Starting phenix.real_space_refine on Fri Feb 16 00:59:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sd0_25044/02_2024/7sd0_25044_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sd0_25044/02_2024/7sd0_25044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sd0_25044/02_2024/7sd0_25044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sd0_25044/02_2024/7sd0_25044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sd0_25044/02_2024/7sd0_25044_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sd0_25044/02_2024/7sd0_25044_updated.pdb" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6177 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Mn 2 7.51 5 P 3 5.49 5 Mg 1 5.21 5 S 40 5.16 5 C 4911 2.51 5 N 1316 2.21 5 O 1456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7729 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3930 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 25, 'TRANS': 473} Chain breaks: 1 Chain: "B" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1407 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 165} Chain: "C" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2357 Classifications: {'peptide': 292} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 278} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.73, per 1000 atoms: 0.61 Number of scatterers: 7729 At special positions: 0 Unit cell: (89.666, 85.476, 104.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 2 24.99 S 40 16.00 P 3 15.00 Mg 1 11.99 O 1456 8.00 N 1316 7.00 C 4911 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.30 Conformation dependent library (CDL) restraints added in 1.3 seconds 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 6 sheets defined 27.8% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 87 through 100 Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 232 through 236 removed outlier: 3.709A pdb=" N GLY A 235 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 removed outlier: 4.265A pdb=" N GLY A 258 " --> pdb=" O LYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.736A pdb=" N GLY A 281 " --> pdb=" O ASP A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 325 through 328 No H-bonds generated for 'chain 'A' and resid 325 through 328' Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.539A pdb=" N PHE A 354 " --> pdb=" O PRO A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 396 through 400 removed outlier: 4.368A pdb=" N GLY A 399 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 442 through 446 removed outlier: 3.553A pdb=" N GLY A 445 " --> pdb=" O HIS A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 468 Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 536 through 539 Processing helix chain 'A' and resid 558 through 563 Processing helix chain 'A' and resid 565 through 573 Processing helix chain 'B' and resid 26 through 35 Processing helix chain 'B' and resid 75 through 84 removed outlier: 5.168A pdb=" N GLU B 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET B 82 " --> pdb=" O GLU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 114 removed outlier: 4.555A pdb=" N ASP B 104 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG B 105 " --> pdb=" O GLU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'B' and resid 138 through 147 Processing helix chain 'B' and resid 164 through 177 removed outlier: 3.693A pdb=" N PHE B 168 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 32 through 48 removed outlier: 3.857A pdb=" N GLU C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE C 45 " --> pdb=" O LYS C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 78 removed outlier: 3.585A pdb=" N LEU C 73 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 74 " --> pdb=" O TYR C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 113 removed outlier: 3.549A pdb=" N ILE C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 126 No H-bonds generated for 'chain 'C' and resid 124 through 126' Processing helix chain 'C' and resid 130 through 133 No H-bonds generated for 'chain 'C' and resid 130 through 133' Processing helix chain 'C' and resid 136 through 143 removed outlier: 3.549A pdb=" N LYS C 141 " --> pdb=" O TYR C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 158 removed outlier: 4.107A pdb=" N CYS C 158 " --> pdb=" O ASP C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 188 Processing helix chain 'C' and resid 200 through 206 removed outlier: 3.622A pdb=" N LEU C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 239 removed outlier: 3.571A pdb=" N ALA C 233 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing sheet with id= A, first strand: chain 'A' and resid 104 through 106 removed outlier: 6.861A pdb=" N GLU A 127 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N THR A 150 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N MET A 173 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR A 196 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N MET A 219 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N THR A 242 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE A 222 " --> pdb=" O THR A 242 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASP A 244 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASN A 265 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL A 245 " --> pdb=" O ASN A 265 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ASP A 267 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ARG A 288 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU A 311 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N SER A 335 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N SER A 359 " --> pdb=" O LEU A 336 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 429 through 431 removed outlier: 5.492A pdb=" N GLU A 452 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LYS A 475 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N HIS A 498 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLU A 521 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE A 545 " --> pdb=" O LEU A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 152 through 154 removed outlier: 8.968A pdb=" N ILE B 153 " --> pdb=" O MET B 121 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU B 123 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE B 88 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL B 124 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE B 90 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASN B 126 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TYR B 92 " --> pdb=" O ASN B 126 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N TYR B 14 " --> pdb=" O TRP B 60 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE B 62 " --> pdb=" O TYR B 14 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU B 16 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP B 64 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL B 18 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU B 66 " --> pdb=" O VAL B 18 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 52 through 55 removed outlier: 7.354A pdb=" N ALA C 162 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N LEU C 55 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE C 164 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU C 243 " --> pdb=" O PHE C 170 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N CYS C 172 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N CYS C 245 " --> pdb=" O CYS C 172 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 59 through 61 Processing sheet with id= F, first strand: chain 'C' and resid 87 through 89 144 hydrogen bonds defined for protein. 351 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: 2.11 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1309 1.30 - 1.43: 1865 1.43 - 1.56: 4627 1.56 - 1.69: 7 1.69 - 1.82: 61 Bond restraints: 7869 Sorted by residual: bond pdb=" CA ASP C 92 " pdb=" C ASP C 92 " ideal model delta sigma weight residual 1.532 1.462 0.070 9.60e-03 1.09e+04 5.33e+01 bond pdb=" C ASP C 208 " pdb=" O ASP C 208 " ideal model delta sigma weight residual 1.240 1.170 0.070 1.24e-02 6.50e+03 3.21e+01 bond pdb=" CA HIS C 125 " pdb=" C HIS C 125 " ideal model delta sigma weight residual 1.524 1.437 0.087 1.66e-02 3.63e+03 2.74e+01 bond pdb=" CA GLN C 262 " pdb=" C GLN C 262 " ideal model delta sigma weight residual 1.522 1.452 0.070 1.40e-02 5.10e+03 2.50e+01 bond pdb=" N GLN C 262 " pdb=" CA GLN C 262 " ideal model delta sigma weight residual 1.458 1.392 0.066 1.33e-02 5.65e+03 2.45e+01 ... (remaining 7864 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.89: 261 106.89 - 114.20: 4588 114.20 - 121.50: 3930 121.50 - 128.81: 1837 128.81 - 136.11: 41 Bond angle restraints: 10657 Sorted by residual: angle pdb=" N SER C 268 " pdb=" CA SER C 268 " pdb=" C SER C 268 " ideal model delta sigma weight residual 112.59 121.87 -9.28 1.22e+00 6.72e-01 5.79e+01 angle pdb=" N HIS C 173 " pdb=" CA HIS C 173 " pdb=" C HIS C 173 " ideal model delta sigma weight residual 111.07 118.65 -7.58 1.07e+00 8.73e-01 5.02e+01 angle pdb=" N TYR C 69 " pdb=" CA TYR C 69 " pdb=" C TYR C 69 " ideal model delta sigma weight residual 112.38 120.62 -8.24 1.22e+00 6.72e-01 4.56e+01 angle pdb=" C ALA C 269 " pdb=" N PRO C 270 " pdb=" CA PRO C 270 " ideal model delta sigma weight residual 120.21 114.20 6.01 9.60e-01 1.09e+00 3.93e+01 angle pdb=" N TYR C 272 " pdb=" CA TYR C 272 " pdb=" C TYR C 272 " ideal model delta sigma weight residual 110.30 119.49 -9.19 1.50e+00 4.44e-01 3.76e+01 ... (remaining 10652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 4345 16.69 - 33.37: 392 33.37 - 50.06: 91 50.06 - 66.74: 13 66.74 - 83.43: 7 Dihedral angle restraints: 4848 sinusoidal: 2029 harmonic: 2819 Sorted by residual: dihedral pdb=" N ASP C 64 " pdb=" C ASP C 64 " pdb=" CA ASP C 64 " pdb=" CB ASP C 64 " ideal model delta harmonic sigma weight residual 122.80 133.86 -11.06 0 2.50e+00 1.60e-01 1.96e+01 dihedral pdb=" C ARG C 246 " pdb=" N ARG C 246 " pdb=" CA ARG C 246 " pdb=" CB ARG C 246 " ideal model delta harmonic sigma weight residual -122.60 -133.30 10.70 0 2.50e+00 1.60e-01 1.83e+01 dihedral pdb=" C ARG C 96 " pdb=" N ARG C 96 " pdb=" CA ARG C 96 " pdb=" CB ARG C 96 " ideal model delta harmonic sigma weight residual -122.60 -132.33 9.73 0 2.50e+00 1.60e-01 1.52e+01 ... (remaining 4845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1104 0.091 - 0.181: 89 0.181 - 0.272: 16 0.272 - 0.363: 11 0.363 - 0.454: 8 Chirality restraints: 1228 Sorted by residual: chirality pdb=" CA ASP C 64 " pdb=" N ASP C 64 " pdb=" C ASP C 64 " pdb=" CB ASP C 64 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CA ARG C 246 " pdb=" N ARG C 246 " pdb=" C ARG C 246 " pdb=" CB ARG C 246 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CA ARG C 261 " pdb=" N ARG C 261 " pdb=" C ARG C 261 " pdb=" CB ARG C 261 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.29e+00 ... (remaining 1225 not shown) Planarity restraints: 1366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 295 " -0.020 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C ILE C 295 " 0.068 2.00e-02 2.50e+03 pdb=" O ILE C 295 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU C 296 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 90 " 0.018 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C LEU C 90 " -0.059 2.00e-02 2.50e+03 pdb=" O LEU C 90 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY C 91 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 89 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.96e+00 pdb=" C PHE C 89 " -0.049 2.00e-02 2.50e+03 pdb=" O PHE C 89 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU C 90 " 0.016 2.00e-02 2.50e+03 ... (remaining 1363 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 27 2.43 - 3.05: 4894 3.05 - 3.67: 11916 3.67 - 4.28: 17942 4.28 - 4.90: 29651 Nonbonded interactions: 64430 Sorted by model distance: nonbonded pdb=" OD1 ASN C 124 " pdb="MN MN C 400 " model vdw 1.813 2.320 nonbonded pdb=" OG1 THR B 45 " pdb="MG MG B 501 " model vdw 1.848 2.170 nonbonded pdb=" O GLN A 474 " pdb=" OG1 THR A 497 " model vdw 2.229 2.440 nonbonded pdb=" O THR A 494 " pdb=" ND2 ASN A 518 " model vdw 2.232 2.520 nonbonded pdb=" O GLY C 80 " pdb=" OH TYR C 87 " model vdw 2.243 2.440 ... (remaining 64425 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 3.950 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 24.960 Find NCS groups from input model: 0.200 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:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 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 : 0.007 0.099 7869 Z= 0.462 Angle : 0.972 11.454 10657 Z= 0.579 Chirality : 0.069 0.454 1228 Planarity : 0.005 0.049 1366 Dihedral : 13.551 83.428 3018 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.91 % Allowed : 2.28 % Favored : 96.81 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 8.70 % 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 (0.27), residues: 957 helix: -1.87 (0.27), residues: 289 sheet: -1.57 (0.48), residues: 138 loop : -0.86 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 206 HIS 0.012 0.002 HIS C 248 PHE 0.011 0.001 PHE C 257 TYR 0.012 0.002 TYR C 93 ARG 0.003 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 446 ASN cc_start: 0.7828 (m110) cc_final: 0.7468 (m110) REVERT: C 31 GLN cc_start: 0.7339 (mt0) cc_final: 0.6813 (tm-30) REVERT: C 32 GLU cc_start: 0.7889 (pm20) cc_final: 0.7668 (pm20) REVERT: C 219 ASN cc_start: 0.7288 (m110) cc_final: 0.6951 (m110) outliers start: 8 outliers final: 3 residues processed: 129 average time/residue: 1.1007 time to fit residues: 151.5074 Evaluate side-chains 80 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 295 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 498 HIS B 58 ASN B 71 GLN B 148 HIS C 125 HIS ** C 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7869 Z= 0.187 Angle : 0.593 9.282 10657 Z= 0.298 Chirality : 0.041 0.155 1228 Planarity : 0.004 0.042 1366 Dihedral : 5.717 76.320 1072 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.71 % Allowed : 10.71 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.84 (0.27), residues: 957 helix: -1.42 (0.28), residues: 306 sheet: -1.52 (0.42), residues: 169 loop : -0.81 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 60 HIS 0.008 0.001 HIS A 247 PHE 0.023 0.001 PHE A 571 TYR 0.015 0.001 TYR C 69 ARG 0.004 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.933 Fit side-chains REVERT: A 446 ASN cc_start: 0.7655 (m110) cc_final: 0.7268 (m110) REVERT: B 59 GLN cc_start: 0.7591 (mm-40) cc_final: 0.7372 (mm-40) REVERT: C 183 MET cc_start: 0.7771 (mpp) cc_final: 0.7454 (mpp) REVERT: C 283 MET cc_start: 0.7799 (ttt) cc_final: 0.7535 (ttm) outliers start: 15 outliers final: 5 residues processed: 96 average time/residue: 1.1110 time to fit residues: 114.3996 Evaluate side-chains 74 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 213 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7869 Z= 0.204 Angle : 0.578 10.759 10657 Z= 0.291 Chirality : 0.041 0.140 1228 Planarity : 0.004 0.044 1366 Dihedral : 5.321 67.070 1070 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.71 % Allowed : 13.55 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.27), residues: 957 helix: -1.20 (0.29), residues: 300 sheet: -1.53 (0.39), residues: 183 loop : -0.72 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 60 HIS 0.007 0.001 HIS A 247 PHE 0.020 0.001 PHE A 66 TYR 0.012 0.001 TYR C 70 ARG 0.003 0.000 ARG C 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.978 Fit side-chains REVERT: A 244 ASP cc_start: 0.6362 (t70) cc_final: 0.6157 (t0) REVERT: A 446 ASN cc_start: 0.7642 (m110) cc_final: 0.7251 (m110) REVERT: C 183 MET cc_start: 0.7934 (mpp) cc_final: 0.7618 (mpp) outliers start: 15 outliers final: 8 residues processed: 82 average time/residue: 1.1038 time to fit residues: 97.4096 Evaluate side-chains 75 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 295 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 0.0670 chunk 45 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 344 GLN A 365 ASN ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 7869 Z= 0.371 Angle : 0.671 9.891 10657 Z= 0.337 Chirality : 0.044 0.141 1228 Planarity : 0.004 0.043 1366 Dihedral : 5.765 67.831 1070 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.08 % Allowed : 14.46 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.95 (0.27), residues: 957 helix: -1.37 (0.28), residues: 292 sheet: -1.91 (0.39), residues: 182 loop : -0.82 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 60 HIS 0.006 0.001 HIS A 247 PHE 0.018 0.002 PHE A 66 TYR 0.014 0.002 TYR C 70 ARG 0.003 0.001 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 72 time to evaluate : 1.040 Fit side-chains REVERT: A 127 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6979 (pm20) REVERT: A 446 ASN cc_start: 0.7697 (m110) cc_final: 0.7301 (m110) REVERT: B 77 MET cc_start: 0.8500 (mmm) cc_final: 0.8286 (mmm) REVERT: C 34 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: C 183 MET cc_start: 0.8132 (mpp) cc_final: 0.7860 (mpp) outliers start: 27 outliers final: 11 residues processed: 94 average time/residue: 0.9847 time to fit residues: 100.0778 Evaluate side-chains 77 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 295 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 317 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7869 Z= 0.167 Angle : 0.579 10.842 10657 Z= 0.285 Chirality : 0.040 0.143 1228 Planarity : 0.003 0.044 1366 Dihedral : 5.120 58.746 1070 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.28 % Allowed : 16.40 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.66 (0.27), residues: 957 helix: -1.15 (0.29), residues: 289 sheet: -1.76 (0.39), residues: 181 loop : -0.63 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 60 HIS 0.008 0.001 HIS A 247 PHE 0.019 0.001 PHE A 66 TYR 0.010 0.001 TYR C 70 ARG 0.003 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 0.980 Fit side-chains REVERT: A 127 GLU cc_start: 0.7300 (pm20) cc_final: 0.6937 (pm20) REVERT: A 446 ASN cc_start: 0.7639 (m110) cc_final: 0.7245 (m110) REVERT: C 33 ASN cc_start: 0.8051 (OUTLIER) cc_final: 0.7766 (m-40) REVERT: C 183 MET cc_start: 0.8010 (mpp) cc_final: 0.7766 (mpp) outliers start: 20 outliers final: 9 residues processed: 96 average time/residue: 1.0266 time to fit residues: 106.4214 Evaluate side-chains 78 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 295 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 0.0570 chunk 7 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 overall best weight: 1.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7869 Z= 0.279 Angle : 0.642 11.549 10657 Z= 0.318 Chirality : 0.042 0.139 1228 Planarity : 0.004 0.045 1366 Dihedral : 5.319 62.535 1070 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.05 % Allowed : 17.77 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.79 (0.27), residues: 957 helix: -1.23 (0.29), residues: 295 sheet: -1.84 (0.40), residues: 181 loop : -0.72 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 60 HIS 0.008 0.001 HIS A 247 PHE 0.018 0.002 PHE C 258 TYR 0.013 0.001 TYR C 70 ARG 0.003 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 76 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7314 (pm20) cc_final: 0.7109 (pm20) REVERT: A 446 ASN cc_start: 0.7668 (m110) cc_final: 0.7258 (m110) REVERT: C 34 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: C 183 MET cc_start: 0.8114 (mpp) cc_final: 0.7880 (mpp) outliers start: 18 outliers final: 13 residues processed: 90 average time/residue: 1.1110 time to fit residues: 107.5853 Evaluate side-chains 83 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 295 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 67 optimal weight: 0.0270 chunk 77 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7869 Z= 0.157 Angle : 0.590 11.642 10657 Z= 0.291 Chirality : 0.040 0.142 1228 Planarity : 0.003 0.047 1366 Dihedral : 4.917 58.145 1068 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.28 % Allowed : 17.77 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.60 (0.28), residues: 957 helix: -1.11 (0.30), residues: 294 sheet: -1.74 (0.40), residues: 181 loop : -0.57 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 401 HIS 0.008 0.001 HIS A 247 PHE 0.022 0.001 PHE C 258 TYR 0.009 0.001 TYR C 70 ARG 0.002 0.000 ARG C 132 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7356 (pm20) cc_final: 0.7037 (pm20) REVERT: A 446 ASN cc_start: 0.7643 (m110) cc_final: 0.7263 (m110) REVERT: A 535 PHE cc_start: 0.8477 (t80) cc_final: 0.8239 (t80) REVERT: C 33 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7830 (m-40) REVERT: C 183 MET cc_start: 0.8054 (mpp) cc_final: 0.7766 (mpp) outliers start: 20 outliers final: 11 residues processed: 90 average time/residue: 0.9662 time to fit residues: 94.1537 Evaluate side-chains 82 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 295 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 0.0050 chunk 8 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7869 Z= 0.162 Angle : 0.592 10.826 10657 Z= 0.294 Chirality : 0.041 0.160 1228 Planarity : 0.003 0.048 1366 Dihedral : 4.872 58.348 1068 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.16 % Allowed : 18.45 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.45 (0.28), residues: 957 helix: -0.94 (0.31), residues: 286 sheet: -1.74 (0.39), residues: 181 loop : -0.48 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 401 HIS 0.007 0.001 HIS A 247 PHE 0.048 0.002 PHE C 258 TYR 0.010 0.001 TYR C 70 ARG 0.002 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 0.957 Fit side-chains REVERT: A 103 MET cc_start: 0.7023 (mmm) cc_final: 0.6701 (mmp) REVERT: A 127 GLU cc_start: 0.7317 (pm20) cc_final: 0.7004 (pm20) REVERT: A 446 ASN cc_start: 0.7620 (m110) cc_final: 0.7233 (m110) REVERT: A 535 PHE cc_start: 0.8577 (t80) cc_final: 0.8322 (t80) REVERT: B 144 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6030 (tpp) REVERT: C 32 GLU cc_start: 0.7500 (pm20) cc_final: 0.6770 (pm20) REVERT: C 33 ASN cc_start: 0.8236 (OUTLIER) cc_final: 0.7501 (m-40) REVERT: C 34 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: C 183 MET cc_start: 0.8062 (mpp) cc_final: 0.7844 (OUTLIER) REVERT: C 267 PHE cc_start: 0.5603 (OUTLIER) cc_final: 0.5187 (m-80) outliers start: 19 outliers final: 10 residues processed: 89 average time/residue: 1.0507 time to fit residues: 100.9316 Evaluate side-chains 80 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 267 PHE Chi-restraints excluded: chain C residue 295 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 67 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 80 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7869 Z= 0.167 Angle : 0.599 10.445 10657 Z= 0.297 Chirality : 0.040 0.139 1228 Planarity : 0.003 0.048 1366 Dihedral : 4.835 58.424 1068 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.82 % Allowed : 19.25 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.45 (0.28), residues: 957 helix: -0.98 (0.31), residues: 285 sheet: -1.61 (0.40), residues: 182 loop : -0.52 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 401 HIS 0.006 0.001 HIS A 247 PHE 0.049 0.002 PHE C 258 TYR 0.010 0.001 TYR C 70 ARG 0.002 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.982 Fit side-chains REVERT: A 103 MET cc_start: 0.7081 (mmm) cc_final: 0.6241 (mmp) REVERT: A 127 GLU cc_start: 0.7268 (pm20) cc_final: 0.6880 (pm20) REVERT: A 446 ASN cc_start: 0.7618 (m110) cc_final: 0.7227 (m110) REVERT: A 535 PHE cc_start: 0.8580 (t80) cc_final: 0.8342 (t80) REVERT: B 144 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.6134 (tpp) REVERT: C 33 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7787 (OUTLIER) REVERT: C 34 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7759 (mp0) REVERT: C 267 PHE cc_start: 0.5596 (OUTLIER) cc_final: 0.5166 (m-80) outliers start: 16 outliers final: 13 residues processed: 85 average time/residue: 0.9634 time to fit residues: 88.9314 Evaluate side-chains 87 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 71 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 267 PHE Chi-restraints excluded: chain C residue 295 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 87 optimal weight: 0.0670 chunk 75 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 20.0000 chunk 59 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7869 Z= 0.169 Angle : 0.603 10.941 10657 Z= 0.300 Chirality : 0.040 0.140 1228 Planarity : 0.004 0.049 1366 Dihedral : 4.795 58.297 1068 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.82 % Allowed : 19.36 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.46 (0.28), residues: 957 helix: -0.99 (0.31), residues: 285 sheet: -1.61 (0.40), residues: 182 loop : -0.52 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 401 HIS 0.006 0.001 HIS A 247 PHE 0.050 0.002 PHE C 258 TYR 0.013 0.001 TYR C 134 ARG 0.002 0.000 ARG C 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.7101 (mmm) cc_final: 0.6253 (mmp) REVERT: A 127 GLU cc_start: 0.7256 (pm20) cc_final: 0.6873 (pm20) REVERT: A 446 ASN cc_start: 0.7599 (m110) cc_final: 0.7206 (m110) REVERT: A 535 PHE cc_start: 0.8590 (t80) cc_final: 0.8337 (t80) REVERT: B 144 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6106 (tpp) REVERT: C 32 GLU cc_start: 0.7153 (pm20) cc_final: 0.6708 (pm20) REVERT: C 33 ASN cc_start: 0.8035 (OUTLIER) cc_final: 0.7700 (m-40) REVERT: C 34 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7833 (OUTLIER) REVERT: C 183 MET cc_start: 0.7894 (mpp) cc_final: 0.7684 (mpp) REVERT: C 267 PHE cc_start: 0.5630 (OUTLIER) cc_final: 0.5179 (m-80) outliers start: 16 outliers final: 12 residues processed: 82 average time/residue: 0.9823 time to fit residues: 87.2096 Evaluate side-chains 83 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 267 PHE Chi-restraints excluded: chain C residue 295 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.112759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.088282 restraints weight = 17128.383| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.82 r_work: 0.3465 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7869 Z= 0.235 Angle : 0.632 11.647 10657 Z= 0.315 Chirality : 0.041 0.139 1228 Planarity : 0.004 0.048 1366 Dihedral : 5.019 60.865 1068 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.82 % Allowed : 19.36 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.64 (0.28), residues: 957 helix: -1.17 (0.30), residues: 293 sheet: -1.81 (0.38), residues: 193 loop : -0.51 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 401 HIS 0.006 0.001 HIS A 247 PHE 0.046 0.002 PHE C 258 TYR 0.011 0.001 TYR C 70 ARG 0.002 0.000 ARG C 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2760.57 seconds wall clock time: 50 minutes 8.06 seconds (3008.06 seconds total)