e+00 angle pdb=" C20 CLR R 702 " pdb=" C22 CLR R 702 " pdb=" C23 CLR R 702 " ideal model delta sigma weight residual 115.57 110.39 5.18 3.00e+00 1.11e-01 2.99e+00 angle pdb=" CA HSM R 701 " pdb=" CB HSM R 701 " pdb=" CG HSM R 701 " ideal model delta sigma weight residual 114.47 109.47 5.00 3.00e+00 1.11e-01 2.78e+00 ... (remaining 12005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.68: 5065 15.68 - 31.35: 161 31.35 - 47.03: 37 47.03 - 62.71: 5 62.71 - 78.38: 1 Dihedral angle restraints: 5269 sinusoidal: 2003 harmonic: 3266 Sorted by residual: dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 159.27 20.73 0 5.00e+00 4.00e-02 1.72e+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 180.00 161.01 18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 162.13 17.87 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 5266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1322 0.093 - 0.186: 66 0.186 - 0.279: 1 0.279 - 0.372: 1 0.372 - 0.465: 1 Chirality restraints: 1391 Sorted by residual: chirality pdb=" C14 CLR R 702 " pdb=" C13 CLR R 702 " pdb=" C15 CLR R 702 " pdb=" C8 CLR R 702 " both_signs ideal model delta sigma weight residual False -2.32 -2.78 0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" C10 CLR R 702 " pdb=" C1 CLR R 702 " pdb=" C5 CLR R 702 " pdb=" C9 CLR R 702 " both_signs ideal model delta sigma weight residual False -2.85 -2.50 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" C17 CLR R 702 " pdb=" C13 CLR R 702 " pdb=" C16 CLR R 702 " pdb=" C20 CLR R 702 " both_signs ideal model delta sigma weight residual False 2.55 2.82 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1388 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO B 236 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 284 " 0.018 5.00e-02 4.00e+02 2.65e-02 1.13e+00 pdb=" N PRO R 285 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO R 285 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 285 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 193 " 0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO R 194 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO R 194 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 194 " 0.014 5.00e-02 4.00e+02 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2213 2.80 - 3.33: 8012 3.33 - 3.85: 14441 3.85 - 4.38: 17491 4.38 - 4.90: 30345 Nonbonded interactions: 72502 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.276 3.040 nonbonded pdb=" O LYS C 20 " pdb=" ND2 ASN C 24 " model vdw 2.293 3.120 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.298 3.040 nonbonded pdb=" O SER E 30 " pdb=" OG SER E 53 " model vdw 2.305 3.040 nonbonded pdb=" O GLY R 44 " pdb=" NH2 ARG R 50 " model vdw 2.311 3.120 ... (remaining 72497 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: 0.290 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.510 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 0.002 0.043 8836 Z= 0.103 Angle : 0.396 7.541 12010 Z= 0.198 Chirality : 0.043 0.465 1391 Planarity : 0.003 0.043 1520 Dihedral : 8.469 78.384 3154 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.33 % Allowed : 2.74 % Favored : 96.93 % 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: 1.49 (0.25), residues: 1109 helix: 1.73 (0.26), residues: 386 sheet: 0.83 (0.29), residues: 288 loop : 0.57 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.002 0.001 HIS B 91 PHE 0.009 0.001 PHE A 228 TYR 0.011 0.001 TYR E 190 ARG 0.002 0.000 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 224 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 94 ARG cc_start: 0.6786 (ptt-90) cc_final: 0.6585 (ttp-170) REVERT: A 132 ARG cc_start: 0.7969 (ttp-110) cc_final: 0.7594 (ttt-90) REVERT: C 17 GLU cc_start: 0.8546 (tp30) cc_final: 0.8194 (tm-30) REVERT: R 233 THR cc_start: 0.8575 (m) cc_final: 0.8230 (p) outliers start: 3 outliers final: 1 residues processed: 225 average time/residue: 1.2767 time to fit residues: 305.0017 Evaluate side-chains 143 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.0040 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 123 ASN A 130 ASN B 91 HIS B 259 GLN E 171 ASN R 46 ASN R 79 GLN R 212 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8836 Z= 0.290 Angle : 0.577 8.637 12010 Z= 0.308 Chirality : 0.044 0.151 1391 Planarity : 0.004 0.039 1520 Dihedral : 4.576 30.614 1295 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.73 % Allowed : 12.18 % Favored : 84.08 % 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: 1.73 (0.25), residues: 1109 helix: 2.38 (0.26), residues: 385 sheet: 0.76 (0.30), residues: 272 loop : 0.41 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 275 HIS 0.005 0.001 HIS B 91 PHE 0.018 0.002 PHE B 199 TYR 0.020 0.002 TYR R 256 ARG 0.009 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 1.041 Fit side-chains REVERT: A 14 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: A 18 MET cc_start: 0.8196 (ttt) cc_final: 0.7984 (ttp) REVERT: A 122 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7976 (mp) REVERT: A 126 LYS cc_start: 0.8385 (mtpp) cc_final: 0.8154 (mtpm) REVERT: A 152 LYS cc_start: 0.8157 (tttt) cc_final: 0.7957 (mtmt) REVERT: A 351 MET cc_start: 0.8234 (mtp) cc_final: 0.7934 (mtm) REVERT: B 13 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8254 (tm-30) REVERT: B 17 GLN cc_start: 0.8688 (tt0) cc_final: 0.8275 (tt0) REVERT: B 44 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7619 (mt0) REVERT: C 17 GLU cc_start: 0.8635 (tp30) cc_final: 0.8122 (tm-30) REVERT: R 31 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8261 (mp) REVERT: R 211 ASP cc_start: 0.7136 (m-30) cc_final: 0.6934 (m-30) outliers start: 34 outliers final: 16 residues processed: 179 average time/residue: 1.3246 time to fit residues: 251.2280 Evaluate side-chains 157 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 99 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8836 Z= 0.232 Angle : 0.523 6.424 12010 Z= 0.282 Chirality : 0.043 0.169 1391 Planarity : 0.004 0.038 1520 Dihedral : 4.380 29.284 1293 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.06 % Allowed : 14.82 % Favored : 81.12 % 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: 1.69 (0.25), residues: 1109 helix: 2.40 (0.26), residues: 392 sheet: 0.49 (0.30), residues: 274 loop : 0.49 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.014 0.001 PHE B 199 TYR 0.014 0.001 TYR E 227 ARG 0.006 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.964 Fit side-chains REVERT: A 14 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: A 122 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8011 (mp) REVERT: A 152 LYS cc_start: 0.8078 (tttt) cc_final: 0.7739 (mtpt) REVERT: A 351 MET cc_start: 0.8229 (mtp) cc_final: 0.7942 (mtm) REVERT: B 17 GLN cc_start: 0.8527 (tt0) cc_final: 0.8319 (tt0) REVERT: B 44 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7658 (mt0) REVERT: B 215 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7832 (mm-30) REVERT: B 217 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.6999 (pmt) REVERT: B 280 LYS cc_start: 0.8631 (tttt) cc_final: 0.8416 (tttp) REVERT: C 17 GLU cc_start: 0.8706 (tp30) cc_final: 0.8178 (tm-30) REVERT: R 31 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8230 (mp) REVERT: R 51 ASN cc_start: 0.7336 (p0) cc_final: 0.6982 (p0) outliers start: 37 outliers final: 17 residues processed: 164 average time/residue: 1.3304 time to fit residues: 231.3799 Evaluate side-chains 150 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 196 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 20.0000 chunk 75 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8836 Z= 0.187 Angle : 0.509 6.273 12010 Z= 0.270 Chirality : 0.042 0.203 1391 Planarity : 0.003 0.042 1520 Dihedral : 4.164 28.953 1293 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.95 % Allowed : 16.14 % Favored : 79.91 % 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: 1.69 (0.25), residues: 1109 helix: 2.54 (0.26), residues: 392 sheet: 0.32 (0.30), residues: 277 loop : 0.47 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.012 0.001 PHE B 199 TYR 0.012 0.001 TYR E 190 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.856 Fit side-chains REVERT: A 14 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7657 (tt0) REVERT: A 21 LYS cc_start: 0.8489 (ttpp) cc_final: 0.8154 (ttmt) REVERT: A 152 LYS cc_start: 0.8109 (tttt) cc_final: 0.7765 (mtpt) REVERT: A 351 MET cc_start: 0.8222 (mtp) cc_final: 0.7953 (mtm) REVERT: B 44 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7653 (mt0) REVERT: B 215 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7785 (mm-30) REVERT: B 217 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7027 (pmt) REVERT: C 17 GLU cc_start: 0.8742 (tp30) cc_final: 0.8164 (tm-30) REVERT: C 18 GLN cc_start: 0.8932 (tp40) cc_final: 0.8608 (tp-100) REVERT: C 42 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7000 (tp30) REVERT: E 191 ARG cc_start: 0.8529 (mtm-85) cc_final: 0.8323 (mtt180) REVERT: R 31 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8202 (mp) REVERT: R 51 ASN cc_start: 0.7428 (p0) cc_final: 0.7052 (p0) outliers start: 36 outliers final: 15 residues processed: 159 average time/residue: 1.3394 time to fit residues: 225.3011 Evaluate side-chains 151 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 240 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 95 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN B 17 GLN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8836 Z= 0.169 Angle : 0.506 7.933 12010 Z= 0.265 Chirality : 0.042 0.161 1391 Planarity : 0.003 0.042 1520 Dihedral : 4.080 29.511 1293 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.73 % Allowed : 17.78 % Favored : 78.49 % 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: 1.68 (0.25), residues: 1109 helix: 2.55 (0.26), residues: 393 sheet: 0.27 (0.30), residues: 277 loop : 0.48 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.011 0.001 PHE A 228 TYR 0.012 0.001 TYR E 190 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.861 Fit side-chains REVERT: A 14 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: A 21 LYS cc_start: 0.8463 (ttpp) cc_final: 0.8121 (ttmt) REVERT: A 152 LYS cc_start: 0.8144 (tttt) cc_final: 0.7770 (mtpt) REVERT: A 351 MET cc_start: 0.8173 (mtp) cc_final: 0.7916 (mtm) REVERT: B 44 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7651 (mt0) REVERT: B 215 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7810 (mm-30) REVERT: B 217 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.6918 (pmt) REVERT: C 17 GLU cc_start: 0.8734 (tp30) cc_final: 0.8153 (tm-30) REVERT: C 18 GLN cc_start: 0.8869 (tp40) cc_final: 0.8586 (tp-100) REVERT: C 42 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.6988 (tp30) REVERT: R 51 ASN cc_start: 0.7429 (p0) cc_final: 0.7078 (p0) REVERT: R 233 THR cc_start: 0.8182 (m) cc_final: 0.7811 (p) outliers start: 34 outliers final: 19 residues processed: 154 average time/residue: 1.4150 time to fit residues: 231.1696 Evaluate side-chains 156 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 240 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN C 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8836 Z= 0.172 Angle : 0.509 9.172 12010 Z= 0.265 Chirality : 0.041 0.137 1391 Planarity : 0.003 0.043 1520 Dihedral : 4.007 28.467 1293 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.62 % Allowed : 18.22 % Favored : 78.16 % 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: 1.73 (0.26), residues: 1109 helix: 2.64 (0.26), residues: 394 sheet: 0.25 (0.30), residues: 277 loop : 0.47 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.018 0.001 PHE E 68 TYR 0.011 0.001 TYR E 190 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7657 (tt0) REVERT: A 21 LYS cc_start: 0.8448 (ttpp) cc_final: 0.8102 (ttmt) REVERT: A 351 MET cc_start: 0.8202 (mtp) cc_final: 0.7951 (mtm) REVERT: B 44 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7690 (mt0) REVERT: B 215 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7803 (mm-30) REVERT: B 217 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.6917 (pmt) REVERT: C 17 GLU cc_start: 0.8741 (tp30) cc_final: 0.8142 (tm-30) REVERT: C 42 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6970 (tp30) REVERT: E 46 GLU cc_start: 0.8042 (tt0) cc_final: 0.7512 (pt0) REVERT: R 51 ASN cc_start: 0.7493 (p0) cc_final: 0.7107 (p0) REVERT: R 233 THR cc_start: 0.8176 (m) cc_final: 0.7801 (p) outliers start: 33 outliers final: 19 residues processed: 153 average time/residue: 1.4845 time to fit residues: 241.1459 Evaluate side-chains 154 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 240 MET 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: 0.9990 chunk 89 optimal weight: 0.3980 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** R 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8836 Z= 0.168 Angle : 0.517 8.417 12010 Z= 0.267 Chirality : 0.041 0.133 1391 Planarity : 0.003 0.042 1520 Dihedral : 3.986 28.590 1293 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.62 % Allowed : 18.33 % Favored : 78.05 % 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: 1.74 (0.26), residues: 1109 helix: 2.65 (0.26), residues: 397 sheet: 0.23 (0.30), residues: 277 loop : 0.47 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.010 0.001 PHE B 199 TYR 0.011 0.001 TYR E 190 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.950 Fit side-chains REVERT: A 14 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7661 (tt0) REVERT: A 21 LYS cc_start: 0.8452 (ttpp) cc_final: 0.8101 (ttmt) REVERT: A 132 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7707 (ttp80) REVERT: A 351 MET cc_start: 0.8189 (mtp) cc_final: 0.7949 (mtm) REVERT: B 44 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7693 (mt0) REVERT: B 215 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7785 (mm-30) REVERT: B 217 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7036 (pmt) REVERT: C 17 GLU cc_start: 0.8741 (tp30) cc_final: 0.8163 (tm-30) REVERT: C 42 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7036 (tp30) REVERT: E 46 GLU cc_start: 0.8022 (tt0) cc_final: 0.7520 (pt0) REVERT: R 31 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8014 (mp) REVERT: R 51 ASN cc_start: 0.7510 (p0) cc_final: 0.7112 (p0) REVERT: R 233 THR cc_start: 0.8153 (m) cc_final: 0.7787 (p) outliers start: 33 outliers final: 18 residues processed: 151 average time/residue: 1.3178 time to fit residues: 211.0352 Evaluate side-chains 158 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 240 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN ** R 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8836 Z= 0.329 Angle : 0.594 8.602 12010 Z= 0.306 Chirality : 0.044 0.139 1391 Planarity : 0.004 0.043 1520 Dihedral : 4.279 28.448 1293 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.62 % Allowed : 18.66 % Favored : 77.72 % 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: 1.56 (0.25), residues: 1109 helix: 2.40 (0.26), residues: 398 sheet: 0.19 (0.30), residues: 281 loop : 0.44 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.006 0.001 HIS B 225 PHE 0.017 0.002 PHE B 199 TYR 0.014 0.002 TYR E 227 ARG 0.008 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: A 18 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7918 (ttt) REVERT: A 71 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8294 (mm-30) REVERT: A 351 MET cc_start: 0.8239 (mtp) cc_final: 0.7977 (mtm) REVERT: B 19 ARG cc_start: 0.7977 (ttp-110) cc_final: 0.7759 (ttm110) REVERT: B 44 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7746 (mt0) REVERT: B 217 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.7090 (pmt) REVERT: C 17 GLU cc_start: 0.8729 (tp30) cc_final: 0.8137 (tm-30) REVERT: C 42 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7113 (tp30) REVERT: R 51 ASN cc_start: 0.7488 (p0) cc_final: 0.7074 (p0) REVERT: R 233 THR cc_start: 0.8224 (m) cc_final: 0.7845 (p) outliers start: 33 outliers final: 18 residues processed: 152 average time/residue: 1.3859 time to fit residues: 222.9987 Evaluate side-chains 155 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 240 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 59 optimal weight: 0.0970 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN ** R 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8836 Z= 0.164 Angle : 0.541 9.556 12010 Z= 0.278 Chirality : 0.042 0.137 1391 Planarity : 0.003 0.045 1520 Dihedral : 4.038 27.916 1293 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.85 % Allowed : 19.98 % Favored : 77.17 % 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: 1.65 (0.26), residues: 1109 helix: 2.54 (0.26), residues: 399 sheet: 0.23 (0.30), residues: 275 loop : 0.43 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.037 0.001 PHE E 68 TYR 0.011 0.001 TYR E 190 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 1.034 Fit side-chains REVERT: A 14 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7623 (tt0) REVERT: A 21 LYS cc_start: 0.8531 (ttpp) cc_final: 0.8200 (ttmt) REVERT: A 351 MET cc_start: 0.8195 (mtp) cc_final: 0.7958 (mtm) REVERT: B 44 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7680 (mt0) REVERT: B 217 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8317 (ppp) REVERT: C 17 GLU cc_start: 0.8686 (tp30) cc_final: 0.8133 (tm-30) REVERT: C 42 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6980 (tp30) REVERT: E 46 GLU cc_start: 0.8040 (tt0) cc_final: 0.7631 (pt0) REVERT: R 51 ASN cc_start: 0.7505 (p0) cc_final: 0.7093 (p0) outliers start: 26 outliers final: 15 residues processed: 151 average time/residue: 1.3643 time to fit residues: 218.1941 Evaluate side-chains 152 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 240 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 175 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN E 231 GLN ** R 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8836 Z= 0.342 Angle : 0.616 9.585 12010 Z= 0.316 Chirality : 0.045 0.155 1391 Planarity : 0.004 0.043 1520 Dihedral : 4.323 28.107 1293 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.51 % Allowed : 19.65 % Favored : 76.84 % 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: 1.49 (0.25), residues: 1109 helix: 2.31 (0.26), residues: 398 sheet: 0.19 (0.29), residues: 282 loop : 0.42 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS B 225 PHE 0.031 0.002 PHE E 68 TYR 0.012 0.002 TYR E 227 ARG 0.009 0.001 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.997 Fit side-chains REVERT: A 14 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7596 (tt0) REVERT: A 18 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7936 (ttt) REVERT: A 21 LYS cc_start: 0.8509 (ttpp) cc_final: 0.8138 (ttmt) REVERT: A 351 MET cc_start: 0.8237 (mtp) cc_final: 0.7983 (mtm) REVERT: B 19 ARG cc_start: 0.7976 (ttp-110) cc_final: 0.7761 (ttm110) REVERT: B 44 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7739 (mt0) REVERT: B 217 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.7187 (pmt) REVERT: C 17 GLU cc_start: 0.8652 (tp30) cc_final: 0.8126 (tm-30) REVERT: C 42 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7117 (tp30) REVERT: E 46 GLU cc_start: 0.8081 (tt0) cc_final: 0.7607 (pt0) REVERT: R 51 ASN cc_start: 0.7486 (p0) cc_final: 0.7103 (p0) REVERT: R 137 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7776 (mp) REVERT: R 233 THR cc_start: 0.8079 (m) cc_final: 0.7734 (p) outliers start: 32 outliers final: 19 residues processed: 151 average time/residue: 1.3795 time to fit residues: 220.6000 Evaluate side-chains 163 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 240 MET Chi-restraints excluded: chain R residue 252 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN ** R 159 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 = 0.3894 r_free = 0.3894 target = 0.160222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114700 restraints weight = 9919.202| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.16 r_work: 0.3128 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8836 Z= 0.193 Angle : 0.569 10.680 12010 Z= 0.293 Chirality : 0.043 0.191 1391 Planarity : 0.003 0.044 1520 Dihedral : 4.149 27.816 1293 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.74 % Allowed : 21.41 % Favored : 75.85 % 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: 1.53 (0.26), residues: 1109 helix: 2.40 (0.26), residues: 400 sheet: 0.14 (0.30), residues: 277 loop : 0.42 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS B 225 PHE 0.011 0.001 PHE B 199 TYR 0.011 0.001 TYR A 115 ARG 0.008 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4013.75 seconds wall clock time: 72 minutes 30.30 seconds (4350.30 seconds total)