Starting phenix.real_space_refine on Fri Dec 8 08:58:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8itm_35707/12_2023/8itm_35707.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8itm_35707/12_2023/8itm_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_35707/12_2023/8itm_35707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8itm_35707/12_2023/8itm_35707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8itm_35707/12_2023/8itm_35707.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8itm_35707/12_2023/8itm_35707.pdb" } 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 Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 138": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 4.72, 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 - 3.50 Amino acid : False - 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: 3.21 Conformation dependent library (CDL) restraints added in 1.5 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: 0.83 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: 2.56 Time building geometry restraints manager: 3.41 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: 97.56 - 104.85: 90 104.85 - 112.15: 4068 112.15 - 119.44: 2527 119.44 - 126.73: 4146 126.73 - 134.03: 117 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 2.440 nonbonded pdb=" O CYS B 204 " pdb=" OH TYR N 117 " model vdw 2.234 2.440 nonbonded pdb=" O GLY B 310 " pdb=" NZ LYS B 337 " model vdw 2.257 2.520 nonbonded pdb=" NZ LYS B 57 " pdb=" OH TYR B 59 " model vdw 2.260 2.520 nonbonded pdb=" OG SER R 118 " pdb=" OD1 ASN R 169 " model vdw 2.270 2.440 ... (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 ========== 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: 1.470 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: 4.000 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.100 Find NCS groups from input model: 0.220 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.730 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.883 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2344 time to fit residues: 43.3582 Evaluate side-chains 119 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.879 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2108 ------------------------------------------------------------------------------- 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: 1.9990 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 0.0040 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 109 ASN A 31 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8060 Z= 0.216 Angle : 0.542 6.557 10948 Z= 0.285 Chirality : 0.041 0.142 1261 Planarity : 0.003 0.030 1397 Dihedral : 4.078 18.961 1130 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.62 % Allowed : 9.09 % Favored : 89.29 % 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: 0.26 (0.27), residues: 1019 helix: 1.99 (0.26), residues: 424 sheet: -0.65 (0.34), residues: 219 loop : -1.46 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.004 0.001 HIS A 220 PHE 0.016 0.001 PHE R 310 TYR 0.028 0.001 TYR R 80 ARG 0.004 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 138 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 0.896 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 131 average time/residue: 0.2205 time to fit residues: 38.8978 Evaluate side-chains 129 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 0.903 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0742 time to fit residues: 2.7561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 0.0970 chunk 73 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8060 Z= 0.275 Angle : 0.544 6.569 10948 Z= 0.285 Chirality : 0.042 0.147 1261 Planarity : 0.003 0.030 1397 Dihedral : 4.094 19.436 1130 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.37 % Allowed : 11.58 % Favored : 87.05 % 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: 0.19 (0.27), residues: 1019 helix: 1.91 (0.26), residues: 428 sheet: -0.59 (0.34), residues: 215 loop : -1.55 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.005 0.001 HIS A 220 PHE 0.016 0.002 PHE R 310 TYR 0.028 0.002 TYR B 59 ARG 0.004 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 136 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 0.953 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 130 average time/residue: 0.2036 time to fit residues: 36.1668 Evaluate side-chains 123 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0858 time to fit residues: 2.1108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 0.2980 chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7439 moved from start: 0.1279 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= 0.192 Angle : 0.499 6.587 10948 Z= 0.264 Chirality : 0.040 0.147 1261 Planarity : 0.003 0.030 1397 Dihedral : 3.961 18.303 1130 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.87 % Allowed : 13.82 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.27), residues: 1019 helix: 2.02 (0.26), residues: 430 sheet: -0.49 (0.33), residues: 221 loop : -1.53 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 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 0.005 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 140 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 0.880 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 136 average time/residue: 0.2173 time to fit residues: 39.5257 Evaluate side-chains 127 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 0.884 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0727 time to fit residues: 2.1607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 83 optimal weight: 0.0030 chunk 67 optimal weight: 2.9990 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: 0.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 109 ASN A 31 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1391 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= 0.171 Angle : 0.497 6.538 10948 Z= 0.262 Chirality : 0.040 0.144 1261 Planarity : 0.003 0.030 1397 Dihedral : 3.855 17.573 1130 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.62 % Allowed : 16.31 % Favored : 83.06 % 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: 0.46 (0.27), residues: 1019 helix: 2.14 (0.26), residues: 426 sheet: -0.38 (0.34), residues: 215 loop : -1.44 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.003 0.001 HIS A 357 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 133 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 0.903 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 132 average time/residue: 0.2131 time to fit residues: 37.9804 Evaluate side-chains 123 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 0.821 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0716 time to fit residues: 1.5515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.5980 chunk 19 optimal weight: 20.0000 chunk 57 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 32 optimal weight: 0.0170 chunk 51 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** 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: 0.7418 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8060 Z= 0.162 Angle : 0.488 6.494 10948 Z= 0.256 Chirality : 0.040 0.141 1261 Planarity : 0.003 0.030 1397 Dihedral : 3.793 17.042 1130 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.75 % Allowed : 17.93 % 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: 0.56 (0.27), residues: 1019 helix: 2.19 (0.26), residues: 427 sheet: -0.22 (0.34), residues: 216 loop : -1.46 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.003 0.000 HIS A 357 PHE 0.016 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 133 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 0.803 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 129 average time/residue: 0.2123 time to fit residues: 36.9492 Evaluate side-chains 125 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 0.826 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0743 time to fit residues: 1.7937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 0.0770 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 58 optimal weight: 0.3980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7421 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8060 Z= 0.174 Angle : 0.511 9.225 10948 Z= 0.266 Chirality : 0.040 0.145 1261 Planarity : 0.003 0.030 1397 Dihedral : 3.785 16.842 1130 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.75 % Allowed : 18.80 % Favored : 80.45 % 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: 0.59 (0.27), residues: 1019 helix: 2.22 (0.26), residues: 427 sheet: -0.20 (0.33), residues: 216 loop : -1.43 (0.31), residues: 376 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 0.016 0.001 PHE R 310 TYR 0.025 0.001 TYR R 80 ARG 0.006 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 131 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 125 time to evaluate : 0.965 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 126 average time/residue: 0.2113 time to fit residues: 36.5954 Evaluate side-chains 127 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 123 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0785 time to fit residues: 1.8512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 76 optimal weight: 0.0870 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7421 moved from start: 0.1655 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= 0.179 Angle : 0.510 8.910 10948 Z= 0.266 Chirality : 0.040 0.166 1261 Planarity : 0.003 0.030 1397 Dihedral : 3.777 16.782 1130 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.75 % Allowed : 18.80 % Favored : 80.45 % 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: 0.60 (0.27), residues: 1019 helix: 2.20 (0.26), residues: 427 sheet: -0.18 (0.34), residues: 216 loop : -1.40 (0.31), residues: 376 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 0.016 0.001 PHE R 310 TYR 0.026 0.001 TYR R 80 ARG 0.008 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 129 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 0.916 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 125 average time/residue: 0.2066 time to fit residues: 35.6742 Evaluate side-chains 122 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0816 time to fit residues: 1.8223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 59 optimal weight: 0.0980 chunk 95 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1681 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= 0.192 Angle : 0.519 8.862 10948 Z= 0.271 Chirality : 0.040 0.142 1261 Planarity : 0.003 0.031 1397 Dihedral : 3.807 17.153 1130 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.12 % Allowed : 19.80 % Favored : 80.07 % 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: 0.59 (0.27), residues: 1019 helix: 2.19 (0.26), residues: 427 sheet: -0.19 (0.34), residues: 216 loop : -1.42 (0.31), residues: 376 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 0.016 0.001 PHE R 310 TYR 0.026 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 128 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 0.937 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.2184 time to fit residues: 38.2216 Evaluate side-chains 120 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.981 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 100 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 109 ASN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8060 Z= 0.309 Angle : 0.581 8.892 10948 Z= 0.302 Chirality : 0.042 0.146 1261 Planarity : 0.004 0.033 1397 Dihedral : 4.055 18.620 1130 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.25 % Allowed : 20.17 % 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: 0.47 (0.27), residues: 1019 helix: 2.11 (0.26), residues: 422 sheet: -0.22 (0.34), residues: 209 loop : -1.45 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.016 0.002 PHE R 310 TYR 0.025 0.002 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 122 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 0.890 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 120 average time/residue: 0.2002 time to fit residues: 33.4273 Evaluate side-chains 120 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 0.943 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1019 time to fit residues: 1.6368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 14 optimal weight: 7.9990 chunk 70 optimal weight: 0.0980 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 31 GLN ** B 13 GLN ** 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 = 0.4077 r_free = 0.4077 target = 0.183471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.141634 restraints weight = 9113.477| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.66 r_work: 0.3294 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8060 Z= 0.180 Angle : 0.526 8.714 10948 Z= 0.274 Chirality : 0.040 0.142 1261 Planarity : 0.003 0.035 1397 Dihedral : 3.891 16.719 1130 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.25 % Allowed : 20.55 % 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: 0.58 (0.27), residues: 1019 helix: 2.24 (0.26), residues: 422 sheet: -0.18 (0.34), residues: 209 loop : -1.43 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.003 0.001 HIS A 357 PHE 0.016 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: 1944.89 seconds wall clock time: 36 minutes 1.18 seconds (2161.18 seconds total)