Starting phenix.real_space_refine on Fri Mar 15 02:03:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdz_14678/03_2024/7zdz_14678.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdz_14678/03_2024/7zdz_14678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdz_14678/03_2024/7zdz_14678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdz_14678/03_2024/7zdz_14678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdz_14678/03_2024/7zdz_14678.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdz_14678/03_2024/7zdz_14678.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians Sr 2 13.11 5 K 1 8.98 5 S 79 5.16 5 C 6687 2.51 5 N 1736 2.21 5 O 1864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 312": "NH1" <-> "NH2" Residue "A GLU 363": "OE1" <-> "OE2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B ARG 312": "NH1" <-> "NH2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C GLU 332": "OE1" <-> "OE2" Residue "D GLU 319": "OE1" <-> "OE2" Residue "D GLU 363": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10369 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2611 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "B" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2575 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 8, 'TRANS': 312} Chain: "C" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2572 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 8, 'TRANS': 312} Chain: "D" Number of atoms: 2608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2608 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' SR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' SR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.78, per 1000 atoms: 0.56 Number of scatterers: 10369 At special positions: 0 Unit cell: (99.76, 96.32, 132.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Sr 2 37.98 K 1 19.00 S 79 16.00 O 1864 8.00 N 1736 7.00 C 6687 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 154 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 154 " distance=2.03 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 154 " distance=2.03 Simple disulfide: pdb=" SG CYS D 122 " - pdb=" SG CYS D 154 " 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: 4.18 Conformation dependent library (CDL) restraints added in 1.8 seconds 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2448 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 19 sheets defined 31.3% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 72 through 79 Processing helix chain 'A' and resid 83 through 110 Processing helix chain 'A' and resid 128 through 141 Processing helix chain 'A' and resid 154 through 185 removed outlier: 3.909A pdb=" N LYS A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 290 removed outlier: 3.542A pdb=" N ILE A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 366 removed outlier: 3.910A pdb=" N TYR A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 64 removed outlier: 4.212A pdb=" N LYS B 64 " --> pdb=" O VAL B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 removed outlier: 3.688A pdb=" N ILE B 79 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG B 80 " --> pdb=" O CYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 115 removed outlier: 3.849A pdb=" N LEU B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 141 Processing helix chain 'B' and resid 154 through 185 Processing helix chain 'B' and resid 283 through 290 removed outlier: 3.535A pdb=" N ILE B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 344 Processing helix chain 'C' and resid 73 through 79 Processing helix chain 'C' and resid 83 through 111 Processing helix chain 'C' and resid 128 through 141 removed outlier: 3.832A pdb=" N ALA C 132 " --> pdb=" O SER C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 181 removed outlier: 3.643A pdb=" N VAL C 158 " --> pdb=" O CYS C 154 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 181 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 340 through 344 removed outlier: 4.392A pdb=" N ARG C 343 " --> pdb=" O ASP C 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 110 removed outlier: 4.712A pdb=" N THR D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N CYS D 76 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG D 80 " --> pdb=" O CYS D 76 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N TRP D 81 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ARG D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TRP D 83 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET D 84 " --> pdb=" O ARG D 80 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU D 85 " --> pdb=" O TRP D 81 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL D 86 " --> pdb=" O ARG D 82 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 115 Processing helix chain 'D' and resid 129 through 141 Processing helix chain 'D' and resid 154 through 184 removed outlier: 4.169A pdb=" N VAL D 158 " --> pdb=" O CYS D 154 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N PHE D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'D' and resid 357 through 364 removed outlier: 3.941A pdb=" N LEU D 361 " --> pdb=" O SER D 357 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA D 362 " --> pdb=" O ALA D 358 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 193 through 194 Processing sheet with id=AA2, first strand: chain 'A' and resid 268 through 269 removed outlier: 3.703A pdb=" N TRP A 212 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 222 through 223 Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 249 removed outlier: 4.587A pdb=" N ARG A 235 " --> pdb=" O PRO A 244 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 293 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 313 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 58 removed outlier: 6.610A pdb=" N GLN B 57 " --> pdb=" O VAL C 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 202 through 204 Processing sheet with id=AA7, first strand: chain 'B' and resid 222 through 223 Processing sheet with id=AA8, first strand: chain 'B' and resid 242 through 249 removed outlier: 5.201A pdb=" N ARG B 235 " --> pdb=" O PRO B 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 324 through 325 Processing sheet with id=AB1, first strand: chain 'B' and resid 330 through 333 Processing sheet with id=AB2, first strand: chain 'C' and resid 194 through 195 removed outlier: 3.551A pdb=" N VAL C 200 " --> pdb=" O MET C 211 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 194 through 195 Processing sheet with id=AB4, first strand: chain 'C' and resid 242 through 249 removed outlier: 4.080A pdb=" N LEU C 245 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS C 233 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN C 247 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C 231 " --> pdb=" O GLN C 247 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASP C 249 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALA C 229 " --> pdb=" O ASP C 249 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLU C 224 " --> pdb=" O MET C 301 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N MET C 301 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU C 299 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AB6, first strand: chain 'D' and resid 193 through 195 removed outlier: 3.908A pdb=" N VAL D 200 " --> pdb=" O MET D 211 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 193 through 195 Processing sheet with id=AB8, first strand: chain 'D' and resid 242 through 249 removed outlier: 5.281A pdb=" N ARG D 235 " --> pdb=" O PRO D 244 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU D 293 " --> pdb=" O LEU D 232 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE D 294 " --> pdb=" O TYR D 315 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR D 315 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER D 313 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 300 through 301 Processing sheet with id=AC1, first strand: chain 'D' and resid 324 through 325 389 hydrogen bonds defined for protein. 1086 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: 2.77 Time building geometry restraints manager: 4.54 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: 3293 1.34 - 1.46: 1831 1.46 - 1.58: 5368 1.58 - 1.70: 0 1.70 - 1.81: 111 Bond restraints: 10603 Sorted by residual: bond pdb=" CA TYR C 68 " pdb=" C TYR C 68 " ideal model delta sigma weight residual 1.523 1.469 0.054 1.34e-02 5.57e+03 1.65e+01 bond pdb=" N ILE C 72 " pdb=" CA ILE C 72 " ideal model delta sigma weight residual 1.459 1.413 0.046 1.25e-02 6.40e+03 1.38e+01 bond pdb=" CA ASP C 71 " pdb=" C ASP C 71 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.34e-02 5.57e+03 9.80e+00 bond pdb=" CA LEU C 69 " pdb=" C LEU C 69 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.34e-02 5.57e+03 8.86e+00 bond pdb=" CA TYR D 280 " pdb=" C TYR D 280 " ideal model delta sigma weight residual 1.522 1.485 0.038 1.37e-02 5.33e+03 7.62e+00 ... (remaining 10598 not shown) Histogram of bond angle deviations from ideal: 96.05 - 103.66: 100 103.66 - 111.26: 4203 111.26 - 118.86: 4319 118.86 - 126.47: 5566 126.47 - 134.07: 165 Bond angle restraints: 14353 Sorted by residual: angle pdb=" N ASN A 127 " pdb=" CA ASN A 127 " pdb=" C ASN A 127 " ideal model delta sigma weight residual 112.03 96.05 15.98 1.31e+00 5.83e-01 1.49e+02 angle pdb=" N LYS B 334 " pdb=" CA LYS B 334 " pdb=" C LYS B 334 " ideal model delta sigma weight residual 108.67 98.31 10.36 1.67e+00 3.59e-01 3.85e+01 angle pdb=" N HIS C 335 " pdb=" CA HIS C 335 " pdb=" C HIS C 335 " ideal model delta sigma weight residual 113.17 105.47 7.70 1.26e+00 6.30e-01 3.73e+01 angle pdb=" N VAL D 264 " pdb=" CA VAL D 264 " pdb=" C VAL D 264 " ideal model delta sigma weight residual 113.71 108.30 5.41 9.50e-01 1.11e+00 3.25e+01 angle pdb=" C ILE C 72 " pdb=" N PHE C 73 " pdb=" CA PHE C 73 " ideal model delta sigma weight residual 121.54 110.92 10.62 1.91e+00 2.74e-01 3.09e+01 ... (remaining 14348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 5502 17.00 - 33.99: 619 33.99 - 50.99: 136 50.99 - 67.99: 15 67.99 - 84.98: 11 Dihedral angle restraints: 6283 sinusoidal: 2506 harmonic: 3777 Sorted by residual: dihedral pdb=" CB CYS C 122 " pdb=" SG CYS C 122 " pdb=" SG CYS C 154 " pdb=" CB CYS C 154 " ideal model delta sinusoidal sigma weight residual 93.00 27.40 65.60 1 1.00e+01 1.00e-02 5.63e+01 dihedral pdb=" CB CYS D 122 " pdb=" SG CYS D 122 " pdb=" SG CYS D 154 " pdb=" CB CYS D 154 " ideal model delta sinusoidal sigma weight residual 93.00 143.20 -50.20 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CA TYR C 336 " pdb=" C TYR C 336 " pdb=" N TYR C 337 " pdb=" CA TYR C 337 " ideal model delta harmonic sigma weight residual -180.00 -158.34 -21.66 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 6280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1205 0.049 - 0.098: 313 0.098 - 0.147: 85 0.147 - 0.196: 6 0.196 - 0.245: 7 Chirality restraints: 1616 Sorted by residual: chirality pdb=" CA ARG C 312 " pdb=" N ARG C 312 " pdb=" C ARG C 312 " pdb=" CB ARG C 312 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA GLU B 303 " pdb=" N GLU B 303 " pdb=" C GLU B 303 " pdb=" CB GLU B 303 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ARG A 312 " pdb=" N ARG A 312 " pdb=" C ARG A 312 " pdb=" CB ARG A 312 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1613 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 96 " -0.029 2.00e-02 2.50e+03 2.37e-02 1.40e+01 pdb=" CG TRP C 96 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP C 96 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 96 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 96 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 96 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 96 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 96 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 96 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 96 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 333 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.22e+00 pdb=" C GLU C 333 " -0.046 2.00e-02 2.50e+03 pdb=" O GLU C 333 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS C 334 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 96 " -0.021 2.00e-02 2.50e+03 1.68e-02 7.05e+00 pdb=" CG TRP D 96 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP D 96 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP D 96 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 96 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 96 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 96 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 96 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 96 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 96 " 0.002 2.00e-02 2.50e+03 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.78: 2205 2.78 - 3.37: 11861 3.37 - 3.96: 18161 3.96 - 4.55: 23246 4.55 - 5.14: 35191 Nonbonded interactions: 90664 Sorted by model distance: nonbonded pdb=" O ARG C 67 " pdb=" C TYR C 68 " model vdw 2.192 3.270 nonbonded pdb=" O ARG D 325 " pdb=" OG1 THR D 347 " model vdw 2.228 2.440 nonbonded pdb=" NH2 ARG D 46 " pdb=" OD2 ASP D 51 " model vdw 2.261 2.520 nonbonded pdb=" O ILE C 137 " pdb=" OG1 THR C 141 " model vdw 2.262 2.440 nonbonded pdb=" O VAL C 61 " pdb=" OH TYR D 341 " model vdw 2.281 2.440 ... (remaining 90659 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 44 through 363) selection = (chain 'B' and resid 44 through 363) selection = (chain 'C' and resid 44 through 363) selection = (chain 'D' and resid 44 through 363) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 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: 2.350 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 29.800 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10603 Z= 0.225 Angle : 0.860 15.979 14353 Z= 0.503 Chirality : 0.048 0.245 1616 Planarity : 0.004 0.032 1808 Dihedral : 15.046 84.983 3823 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.14 % Favored : 88.55 % Rotamer: Outliers : 0.35 % Allowed : 1.14 % Favored : 98.50 % 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: -1.61 (0.23), residues: 1284 helix: 1.13 (0.27), residues: 367 sheet: -1.09 (0.39), residues: 157 loop : -2.32 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP C 96 HIS 0.008 0.001 HIS D 221 PHE 0.029 0.002 PHE D 103 TYR 0.019 0.001 TYR C 337 ARG 0.006 0.000 ARG C 312 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 259 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8594 (tm-30) REVERT: A 211 MET cc_start: 0.3964 (ttm) cc_final: 0.3406 (ttm) REVERT: A 247 GLN cc_start: 0.7961 (mp10) cc_final: 0.7543 (mp10) REVERT: A 295 VAL cc_start: 0.9078 (t) cc_final: 0.8826 (m) REVERT: B 134 LEU cc_start: 0.8661 (tt) cc_final: 0.8427 (tt) REVERT: B 360 ASP cc_start: 0.8541 (m-30) cc_final: 0.8277 (m-30) REVERT: C 211 MET cc_start: 0.4424 (ptm) cc_final: 0.3492 (ptm) REVERT: C 310 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7933 (tm-30) REVERT: C 312 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8621 (mtt180) REVERT: D 103 PHE cc_start: 0.7728 (m-80) cc_final: 0.7405 (m-80) REVERT: D 160 MET cc_start: 0.7867 (ttt) cc_final: 0.7550 (tpt) REVERT: D 285 GLN cc_start: 0.8382 (pp30) cc_final: 0.8008 (pp30) REVERT: D 299 GLU cc_start: 0.7847 (pt0) cc_final: 0.7631 (pp20) REVERT: D 341 TYR cc_start: 0.5369 (p90) cc_final: 0.5123 (p90) outliers start: 4 outliers final: 1 residues processed: 262 average time/residue: 0.1833 time to fit residues: 71.0338 Evaluate side-chains 228 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 226 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 HIS ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10603 Z= 0.383 Angle : 0.726 6.782 14353 Z= 0.396 Chirality : 0.047 0.160 1616 Planarity : 0.005 0.043 1808 Dihedral : 5.871 29.527 1397 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.33 % Favored : 85.44 % Rotamer: Outliers : 0.09 % Allowed : 10.65 % Favored : 89.26 % 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: -2.03 (0.23), residues: 1284 helix: 0.63 (0.26), residues: 366 sheet: -1.47 (0.39), residues: 161 loop : -2.48 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 96 HIS 0.012 0.002 HIS C 221 PHE 0.032 0.002 PHE D 133 TYR 0.019 0.002 TYR D 280 ARG 0.010 0.001 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 249 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 GLN cc_start: 0.8169 (mp10) cc_final: 0.7669 (mp10) REVERT: A 310 GLN cc_start: 0.8548 (pp30) cc_final: 0.8288 (pp30) REVERT: B 134 LEU cc_start: 0.8931 (tt) cc_final: 0.8701 (tp) REVERT: B 299 GLU cc_start: 0.8085 (tt0) cc_final: 0.7776 (tt0) REVERT: C 211 MET cc_start: 0.4923 (ptm) cc_final: 0.4170 (ptm) REVERT: C 216 ASN cc_start: 0.7803 (m110) cc_final: 0.7563 (m-40) REVERT: D 211 MET cc_start: 0.7085 (ptp) cc_final: 0.6729 (ptp) REVERT: D 285 GLN cc_start: 0.8415 (pp30) cc_final: 0.8031 (pp30) REVERT: D 331 PHE cc_start: 0.7926 (t80) cc_final: 0.7668 (t80) outliers start: 1 outliers final: 0 residues processed: 249 average time/residue: 0.1744 time to fit residues: 64.8078 Evaluate side-chains 215 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 96 optimal weight: 0.0980 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 39 optimal weight: 30.0000 chunk 93 optimal weight: 9.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10603 Z= 0.286 Angle : 0.681 7.935 14353 Z= 0.367 Chirality : 0.046 0.171 1616 Planarity : 0.004 0.034 1808 Dihedral : 5.785 27.234 1397 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.86 % Favored : 85.83 % Rotamer: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % 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: -2.07 (0.23), residues: 1284 helix: 0.56 (0.25), residues: 369 sheet: -1.30 (0.41), residues: 154 loop : -2.54 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 96 HIS 0.008 0.002 HIS C 221 PHE 0.027 0.002 PHE D 133 TYR 0.025 0.002 TYR C 337 ARG 0.010 0.001 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLN cc_start: 0.9036 (tm-30) cc_final: 0.8729 (tm-30) REVERT: A 247 GLN cc_start: 0.8217 (mp10) cc_final: 0.7669 (mp10) REVERT: B 360 ASP cc_start: 0.8421 (m-30) cc_final: 0.8126 (m-30) REVERT: C 82 ARG cc_start: 0.6268 (mtt90) cc_final: 0.5870 (mmm160) REVERT: C 189 ARG cc_start: 0.7135 (ptp90) cc_final: 0.6639 (ptp90) REVERT: C 211 MET cc_start: 0.4913 (ptm) cc_final: 0.4287 (ptm) REVERT: C 310 GLN cc_start: 0.8371 (tm-30) cc_final: 0.7917 (tm-30) REVERT: C 331 PHE cc_start: 0.8739 (m-80) cc_final: 0.8484 (m-80) REVERT: D 92 PHE cc_start: 0.7812 (t80) cc_final: 0.7578 (t80) REVERT: D 211 MET cc_start: 0.6975 (ptp) cc_final: 0.6696 (ptp) REVERT: D 285 GLN cc_start: 0.8484 (pp30) cc_final: 0.8069 (pp30) REVERT: D 331 PHE cc_start: 0.7854 (t80) cc_final: 0.7639 (t80) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.1957 time to fit residues: 78.0677 Evaluate side-chains 234 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS ** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10603 Z= 0.218 Angle : 0.643 8.197 14353 Z= 0.344 Chirality : 0.045 0.155 1616 Planarity : 0.004 0.051 1808 Dihedral : 5.536 28.091 1397 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.94 % Favored : 85.75 % Rotamer: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % 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: -1.94 (0.23), residues: 1284 helix: 0.80 (0.26), residues: 370 sheet: -1.03 (0.42), residues: 155 loop : -2.58 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 96 HIS 0.011 0.001 HIS D 271 PHE 0.031 0.002 PHE B 159 TYR 0.024 0.001 TYR C 337 ARG 0.006 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7597 (mmp-170) cc_final: 0.6739 (mmt-90) REVERT: A 164 GLN cc_start: 0.9022 (tm-30) cc_final: 0.8772 (tm-30) REVERT: B 341 TYR cc_start: 0.7603 (m-80) cc_final: 0.7324 (m-80) REVERT: B 360 ASP cc_start: 0.8468 (m-30) cc_final: 0.8136 (m-30) REVERT: C 82 ARG cc_start: 0.6283 (mtt90) cc_final: 0.5782 (mmm160) REVERT: C 160 MET cc_start: 0.8132 (ttp) cc_final: 0.7889 (ttm) REVERT: C 189 ARG cc_start: 0.7120 (ptp90) cc_final: 0.6489 (ttt180) REVERT: C 211 MET cc_start: 0.4859 (ptm) cc_final: 0.4210 (ptm) REVERT: C 310 GLN cc_start: 0.8393 (tm-30) cc_final: 0.7894 (tm-30) REVERT: C 331 PHE cc_start: 0.8736 (m-80) cc_final: 0.8521 (m-80) REVERT: D 160 MET cc_start: 0.8076 (ttt) cc_final: 0.7771 (tpp) REVERT: D 211 MET cc_start: 0.7070 (ptp) cc_final: 0.6766 (ptp) REVERT: D 285 GLN cc_start: 0.8453 (pp30) cc_final: 0.8067 (pp30) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.1894 time to fit residues: 75.3261 Evaluate side-chains 221 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 30.0000 chunk 111 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10603 Z= 0.400 Angle : 0.774 7.869 14353 Z= 0.422 Chirality : 0.050 0.216 1616 Planarity : 0.005 0.054 1808 Dihedral : 6.430 29.239 1397 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 0.31 % Allowed : 15.81 % Favored : 83.88 % Rotamer: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % 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: -2.42 (0.22), residues: 1284 helix: 0.05 (0.25), residues: 363 sheet: -1.24 (0.42), residues: 152 loop : -2.67 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 96 HIS 0.019 0.002 HIS B 271 PHE 0.052 0.003 PHE D 133 TYR 0.032 0.002 TYR C 337 ARG 0.016 0.001 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 HIS cc_start: 0.8152 (t-90) cc_final: 0.7526 (t-170) REVERT: B 164 GLN cc_start: 0.9079 (pp30) cc_final: 0.8852 (pp30) REVERT: B 360 ASP cc_start: 0.8432 (m-30) cc_final: 0.8050 (m-30) REVERT: C 160 MET cc_start: 0.8170 (ttp) cc_final: 0.7905 (ttm) REVERT: C 189 ARG cc_start: 0.6681 (ptp90) cc_final: 0.6336 (ttt180) REVERT: C 211 MET cc_start: 0.5230 (ptm) cc_final: 0.4682 (ptm) REVERT: C 216 ASN cc_start: 0.8100 (m110) cc_final: 0.7866 (m-40) REVERT: C 310 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8027 (tm-30) REVERT: D 160 MET cc_start: 0.8137 (ttt) cc_final: 0.7787 (tpp) REVERT: D 211 MET cc_start: 0.7202 (ptp) cc_final: 0.6865 (ptp) REVERT: D 285 GLN cc_start: 0.8534 (pp30) cc_final: 0.8101 (pp30) REVERT: D 331 PHE cc_start: 0.7917 (t80) cc_final: 0.7670 (t80) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.1895 time to fit residues: 72.4756 Evaluate side-chains 214 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 HIS C 110 HIS ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10603 Z= 0.224 Angle : 0.672 9.023 14353 Z= 0.359 Chirality : 0.046 0.191 1616 Planarity : 0.004 0.058 1808 Dihedral : 5.815 29.641 1397 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.86 % Favored : 85.83 % Rotamer: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % 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: -2.12 (0.22), residues: 1284 helix: 0.58 (0.25), residues: 362 sheet: -1.15 (0.43), residues: 149 loop : -2.62 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP D 96 HIS 0.012 0.002 HIS B 271 PHE 0.033 0.002 PHE D 133 TYR 0.023 0.002 TYR C 337 ARG 0.011 0.001 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7571 (mmp-170) cc_final: 0.6776 (mmt-90) REVERT: A 183 MET cc_start: 0.7637 (mmm) cc_final: 0.7414 (mtt) REVERT: B 164 GLN cc_start: 0.9079 (pp30) cc_final: 0.8846 (pp30) REVERT: B 293 GLU cc_start: 0.8197 (tp30) cc_final: 0.7956 (tp30) REVERT: B 360 ASP cc_start: 0.8420 (m-30) cc_final: 0.8087 (m-30) REVERT: C 160 MET cc_start: 0.8089 (ttp) cc_final: 0.7772 (ttm) REVERT: C 211 MET cc_start: 0.4886 (ptm) cc_final: 0.4369 (ptm) REVERT: C 331 PHE cc_start: 0.8703 (m-80) cc_final: 0.8462 (m-80) REVERT: D 103 PHE cc_start: 0.8030 (m-80) cc_final: 0.7786 (m-80) REVERT: D 160 MET cc_start: 0.8114 (ttt) cc_final: 0.7888 (tpp) REVERT: D 211 MET cc_start: 0.6929 (ptp) cc_final: 0.6670 (ptp) REVERT: D 285 GLN cc_start: 0.8568 (pp30) cc_final: 0.8056 (pp30) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.1892 time to fit residues: 77.0188 Evaluate side-chains 220 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 104 optimal weight: 0.0000 chunk 69 optimal weight: 0.8980 chunk 123 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS A 230 GLN B 110 HIS B 230 GLN B 335 HIS C 190 ASN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10603 Z= 0.173 Angle : 0.664 9.884 14353 Z= 0.347 Chirality : 0.046 0.228 1616 Planarity : 0.003 0.042 1808 Dihedral : 5.373 28.448 1397 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.62 % Favored : 87.07 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: -1.91 (0.23), residues: 1284 helix: 0.87 (0.26), residues: 368 sheet: -1.01 (0.42), residues: 148 loop : -2.58 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 96 HIS 0.008 0.001 HIS B 335 PHE 0.029 0.002 PHE A 88 TYR 0.020 0.001 TYR D 341 ARG 0.005 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.7661 (mmm) cc_final: 0.7441 (mtt) REVERT: B 164 GLN cc_start: 0.9045 (pp30) cc_final: 0.8834 (pp30) REVERT: B 293 GLU cc_start: 0.8140 (tp30) cc_final: 0.7892 (tp30) REVERT: B 360 ASP cc_start: 0.8470 (m-30) cc_final: 0.8089 (m-30) REVERT: C 164 GLN cc_start: 0.9018 (pp30) cc_final: 0.8757 (pp30) REVERT: C 211 MET cc_start: 0.4776 (ptm) cc_final: 0.4153 (ptm) REVERT: C 310 GLN cc_start: 0.8377 (tm-30) cc_final: 0.7705 (tm-30) REVERT: C 331 PHE cc_start: 0.8553 (m-80) cc_final: 0.8349 (m-80) REVERT: D 211 MET cc_start: 0.7008 (ptp) cc_final: 0.6625 (ptp) REVERT: D 285 GLN cc_start: 0.8505 (pp30) cc_final: 0.8063 (pp30) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.1831 time to fit residues: 76.3001 Evaluate side-chains 229 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10603 Z= 0.202 Angle : 0.674 9.176 14353 Z= 0.351 Chirality : 0.046 0.244 1616 Planarity : 0.004 0.056 1808 Dihedral : 5.369 28.059 1397 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.93 % Favored : 86.76 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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: -1.90 (0.23), residues: 1284 helix: 0.83 (0.26), residues: 368 sheet: -1.01 (0.41), residues: 152 loop : -2.54 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 96 HIS 0.012 0.001 HIS D 221 PHE 0.033 0.003 PHE A 92 TYR 0.020 0.001 TYR C 337 ARG 0.013 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.7504 (mmm) cc_final: 0.7053 (mmm) REVERT: A 363 GLU cc_start: 0.5713 (tp30) cc_final: 0.5455 (tp30) REVERT: B 293 GLU cc_start: 0.8151 (tp30) cc_final: 0.7951 (tp30) REVERT: B 360 ASP cc_start: 0.8438 (m-30) cc_final: 0.8124 (m-30) REVERT: C 103 PHE cc_start: 0.7506 (m-80) cc_final: 0.7030 (m-80) REVERT: C 211 MET cc_start: 0.4835 (ptm) cc_final: 0.4226 (ptm) REVERT: C 216 ASN cc_start: 0.7756 (m-40) cc_final: 0.7428 (t0) REVERT: C 310 GLN cc_start: 0.8413 (tm-30) cc_final: 0.7859 (tm-30) REVERT: C 331 PHE cc_start: 0.8609 (m-80) cc_final: 0.8383 (m-80) REVERT: D 103 PHE cc_start: 0.8053 (m-80) cc_final: 0.7613 (m-80) REVERT: D 211 MET cc_start: 0.7046 (ptp) cc_final: 0.6660 (ptp) REVERT: D 285 GLN cc_start: 0.8473 (pp30) cc_final: 0.8066 (pp30) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.1805 time to fit residues: 73.9655 Evaluate side-chains 228 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 7.9990 chunk 107 optimal weight: 0.4980 chunk 114 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN C 190 ASN C 216 ASN C 221 HIS C 324 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10603 Z= 0.178 Angle : 0.682 9.411 14353 Z= 0.352 Chirality : 0.045 0.144 1616 Planarity : 0.004 0.064 1808 Dihedral : 5.233 27.649 1397 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.92 % Favored : 87.85 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: -1.81 (0.23), residues: 1284 helix: 0.91 (0.26), residues: 371 sheet: -0.99 (0.38), residues: 174 loop : -2.53 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 96 HIS 0.008 0.001 HIS D 221 PHE 0.032 0.003 PHE B 159 TYR 0.021 0.001 TYR C 337 ARG 0.014 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.7482 (m-80) cc_final: 0.7267 (m-80) REVERT: A 307 MET cc_start: 0.7452 (mmm) cc_final: 0.7043 (mmm) REVERT: A 363 GLU cc_start: 0.5755 (tp30) cc_final: 0.5541 (tp30) REVERT: B 293 GLU cc_start: 0.8100 (tp30) cc_final: 0.7887 (tp30) REVERT: B 360 ASP cc_start: 0.8474 (m-30) cc_final: 0.8112 (m-30) REVERT: C 92 PHE cc_start: 0.7564 (t80) cc_final: 0.7160 (t80) REVERT: C 103 PHE cc_start: 0.7461 (m-80) cc_final: 0.7009 (m-80) REVERT: C 211 MET cc_start: 0.4654 (ptm) cc_final: 0.4046 (ptm) REVERT: C 310 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7484 (tm-30) REVERT: D 211 MET cc_start: 0.7001 (ptp) cc_final: 0.6572 (ptp) REVERT: D 285 GLN cc_start: 0.8451 (pp30) cc_final: 0.8111 (pp30) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.1804 time to fit residues: 73.3846 Evaluate side-chains 234 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10603 Z= 0.303 Angle : 0.743 8.666 14353 Z= 0.392 Chirality : 0.048 0.165 1616 Planarity : 0.004 0.072 1808 Dihedral : 5.848 29.173 1397 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.31 % Allowed : 14.72 % Favored : 84.97 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -2.10 (0.22), residues: 1284 helix: 0.57 (0.25), residues: 369 sheet: -1.16 (0.41), residues: 153 loop : -2.62 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP C 96 HIS 0.009 0.002 HIS D 221 PHE 0.034 0.003 PHE D 133 TYR 0.029 0.002 TYR C 337 ARG 0.015 0.001 ARG D 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.7934 (mmm) cc_final: 0.7573 (mmm) REVERT: A 363 GLU cc_start: 0.5651 (tp30) cc_final: 0.5419 (tp30) REVERT: B 164 GLN cc_start: 0.9143 (pp30) cc_final: 0.8919 (pp30) REVERT: B 293 GLU cc_start: 0.8313 (tp30) cc_final: 0.7985 (tp30) REVERT: B 360 ASP cc_start: 0.8437 (m-30) cc_final: 0.8117 (m-30) REVERT: C 103 PHE cc_start: 0.7542 (m-80) cc_final: 0.7228 (m-80) REVERT: C 211 MET cc_start: 0.5206 (ptm) cc_final: 0.4599 (ptm) REVERT: C 310 GLN cc_start: 0.8337 (tm-30) cc_final: 0.7670 (tm-30) REVERT: C 324 HIS cc_start: 0.8474 (m-70) cc_final: 0.8215 (m-70) REVERT: D 211 MET cc_start: 0.7241 (ptp) cc_final: 0.6813 (ptp) REVERT: D 285 GLN cc_start: 0.8485 (pp30) cc_final: 0.8142 (pp30) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.1750 time to fit residues: 71.7401 Evaluate side-chains 223 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 30.0000 chunk 93 optimal weight: 3.9990 chunk 14 optimal weight: 0.0070 chunk 28 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 104 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 HIS ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.180491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.146906 restraints weight = 22035.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.150346 restraints weight = 15886.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.152335 restraints weight = 11986.592| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10603 Z= 0.191 Angle : 0.707 9.508 14353 Z= 0.368 Chirality : 0.047 0.166 1616 Planarity : 0.004 0.053 1808 Dihedral : 5.487 28.636 1397 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.69 % Favored : 87.07 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -1.92 (0.23), residues: 1284 helix: 0.78 (0.26), residues: 372 sheet: -1.15 (0.39), residues: 170 loop : -2.54 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.102 0.002 TRP C 96 HIS 0.008 0.001 HIS B 335 PHE 0.032 0.002 PHE D 133 TYR 0.022 0.001 TYR C 337 ARG 0.011 0.000 ARG D 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2217.24 seconds wall clock time: 40 minutes 57.51 seconds (2457.51 seconds total)