Starting phenix.real_space_refine on Fri Nov 15 00:56:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8itm_35707/11_2024/8itm_35707.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8itm_35707/11_2024/8itm_35707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8itm_35707/11_2024/8itm_35707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8itm_35707/11_2024/8itm_35707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8itm_35707/11_2024/8itm_35707.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8itm_35707/11_2024/8itm_35707.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.092 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 47 5.16 5 C 5008 2.51 5 N 1410 2.21 5 O 1440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7905 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2153 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 6, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 111 Chain: "A" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1868 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 2552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2552 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 54 Chain: "G" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 382 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "N" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 950 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 4.73, per 1000 atoms: 0.60 Number of scatterers: 7905 At special positions: 0 Unit cell: (76.041, 101.745, 127.449, 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 47 16.00 O 1440 8.00 N 1410 7.00 C 5008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 155 " - pdb=" SG CYS R 225 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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: 2.03 Conformation dependent library (CDL) restraints added in 1.1 seconds 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1942 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 11 sheets defined 43.1% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'R' and resid 63 through 101 Processing helix chain 'R' and resid 106 through 133 removed outlier: 3.723A pdb=" N LEU R 127 " --> pdb=" O ALA R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 186 removed outlier: 3.935A pdb=" N TYR R 170 " --> pdb=" O VAL R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 194 through 220 Proline residue: R 206 - end of helix Proline residue: R 212 - end of helix Processing helix chain 'R' and resid 231 through 268 removed outlier: 3.856A pdb=" N ILE R 237 " --> pdb=" O ALA R 233 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE R 238 " --> pdb=" O ILE R 234 " (cutoff:3.500A) Proline residue: R 241 - end of helix removed outlier: 3.783A pdb=" N ARG R 267 " --> pdb=" O LYS R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 290 removed outlier: 3.910A pdb=" N ARG R 277 " --> pdb=" O ASP R 273 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU R 278 " --> pdb=" O TYR R 274 " (cutoff:3.500A) Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 290 through 296 Processing helix chain 'R' and resid 306 through 331 removed outlier: 4.265A pdb=" N PHE R 310 " --> pdb=" O GLY R 306 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE R 317 " --> pdb=" O LEU R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 354 Processing helix chain 'A' and resid 10 through 40 removed outlier: 3.757A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.060A 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 234 through 239 removed outlier: 3.694A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.529A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.837A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.318A 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 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.573A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 209 removed outlier: 3.623A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 209 removed outlier: 6.615A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.274A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.904A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.567A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.436A 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: 3.526A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.597A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.793A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.584A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 5 through 6 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.741A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1242 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: 2.18 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2619 1.34 - 1.46: 1947 1.46 - 1.58: 3429 1.58 - 1.70: 0 1.70 - 1.83: 65 Bond restraints: 8060 Sorted by residual: bond pdb=" C VAL R 286 " pdb=" N PRO R 287 " ideal model delta sigma weight residual 1.335 1.354 -0.020 1.28e-02 6.10e+03 2.37e+00 bond pdb=" CA GLU R 301 " pdb=" C GLU R 301 " ideal model delta sigma weight residual 1.525 1.508 0.017 1.29e-02 6.01e+03 1.79e+00 bond pdb=" C ALA R 297 " pdb=" O ALA R 297 " ideal model delta sigma weight residual 1.244 1.231 0.012 1.00e-02 1.00e+04 1.54e+00 bond pdb=" CA THR R 300 " pdb=" C THR R 300 " ideal model delta sigma weight residual 1.528 1.512 0.015 1.33e-02 5.65e+03 1.33e+00 bond pdb=" CB ASN R 249 " pdb=" CG ASN R 249 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.28e+00 ... (remaining 8055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 10685 1.62 - 3.23: 208 3.23 - 4.85: 36 4.85 - 6.46: 14 6.46 - 8.08: 5 Bond angle restraints: 10948 Sorted by residual: angle pdb=" C VAL R 286 " pdb=" CA VAL R 286 " pdb=" CB VAL R 286 " ideal model delta sigma weight residual 113.70 110.17 3.53 9.50e-01 1.11e+00 1.38e+01 angle pdb=" N GLU R 316 " pdb=" CA GLU R 316 " pdb=" CB GLU R 316 " ideal model delta sigma weight residual 110.16 115.59 -5.43 1.48e+00 4.57e-01 1.34e+01 angle pdb=" N GLU R 301 " pdb=" CA GLU R 301 " pdb=" C GLU R 301 " ideal model delta sigma weight residual 112.04 107.15 4.89 1.44e+00 4.82e-01 1.15e+01 angle pdb=" CA ALA R 297 " pdb=" C ALA R 297 " pdb=" N PRO R 298 " ideal model delta sigma weight residual 120.77 117.70 3.07 9.70e-01 1.06e+00 1.00e+01 angle pdb=" N ARG R 305 " pdb=" CA ARG R 305 " pdb=" C ARG R 305 " ideal model delta sigma weight residual 109.76 114.66 -4.90 1.59e+00 3.96e-01 9.50e+00 ... (remaining 10943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 4283 17.46 - 34.92: 401 34.92 - 52.37: 73 52.37 - 69.83: 9 69.83 - 87.29: 8 Dihedral angle restraints: 4774 sinusoidal: 1770 harmonic: 3004 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -17.74 -68.26 1 1.00e+01 1.00e-02 6.04e+01 dihedral pdb=" CB CYS R 155 " pdb=" SG CYS R 155 " pdb=" SG CYS R 225 " pdb=" CB CYS R 225 " ideal model delta sinusoidal sigma weight residual 93.00 45.78 47.22 1 1.00e+01 1.00e-02 3.08e+01 dihedral pdb=" CA ALA B 60 " pdb=" C ALA B 60 " pdb=" N MET B 61 " pdb=" CA MET B 61 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 4771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 719 0.029 - 0.058: 352 0.058 - 0.087: 110 0.087 - 0.117: 62 0.117 - 0.146: 18 Chirality restraints: 1261 Sorted by residual: chirality pdb=" CG LEU B 14 " pdb=" CB LEU B 14 " pdb=" CD1 LEU B 14 " pdb=" CD2 LEU B 14 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CG LEU R 183 " pdb=" CB LEU R 183 " pdb=" CD1 LEU R 183 " pdb=" CD2 LEU R 183 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA ILE A 207 " pdb=" N ILE A 207 " pdb=" C ILE A 207 " pdb=" CB ILE A 207 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 1258 not shown) Planarity restraints: 1397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 327 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" C VAL R 327 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL R 327 " 0.012 2.00e-02 2.50e+03 pdb=" N SER R 328 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 312 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C LYS R 312 " -0.028 2.00e-02 2.50e+03 pdb=" O LYS R 312 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU R 313 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " 0.013 2.00e-02 2.50e+03 1.11e-02 2.48e+00 pdb=" CG TYR B 59 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.001 2.00e-02 2.50e+03 ... (remaining 1394 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1135 2.75 - 3.29: 7700 3.29 - 3.83: 13201 3.83 - 4.36: 14907 4.36 - 4.90: 26941 Nonbonded interactions: 63884 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.218 3.040 nonbonded pdb=" O CYS B 204 " pdb=" OH TYR N 117 " model vdw 2.234 3.040 nonbonded pdb=" O GLY B 310 " pdb=" NZ LYS B 337 " model vdw 2.257 3.120 nonbonded pdb=" NZ LYS B 57 " pdb=" OH TYR B 59 " model vdw 2.260 3.120 nonbonded pdb=" OG SER R 118 " pdb=" OD1 ASN R 169 " model vdw 2.270 3.040 ... (remaining 63879 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: 0.820 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.350 Find NCS groups from input model: 0.070 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 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 0.037 8060 Z= 0.255 Angle : 0.609 8.076 10948 Z= 0.346 Chirality : 0.042 0.146 1261 Planarity : 0.003 0.031 1397 Dihedral : 14.137 87.289 2823 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.27), residues: 1019 helix: 1.81 (0.26), residues: 422 sheet: -0.77 (0.35), residues: 226 loop : -1.55 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 234 HIS 0.008 0.001 HIS A 220 PHE 0.016 0.001 PHE R 310 TYR 0.027 0.002 TYR B 59 ARG 0.012 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: R 191 GLU cc_start: 0.5105 (pp20) cc_final: 0.3897 (pm20) REVERT: R 234 ILE cc_start: 0.7892 (mm) cc_final: 0.7567 (pt) REVERT: A 31 GLN cc_start: 0.7830 (tp-100) cc_final: 0.7358 (tp-100) REVERT: A 381 ASP cc_start: 0.8420 (t0) cc_final: 0.8156 (t0) REVERT: B 243 THR cc_start: 0.8781 (p) cc_final: 0.8521 (p) REVERT: B 262 MET cc_start: 0.7858 (ppp) cc_final: 0.7612 (ppp) REVERT: B 264 TYR cc_start: 0.8516 (m-80) cc_final: 0.8006 (m-80) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2274 time to fit residues: 41.8975 Evaluate side-chains 121 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 0.0770 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 109 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8060 Z= 0.198 Angle : 0.551 6.534 10948 Z= 0.290 Chirality : 0.042 0.140 1261 Planarity : 0.004 0.030 1397 Dihedral : 4.076 18.794 1130 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.49 % Allowed : 8.59 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.27), residues: 1019 helix: 2.05 (0.26), residues: 424 sheet: -0.63 (0.34), residues: 213 loop : -1.51 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.005 0.001 HIS A 220 PHE 0.016 0.001 PHE R 310 TYR 0.028 0.001 TYR R 80 ARG 0.005 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.6911 (mm) REVERT: R 191 GLU cc_start: 0.4872 (pp20) cc_final: 0.3949 (pm20) REVERT: R 234 ILE cc_start: 0.7891 (mm) cc_final: 0.7568 (pt) REVERT: A 31 GLN cc_start: 0.7988 (tp-100) cc_final: 0.7515 (tp-100) REVERT: A 381 ASP cc_start: 0.8421 (t0) cc_final: 0.8160 (t0) REVERT: A 386 MET cc_start: 0.7611 (tmm) cc_final: 0.7340 (tmm) REVERT: B 243 THR cc_start: 0.8645 (p) cc_final: 0.8413 (p) REVERT: B 264 TYR cc_start: 0.8491 (m-80) cc_final: 0.8083 (m-80) REVERT: N 82 GLN cc_start: 0.8076 (tp40) cc_final: 0.7771 (tp-100) outliers start: 12 outliers final: 7 residues processed: 137 average time/residue: 0.2147 time to fit residues: 39.8358 Evaluate side-chains 127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 11 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 90 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8060 Z= 0.208 Angle : 0.525 6.537 10948 Z= 0.277 Chirality : 0.041 0.146 1261 Planarity : 0.003 0.030 1397 Dihedral : 4.001 18.236 1130 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.87 % Allowed : 10.83 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.27), residues: 1019 helix: 2.05 (0.26), residues: 428 sheet: -0.53 (0.34), residues: 215 loop : -1.59 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.004 0.001 HIS A 220 PHE 0.017 0.001 PHE R 310 TYR 0.027 0.001 TYR R 80 ARG 0.005 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.6905 (mm) REVERT: R 191 GLU cc_start: 0.4786 (pp20) cc_final: 0.3859 (pm20) REVERT: R 234 ILE cc_start: 0.7894 (mm) cc_final: 0.7593 (pt) REVERT: A 31 GLN cc_start: 0.7995 (tp-100) cc_final: 0.7505 (tp-100) REVERT: A 381 ASP cc_start: 0.8434 (t70) cc_final: 0.8160 (t0) REVERT: A 386 MET cc_start: 0.7510 (tmm) cc_final: 0.7266 (tmm) REVERT: B 243 THR cc_start: 0.8630 (p) cc_final: 0.8392 (p) REVERT: B 264 TYR cc_start: 0.8497 (m-80) cc_final: 0.7982 (m-80) outliers start: 15 outliers final: 10 residues processed: 135 average time/residue: 0.2271 time to fit residues: 41.4719 Evaluate side-chains 134 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.0970 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 81 optimal weight: 0.3980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8060 Z= 0.175 Angle : 0.501 6.482 10948 Z= 0.263 Chirality : 0.041 0.162 1261 Planarity : 0.003 0.031 1397 Dihedral : 3.877 17.925 1130 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.74 % Allowed : 12.45 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.27), residues: 1019 helix: 2.13 (0.26), residues: 428 sheet: -0.46 (0.33), residues: 215 loop : -1.58 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.003 0.001 HIS A 220 PHE 0.017 0.001 PHE R 310 TYR 0.025 0.001 TYR R 80 ARG 0.005 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6938 (mm) REVERT: R 191 GLU cc_start: 0.4766 (pp20) cc_final: 0.3907 (pm20) REVERT: R 234 ILE cc_start: 0.7925 (mm) cc_final: 0.7630 (pt) REVERT: R 331 TYR cc_start: 0.6022 (OUTLIER) cc_final: 0.5551 (t80) REVERT: A 31 GLN cc_start: 0.8005 (tp-100) cc_final: 0.7519 (tp-100) REVERT: A 372 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7596 (mp) REVERT: A 381 ASP cc_start: 0.8418 (t70) cc_final: 0.8142 (t0) REVERT: A 386 MET cc_start: 0.7546 (tmm) cc_final: 0.7290 (tmm) REVERT: B 55 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7989 (pt) REVERT: B 243 THR cc_start: 0.8605 (p) cc_final: 0.8352 (p) REVERT: B 262 MET cc_start: 0.7777 (ppp) cc_final: 0.7438 (ptm) REVERT: B 264 TYR cc_start: 0.8505 (m-80) cc_final: 0.7908 (m-80) REVERT: N 32 TYR cc_start: 0.8703 (m-80) cc_final: 0.8376 (m-80) outliers start: 22 outliers final: 10 residues processed: 145 average time/residue: 0.2077 time to fit residues: 40.7515 Evaluate side-chains 143 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 331 TYR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 75 GLN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8060 Z= 0.200 Angle : 0.514 6.748 10948 Z= 0.266 Chirality : 0.041 0.184 1261 Planarity : 0.003 0.029 1397 Dihedral : 3.872 17.993 1130 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.24 % Allowed : 13.82 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.27), residues: 1019 helix: 2.25 (0.26), residues: 421 sheet: -0.31 (0.34), residues: 209 loop : -1.53 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 220 PHE 0.016 0.001 PHE R 310 TYR 0.026 0.001 TYR R 80 ARG 0.005 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7174 (mm) REVERT: R 191 GLU cc_start: 0.4784 (pp20) cc_final: 0.3930 (pm20) REVERT: R 234 ILE cc_start: 0.7939 (mm) cc_final: 0.7638 (pt) REVERT: R 331 TYR cc_start: 0.6145 (OUTLIER) cc_final: 0.5632 (t80) REVERT: A 31 GLN cc_start: 0.8031 (tp-100) cc_final: 0.7547 (tp-100) REVERT: A 60 MET cc_start: 0.4915 (ptt) cc_final: 0.4274 (ptt) REVERT: A 381 ASP cc_start: 0.8411 (t70) cc_final: 0.8112 (t0) REVERT: B 55 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8000 (pt) REVERT: B 243 THR cc_start: 0.8611 (p) cc_final: 0.8329 (p) REVERT: B 262 MET cc_start: 0.7801 (ppp) cc_final: 0.7534 (ptm) REVERT: B 264 TYR cc_start: 0.8534 (m-80) cc_final: 0.7920 (m-80) REVERT: N 32 TYR cc_start: 0.8729 (m-80) cc_final: 0.8361 (m-80) outliers start: 26 outliers final: 17 residues processed: 137 average time/residue: 0.2183 time to fit residues: 40.5745 Evaluate side-chains 139 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 331 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.0980 chunk 19 optimal weight: 7.9990 chunk 57 optimal weight: 0.4980 chunk 24 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8060 Z= 0.186 Angle : 0.507 9.228 10948 Z= 0.262 Chirality : 0.040 0.141 1261 Planarity : 0.003 0.029 1397 Dihedral : 3.831 17.800 1130 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.74 % Allowed : 15.82 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.27), residues: 1019 helix: 2.27 (0.26), residues: 421 sheet: -0.26 (0.34), residues: 209 loop : -1.54 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.001 PHE R 310 TYR 0.025 0.001 TYR R 80 ARG 0.006 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.6946 (mm) REVERT: R 120 MET cc_start: 0.6891 (mmm) cc_final: 0.6567 (mmt) REVERT: R 191 GLU cc_start: 0.4767 (pp20) cc_final: 0.3856 (pm20) REVERT: R 234 ILE cc_start: 0.7936 (mm) cc_final: 0.7643 (pt) REVERT: R 331 TYR cc_start: 0.6185 (OUTLIER) cc_final: 0.5688 (t80) REVERT: A 31 GLN cc_start: 0.8036 (tp-100) cc_final: 0.7552 (tp-100) REVERT: A 60 MET cc_start: 0.5256 (ptt) cc_final: 0.4983 (ptt) REVERT: A 381 ASP cc_start: 0.8404 (t70) cc_final: 0.8134 (t0) REVERT: B 55 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7963 (pt) REVERT: B 243 THR cc_start: 0.8615 (p) cc_final: 0.8326 (p) REVERT: B 262 MET cc_start: 0.7799 (ppp) cc_final: 0.7437 (ptm) REVERT: B 264 TYR cc_start: 0.8500 (m-80) cc_final: 0.7880 (m-80) REVERT: N 32 TYR cc_start: 0.8713 (m-80) cc_final: 0.8356 (m-80) REVERT: N 120 GLN cc_start: 0.7689 (mm-40) cc_final: 0.7100 (mm110) outliers start: 22 outliers final: 16 residues processed: 134 average time/residue: 0.2024 time to fit residues: 36.8069 Evaluate side-chains 141 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 331 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 0.0770 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 97 optimal weight: 0.2980 chunk 60 optimal weight: 0.0970 chunk 59 optimal weight: 0.0770 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN B 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8060 Z= 0.124 Angle : 0.484 9.713 10948 Z= 0.250 Chirality : 0.039 0.140 1261 Planarity : 0.003 0.030 1397 Dihedral : 3.647 16.508 1130 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.62 % Allowed : 16.06 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.27), residues: 1019 helix: 2.38 (0.26), residues: 422 sheet: -0.18 (0.34), residues: 215 loop : -1.42 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.002 0.000 HIS A 357 PHE 0.014 0.001 PHE R 310 TYR 0.026 0.001 TYR R 80 ARG 0.008 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.6909 (mm) REVERT: R 120 MET cc_start: 0.6947 (mmm) cc_final: 0.6632 (mmt) REVERT: R 191 GLU cc_start: 0.4767 (pp20) cc_final: 0.3819 (pm20) REVERT: R 234 ILE cc_start: 0.7888 (mm) cc_final: 0.7604 (pt) REVERT: R 331 TYR cc_start: 0.6103 (OUTLIER) cc_final: 0.5694 (t80) REVERT: A 27 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6888 (tp30) REVERT: A 31 GLN cc_start: 0.8006 (tp-100) cc_final: 0.7543 (tp-100) REVERT: B 55 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.8005 (pp) REVERT: B 234 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.7544 (t80) REVERT: B 243 THR cc_start: 0.8592 (p) cc_final: 0.8324 (p) REVERT: B 262 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7340 (ptm) REVERT: B 264 TYR cc_start: 0.8388 (m-80) cc_final: 0.7787 (m-80) REVERT: N 32 TYR cc_start: 0.8602 (m-80) cc_final: 0.8351 (m-80) outliers start: 21 outliers final: 12 residues processed: 147 average time/residue: 0.2143 time to fit residues: 43.1063 Evaluate side-chains 145 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 331 TYR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 88 optimal weight: 0.1980 chunk 93 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8060 Z= 0.181 Angle : 0.502 9.658 10948 Z= 0.260 Chirality : 0.040 0.140 1261 Planarity : 0.003 0.029 1397 Dihedral : 3.711 16.732 1130 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.86 % Allowed : 16.81 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.27), residues: 1019 helix: 2.39 (0.26), residues: 422 sheet: -0.04 (0.34), residues: 204 loop : -1.47 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE R 310 TYR 0.027 0.001 TYR R 80 ARG 0.007 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: R 88 LEU cc_start: 0.7512 (mm) cc_final: 0.7220 (mm) REVERT: R 92 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7046 (mm) REVERT: R 191 GLU cc_start: 0.4759 (pp20) cc_final: 0.3816 (pm20) REVERT: R 234 ILE cc_start: 0.7922 (mm) cc_final: 0.7625 (pt) REVERT: R 331 TYR cc_start: 0.6187 (OUTLIER) cc_final: 0.5740 (t80) REVERT: A 31 GLN cc_start: 0.8023 (tp-100) cc_final: 0.7757 (tp-100) REVERT: B 55 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8065 (pp) REVERT: B 234 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.7603 (t80) REVERT: B 243 THR cc_start: 0.8624 (p) cc_final: 0.8323 (p) REVERT: B 262 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7503 (ptm) REVERT: N 32 TYR cc_start: 0.8756 (m-80) cc_final: 0.8416 (m-80) REVERT: N 46 GLU cc_start: 0.8230 (pt0) cc_final: 0.7956 (pt0) outliers start: 23 outliers final: 17 residues processed: 142 average time/residue: 0.1838 time to fit residues: 36.6643 Evaluate side-chains 145 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 331 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 chunk 95 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8060 Z= 0.188 Angle : 0.524 9.405 10948 Z= 0.269 Chirality : 0.040 0.142 1261 Planarity : 0.003 0.032 1397 Dihedral : 3.749 16.987 1130 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.11 % Allowed : 17.31 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.27), residues: 1019 helix: 2.40 (0.26), residues: 421 sheet: -0.00 (0.34), residues: 199 loop : -1.50 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE R 310 TYR 0.025 0.001 TYR R 80 ARG 0.008 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.6897 (mm) REVERT: R 191 GLU cc_start: 0.4733 (pp20) cc_final: 0.3817 (pm20) REVERT: R 234 ILE cc_start: 0.7894 (mm) cc_final: 0.7598 (pt) REVERT: R 331 TYR cc_start: 0.6264 (OUTLIER) cc_final: 0.5802 (t80) REVERT: A 31 GLN cc_start: 0.8212 (tp-100) cc_final: 0.7760 (tp-100) REVERT: B 55 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8085 (pp) REVERT: B 234 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.7668 (t80) REVERT: B 243 THR cc_start: 0.8620 (p) cc_final: 0.8321 (p) REVERT: B 262 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7443 (ptm) REVERT: B 264 TYR cc_start: 0.8484 (m-80) cc_final: 0.7862 (m-80) REVERT: N 32 TYR cc_start: 0.8778 (m-80) cc_final: 0.8408 (m-80) outliers start: 25 outliers final: 18 residues processed: 139 average time/residue: 0.1964 time to fit residues: 37.6677 Evaluate side-chains 145 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 331 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 100 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8060 Z= 0.194 Angle : 0.528 11.979 10948 Z= 0.270 Chirality : 0.041 0.190 1261 Planarity : 0.003 0.033 1397 Dihedral : 3.773 16.779 1130 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.86 % Allowed : 17.93 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.27), residues: 1019 helix: 2.40 (0.26), residues: 421 sheet: -0.03 (0.34), residues: 205 loop : -1.46 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE R 310 TYR 0.025 0.001 TYR R 80 ARG 0.008 0.000 ARG A 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.6813 (mm) REVERT: R 191 GLU cc_start: 0.4735 (pp20) cc_final: 0.3808 (pm20) REVERT: R 234 ILE cc_start: 0.7895 (mm) cc_final: 0.7588 (pt) REVERT: R 331 TYR cc_start: 0.6281 (OUTLIER) cc_final: 0.5807 (t80) REVERT: A 31 GLN cc_start: 0.8214 (tp-100) cc_final: 0.7761 (tp-100) REVERT: A 381 ASP cc_start: 0.8375 (t70) cc_final: 0.8095 (t0) REVERT: B 44 GLN cc_start: 0.7836 (tp40) cc_final: 0.7491 (mt0) REVERT: B 55 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8025 (pp) REVERT: B 234 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.7671 (t80) REVERT: B 243 THR cc_start: 0.8618 (p) cc_final: 0.8329 (p) REVERT: B 262 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7442 (ptm) REVERT: B 264 TYR cc_start: 0.8492 (m-80) cc_final: 0.7870 (m-80) REVERT: N 32 TYR cc_start: 0.8780 (m-80) cc_final: 0.8404 (m-80) outliers start: 23 outliers final: 18 residues processed: 139 average time/residue: 0.1973 time to fit residues: 37.7467 Evaluate side-chains 147 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 331 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 33 optimal weight: 0.3980 chunk 82 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 57 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: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.183977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.141905 restraints weight = 9108.345| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.73 r_work: 0.3290 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8060 Z= 0.207 Angle : 0.536 11.942 10948 Z= 0.275 Chirality : 0.041 0.155 1261 Planarity : 0.003 0.034 1397 Dihedral : 3.807 17.209 1130 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.99 % Allowed : 18.18 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.27), residues: 1019 helix: 2.39 (0.26), residues: 421 sheet: 0.06 (0.35), residues: 199 loop : -1.48 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE R 310 TYR 0.025 0.001 TYR R 80 ARG 0.008 0.000 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1929.92 seconds wall clock time: 35 minutes 45.81 seconds (2145.81 seconds total)