Starting phenix.real_space_refine on Tue Feb 11 16:23:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7akv_11814/02_2025/7akv_11814.cif Found real_map, /net/cci-nas-00/data/ceres_data/7akv_11814/02_2025/7akv_11814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7akv_11814/02_2025/7akv_11814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7akv_11814/02_2025/7akv_11814.map" model { file = "/net/cci-nas-00/data/ceres_data/7akv_11814/02_2025/7akv_11814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7akv_11814/02_2025/7akv_11814.cif" } resolution = 3.6 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= 0.001 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: 5 Type Number sf(0) Gaussians S 20 5.16 5 C 3721 2.51 5 N 1052 2.21 5 O 1163 1.98 5 H 245 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6201 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2979 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 19, 'TRANS': 358} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Chain: "G" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3222 Classifications: {'peptide': 421} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 411} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 4.52, per 1000 atoms: 0.73 Number of scatterers: 6201 At special positions: 0 Unit cell: (77.004, 105.156, 103.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 O 1163 8.00 N 1052 7.00 C 3721 6.00 H 245 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 123 " - pdb=" SG CYS A 428 " distance=2.03 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 205 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 935.8 milliseconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1458 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 12 sheets defined 15.8% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 132 through 138 removed outlier: 4.183A pdb=" N HIS A 136 " --> pdb=" O ASP A 132 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 132 through 138' Processing helix chain 'A' and resid 138 through 161 Processing helix chain 'A' and resid 170 through 184 Processing helix chain 'A' and resid 187 through 198 Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 366 through 374 Processing helix chain 'A' and resid 375 through 388 Processing helix chain 'A' and resid 409 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 169 Processing sheet with id=AA2, first strand: chain 'A' and resid 249 through 250 removed outlier: 8.140A pdb=" N ARG A 249 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE A 224 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN A 442 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLU A 448 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 401 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 309 through 313 Processing sheet with id=AA4, first strand: chain 'G' and resid 111 through 113 removed outlier: 6.756A pdb=" N PHE G 216 " --> pdb=" O THR G 242 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N THR G 244 " --> pdb=" O PHE G 216 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU G 218 " --> pdb=" O THR G 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 149 through 150 Processing sheet with id=AA6, first strand: chain 'G' and resid 158 through 160 removed outlier: 5.997A pdb=" N LEU G 158 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL G 183 " --> pdb=" O HIS G 209 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLN G 211 " --> pdb=" O VAL G 183 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU G 185 " --> pdb=" O GLN G 211 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU G 258 " --> pdb=" O TRP G 285 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU G 287 " --> pdb=" O LEU G 258 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL G 260 " --> pdb=" O LEU G 287 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL G 309 " --> pdb=" O ALA G 283 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TRP G 285 " --> pdb=" O VAL G 309 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL G 311 " --> pdb=" O TRP G 285 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU G 287 " --> pdb=" O VAL G 311 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N HIS G 307 " --> pdb=" O GLY G 333 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL G 335 " --> pdb=" O HIS G 307 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL G 309 " --> pdb=" O VAL G 335 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N THR G 337 " --> pdb=" O VAL G 309 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL G 311 " --> pdb=" O THR G 337 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 301 through 302 removed outlier: 3.805A pdb=" N ASP G 327 " --> pdb=" O THR G 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 343 through 344 removed outlier: 6.035A pdb=" N VAL G 343 " --> pdb=" O ASP G 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 390 through 391 removed outlier: 6.722A pdb=" N LEU G 390 " --> pdb=" O LYS G 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 404 through 405 removed outlier: 6.802A pdb=" N ILE G 404 " --> pdb=" O ALA G 428 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 413 through 414 Processing sheet with id=AB3, first strand: chain 'G' and resid 422 through 423 179 hydrogen bonds defined for protein. 498 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: 2.03 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 245 1.05 - 1.24: 787 1.24 - 1.43: 1663 1.43 - 1.62: 3565 1.62 - 1.81: 36 Bond restraints: 6296 Sorted by residual: bond pdb=" CA GLY G 72 " pdb=" C GLY G 72 " ideal model delta sigma weight residual 1.514 1.499 0.015 1.41e-02 5.03e+03 1.13e+00 bond pdb=" CA GLU G 261 " pdb=" CB GLU G 261 " ideal model delta sigma weight residual 1.521 1.536 -0.016 1.48e-02 4.57e+03 1.12e+00 bond pdb=" CA VAL G 231 " pdb=" CB VAL G 231 " ideal model delta sigma weight residual 1.539 1.526 0.012 1.19e-02 7.06e+03 1.08e+00 bond pdb=" CG1 ILE G 404 " pdb=" CD1 ILE G 404 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.54e-01 bond pdb=" CA VAL G 184 " pdb=" CB VAL G 184 " ideal model delta sigma weight residual 1.542 1.531 0.011 1.26e-02 6.30e+03 7.34e-01 ... (remaining 6291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 8468 1.68 - 3.36: 210 3.36 - 5.05: 23 5.05 - 6.73: 5 6.73 - 8.41: 2 Bond angle restraints: 8708 Sorted by residual: angle pdb=" N PRO G 163 " pdb=" CA PRO G 163 " pdb=" CB PRO G 163 " ideal model delta sigma weight residual 103.25 111.06 -7.81 1.05e+00 9.07e-01 5.54e+01 angle pdb=" C GLY G 162 " pdb=" N PRO G 163 " pdb=" CA PRO G 163 " ideal model delta sigma weight residual 119.84 124.73 -4.89 1.25e+00 6.40e-01 1.53e+01 angle pdb=" N GLU G 261 " pdb=" CA GLU G 261 " pdb=" C GLU G 261 " ideal model delta sigma weight residual 107.20 113.22 -6.02 1.70e+00 3.46e-01 1.26e+01 angle pdb=" N GLY G 451 " pdb=" CA GLY G 451 " pdb=" C GLY G 451 " ideal model delta sigma weight residual 110.73 116.77 -6.04 1.90e+00 2.77e-01 1.01e+01 angle pdb=" C ASP A 483 " pdb=" N GLN A 484 " pdb=" CA GLN A 484 " ideal model delta sigma weight residual 121.54 126.70 -5.16 1.91e+00 2.74e-01 7.29e+00 ... (remaining 8703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 3431 16.84 - 33.69: 336 33.69 - 50.53: 63 50.53 - 67.38: 22 67.38 - 84.22: 6 Dihedral angle restraints: 3858 sinusoidal: 1596 harmonic: 2262 Sorted by residual: dihedral pdb=" CB CYS A 130 " pdb=" SG CYS A 130 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual 93.00 141.46 -48.46 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" CA LYS G 418 " pdb=" C LYS G 418 " pdb=" N ASP G 419 " pdb=" CA ASP G 419 " ideal model delta harmonic sigma weight residual 180.00 153.52 26.48 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA SER G 206 " pdb=" C SER G 206 " pdb=" N ALA G 207 " pdb=" CA ALA G 207 " ideal model delta harmonic sigma weight residual 180.00 155.40 24.60 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 3855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 841 0.061 - 0.122: 130 0.122 - 0.183: 12 0.183 - 0.243: 0 0.243 - 0.304: 1 Chirality restraints: 984 Sorted by residual: chirality pdb=" CA PRO G 163 " pdb=" N PRO G 163 " pdb=" C PRO G 163 " pdb=" CB PRO G 163 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA ILE G 417 " pdb=" N ILE G 417 " pdb=" C ILE G 417 " pdb=" CB ILE G 417 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.40e-01 chirality pdb=" CA ILE G 223 " pdb=" N ILE G 223 " pdb=" C ILE G 223 " pdb=" CB ILE G 223 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 981 not shown) Planarity restraints: 1311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 186 " 0.016 2.00e-02 2.50e+03 1.60e-02 6.38e+00 pdb=" CG TRP G 186 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP G 186 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP G 186 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 186 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP G 186 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP G 186 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 186 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 186 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP G 186 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 497 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO A 498 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 498 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 498 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 199 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.95e+00 pdb=" N PRO A 200 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 200 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 200 " 0.024 5.00e-02 4.00e+02 ... (remaining 1308 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 82 2.24 - 2.83: 3176 2.83 - 3.42: 8852 3.42 - 4.01: 12891 4.01 - 4.60: 18778 Nonbonded interactions: 43779 Sorted by model distance: nonbonded pdb=" OD1 ASP G 426 " pdb=" H ARG G 452 " model vdw 1.652 2.450 nonbonded pdb=" O ILE G 223 " pdb=" H THR G 249 " model vdw 1.691 2.450 nonbonded pdb=" O ILE G 118 " pdb=" H THR G 120 " model vdw 1.694 2.450 nonbonded pdb=" H LEU G 461 " pdb=" O LYS G 479 " model vdw 1.732 2.450 nonbonded pdb=" H ILE G 84 " pdb=" O ILE G 117 " model vdw 1.774 2.450 ... (remaining 43774 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.660 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: 0.180 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.730 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6051 Z= 0.246 Angle : 0.653 8.412 8218 Z= 0.379 Chirality : 0.043 0.304 984 Planarity : 0.004 0.045 1066 Dihedral : 14.255 84.220 2165 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 76.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 17.65 % Favored : 82.22 % Rotamer: Outliers : 0.16 % Allowed : 0.00 % Favored : 99.84 % 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: -4.19 (0.26), residues: 793 helix: -0.33 (0.47), residues: 123 sheet: -2.84 (0.32), residues: 222 loop : -3.62 (0.24), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP G 186 HIS 0.004 0.001 HIS G 209 PHE 0.014 0.001 PHE A 335 TYR 0.009 0.002 TYR G 234 ARG 0.003 0.000 ARG G 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ALA 125 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue ALA 157 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue ALA 172 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 200 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue ALA 213 is missing expected H atoms. Skipping. Residue SER 215 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue ILE 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue MET 239 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue THR 246 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue THR 249 is missing expected H atoms. Skipping. Residue THR 250 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue VAL 260 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue ALA 284 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue ALA 288 is missing expected H atoms. Skipping. Residue SER 291 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue THR 301 is missing expected H atoms. Skipping. Residue SER 306 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue ALA 326 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 340 is missing expected H atoms. Skipping. Residue ALA 341 is missing expected H atoms. Skipping. Residue MET 342 is missing expected H atoms. Skipping. Residue VAL 343 is missing expected H atoms. Skipping. Residue ALA 345 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue VAL 349 is missing expected H atoms. Skipping. Residue ALA 356 is missing expected H atoms. Skipping. Residue ALA 357 is missing expected H atoms. Skipping. Residue ALA 358 is missing expected H atoms. Skipping. Residue ALA 377 is missing expected H atoms. Skipping. Residue ALA 378 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue VAL 388 is missing expected H atoms. Skipping. Residue SER 389 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue ALA 394 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue ALA 421 is missing expected H atoms. Skipping. Residue LEU 423 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue ALA 450 is missing expected H atoms. Skipping. Residue THR 453 is missing expected H atoms. Skipping. Residue VAL 456 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue LEU 461 is missing expected H atoms. Skipping. Residue VAL 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue VAL 469 is missing expected H atoms. Skipping. Residue VAL 475 is missing expected H atoms. Skipping. Residue ALA 476 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue LYS 479 is missing expected H atoms. Skipping. Residue LEU 480 is missing expected H atoms. Skipping. Evaluate side-chains 64 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 294 TYR cc_start: 0.8711 (p90) cc_final: 0.8336 (p90) REVERT: A 324 MET cc_start: 0.7903 (mtp) cc_final: 0.7682 (mtt) REVERT: G 94 LEU cc_start: 0.8853 (tp) cc_final: 0.8337 (tp) outliers start: 1 outliers final: 1 residues processed: 64 average time/residue: 0.1439 time to fit residues: 13.5060 Evaluate side-chains 51 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.092019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.069112 restraints weight = 15442.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.071285 restraints weight = 9462.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.072854 restraints weight = 6797.859| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6051 Z= 0.367 Angle : 0.668 6.504 8218 Z= 0.352 Chirality : 0.044 0.163 984 Planarity : 0.004 0.042 1066 Dihedral : 5.901 31.098 841 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 70.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 20.55 % Favored : 79.32 % Rotamer: Outliers : 1.86 % Allowed : 9.15 % Favored : 88.99 % 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: -4.03 (0.27), residues: 793 helix: -0.29 (0.46), residues: 128 sheet: -2.69 (0.34), residues: 196 loop : -3.54 (0.24), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 186 HIS 0.006 0.001 HIS G 209 PHE 0.014 0.002 PHE A 335 TYR 0.014 0.002 TYR A 294 ARG 0.003 0.000 ARG G 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ALA 125 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue ALA 157 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue ALA 172 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 200 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue ALA 213 is missing expected H atoms. Skipping. Residue SER 215 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue ILE 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue MET 239 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue THR 246 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue THR 249 is missing expected H atoms. Skipping. Residue THR 250 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue VAL 260 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue ALA 284 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue ALA 288 is missing expected H atoms. Skipping. Residue SER 291 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue THR 301 is missing expected H atoms. Skipping. Residue SER 306 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue ALA 326 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 340 is missing expected H atoms. Skipping. Residue ALA 341 is missing expected H atoms. Skipping. Residue MET 342 is missing expected H atoms. Skipping. Residue VAL 343 is missing expected H atoms. Skipping. Residue ALA 345 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue VAL 349 is missing expected H atoms. Skipping. Residue ALA 356 is missing expected H atoms. Skipping. Residue ALA 357 is missing expected H atoms. Skipping. Residue ALA 358 is missing expected H atoms. Skipping. Residue ALA 377 is missing expected H atoms. Skipping. Residue ALA 378 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue VAL 388 is missing expected H atoms. Skipping. Residue SER 389 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue ALA 394 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue ALA 421 is missing expected H atoms. Skipping. Residue LEU 423 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue ALA 450 is missing expected H atoms. Skipping. Residue THR 453 is missing expected H atoms. Skipping. Residue VAL 456 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue LEU 461 is missing expected H atoms. Skipping. Residue VAL 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue VAL 469 is missing expected H atoms. Skipping. Residue VAL 475 is missing expected H atoms. Skipping. Residue ALA 476 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue LYS 479 is missing expected H atoms. Skipping. Residue LEU 480 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.8652 (mmp) cc_final: 0.7924 (mmp) REVERT: A 324 MET cc_start: 0.8040 (mtp) cc_final: 0.7779 (mtt) REVERT: G 94 LEU cc_start: 0.9035 (tp) cc_final: 0.8656 (tp) outliers start: 12 outliers final: 11 residues processed: 56 average time/residue: 0.1747 time to fit residues: 13.7552 Evaluate side-chains 61 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 453 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.4980 chunk 75 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 0.0570 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 387 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.093913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.070792 restraints weight = 15520.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.073074 restraints weight = 9331.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.074715 restraints weight = 6606.545| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6051 Z= 0.205 Angle : 0.539 5.119 8218 Z= 0.289 Chirality : 0.041 0.149 984 Planarity : 0.004 0.040 1066 Dihedral : 5.228 26.581 839 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 65.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.26 % Favored : 84.62 % Rotamer: Outliers : 1.71 % Allowed : 12.40 % Favored : 85.89 % 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: -3.76 (0.27), residues: 793 helix: 0.24 (0.46), residues: 128 sheet: -2.60 (0.33), residues: 215 loop : -3.42 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.004 0.001 HIS G 209 PHE 0.012 0.001 PHE A 335 TYR 0.011 0.002 TYR A 154 ARG 0.002 0.000 ARG G 405 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ALA 125 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue ALA 157 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue ALA 172 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 200 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue ALA 213 is missing expected H atoms. Skipping. Residue SER 215 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue ILE 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue MET 239 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue THR 246 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue THR 249 is missing expected H atoms. Skipping. Residue THR 250 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue VAL 260 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue ALA 284 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue ALA 288 is missing expected H atoms. Skipping. Residue SER 291 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue THR 301 is missing expected H atoms. Skipping. Residue SER 306 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue ALA 326 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 340 is missing expected H atoms. Skipping. Residue ALA 341 is missing expected H atoms. Skipping. Residue MET 342 is missing expected H atoms. Skipping. Residue VAL 343 is missing expected H atoms. Skipping. Residue ALA 345 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue VAL 349 is missing expected H atoms. Skipping. Residue ALA 356 is missing expected H atoms. Skipping. Residue ALA 357 is missing expected H atoms. Skipping. Residue ALA 358 is missing expected H atoms. Skipping. Residue ALA 377 is missing expected H atoms. Skipping. Residue ALA 378 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue VAL 388 is missing expected H atoms. Skipping. Residue SER 389 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue ALA 394 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue ALA 421 is missing expected H atoms. Skipping. Residue LEU 423 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue ALA 450 is missing expected H atoms. Skipping. Residue THR 453 is missing expected H atoms. Skipping. Residue VAL 456 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue LEU 461 is missing expected H atoms. Skipping. Residue VAL 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue VAL 469 is missing expected H atoms. Skipping. Residue VAL 475 is missing expected H atoms. Skipping. Residue ALA 476 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue LYS 479 is missing expected H atoms. Skipping. Residue LEU 480 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 160 MET cc_start: 0.8092 (tpp) cc_final: 0.7826 (tpp) REVERT: A 294 TYR cc_start: 0.8714 (p90) cc_final: 0.8399 (p90) REVERT: G 94 LEU cc_start: 0.8996 (tp) cc_final: 0.8527 (tp) outliers start: 11 outliers final: 9 residues processed: 60 average time/residue: 0.1353 time to fit residues: 12.5114 Evaluate side-chains 58 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 453 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.094131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.070895 restraints weight = 15578.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.073253 restraints weight = 9357.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.074870 restraints weight = 6584.345| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6051 Z= 0.204 Angle : 0.524 4.979 8218 Z= 0.280 Chirality : 0.040 0.146 984 Planarity : 0.003 0.036 1066 Dihedral : 4.995 26.089 839 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 65.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.52 % Favored : 83.35 % Rotamer: Outliers : 2.17 % Allowed : 15.19 % Favored : 82.64 % 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: -3.61 (0.27), residues: 793 helix: 0.48 (0.46), residues: 127 sheet: -2.48 (0.33), residues: 215 loop : -3.38 (0.25), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 482 HIS 0.004 0.001 HIS G 209 PHE 0.011 0.001 PHE A 335 TYR 0.009 0.001 TYR A 294 ARG 0.002 0.000 ARG G 405 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ALA 125 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue ALA 157 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue ALA 172 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 200 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue ALA 213 is missing expected H atoms. Skipping. Residue SER 215 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue ILE 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue MET 239 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue THR 246 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue THR 249 is missing expected H atoms. Skipping. Residue THR 250 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue VAL 260 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue ALA 284 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue ALA 288 is missing expected H atoms. Skipping. Residue SER 291 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue THR 301 is missing expected H atoms. Skipping. Residue SER 306 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue ALA 326 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 340 is missing expected H atoms. Skipping. Residue ALA 341 is missing expected H atoms. Skipping. Residue MET 342 is missing expected H atoms. Skipping. Residue VAL 343 is missing expected H atoms. Skipping. Residue ALA 345 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue VAL 349 is missing expected H atoms. Skipping. Residue ALA 356 is missing expected H atoms. Skipping. Residue ALA 357 is missing expected H atoms. Skipping. Residue ALA 358 is missing expected H atoms. Skipping. Residue ALA 377 is missing expected H atoms. Skipping. Residue ALA 378 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue VAL 388 is missing expected H atoms. Skipping. Residue SER 389 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue ALA 394 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue ALA 421 is missing expected H atoms. Skipping. Residue LEU 423 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue ALA 450 is missing expected H atoms. Skipping. Residue THR 453 is missing expected H atoms. Skipping. Residue VAL 456 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue LEU 461 is missing expected H atoms. Skipping. Residue VAL 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue VAL 469 is missing expected H atoms. Skipping. Residue VAL 475 is missing expected H atoms. Skipping. Residue ALA 476 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue LYS 479 is missing expected H atoms. Skipping. Residue LEU 480 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 160 MET cc_start: 0.7980 (tpp) cc_final: 0.7708 (tpp) REVERT: A 245 SER cc_start: 0.9024 (m) cc_final: 0.8627 (p) REVERT: A 310 MET cc_start: 0.8738 (mmp) cc_final: 0.7986 (mmp) REVERT: G 94 LEU cc_start: 0.9045 (tp) cc_final: 0.8624 (tp) REVERT: G 262 ASP cc_start: 0.5894 (t70) cc_final: 0.5417 (t70) outliers start: 14 outliers final: 12 residues processed: 60 average time/residue: 0.1234 time to fit residues: 11.3719 Evaluate side-chains 60 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 199 GLN Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 453 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 70 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.091874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.068811 restraints weight = 15980.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.070993 restraints weight = 9661.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.072576 restraints weight = 6910.784| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 6051 Z= 0.380 Angle : 0.640 5.846 8218 Z= 0.338 Chirality : 0.043 0.151 984 Planarity : 0.004 0.038 1066 Dihedral : 5.532 27.862 839 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 67.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 19.04 % Favored : 80.83 % Rotamer: Outliers : 4.19 % Allowed : 17.36 % Favored : 78.45 % 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: -3.76 (0.27), residues: 793 helix: 0.04 (0.45), residues: 128 sheet: -2.50 (0.34), residues: 196 loop : -3.41 (0.24), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP G 186 HIS 0.005 0.001 HIS G 209 PHE 0.012 0.001 PHE A 335 TYR 0.008 0.002 TYR A 294 ARG 0.002 0.000 ARG G 405 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ALA 125 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue ALA 157 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue ALA 172 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 200 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue ALA 213 is missing expected H atoms. Skipping. Residue SER 215 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue ILE 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue MET 239 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue THR 246 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue THR 249 is missing expected H atoms. Skipping. Residue THR 250 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue VAL 260 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue ALA 284 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue ALA 288 is missing expected H atoms. Skipping. Residue SER 291 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue THR 301 is missing expected H atoms. Skipping. Residue SER 306 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue ALA 326 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 340 is missing expected H atoms. Skipping. Residue ALA 341 is missing expected H atoms. Skipping. Residue MET 342 is missing expected H atoms. Skipping. Residue VAL 343 is missing expected H atoms. Skipping. Residue ALA 345 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue VAL 349 is missing expected H atoms. Skipping. Residue ALA 356 is missing expected H atoms. Skipping. Residue ALA 357 is missing expected H atoms. Skipping. Residue ALA 358 is missing expected H atoms. Skipping. Residue ALA 377 is missing expected H atoms. Skipping. Residue ALA 378 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue VAL 388 is missing expected H atoms. Skipping. Residue SER 389 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue ALA 394 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue ALA 421 is missing expected H atoms. Skipping. Residue LEU 423 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue ALA 450 is missing expected H atoms. Skipping. Residue THR 453 is missing expected H atoms. Skipping. Residue VAL 456 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue LEU 461 is missing expected H atoms. Skipping. Residue VAL 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue VAL 469 is missing expected H atoms. Skipping. Residue VAL 475 is missing expected H atoms. Skipping. Residue ALA 476 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue LYS 479 is missing expected H atoms. Skipping. Residue LEU 480 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 46 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 160 MET cc_start: 0.8075 (tpp) cc_final: 0.7796 (tpp) REVERT: A 245 SER cc_start: 0.9123 (m) cc_final: 0.8737 (p) REVERT: A 310 MET cc_start: 0.8647 (mmp) cc_final: 0.7896 (mmp) REVERT: G 94 LEU cc_start: 0.9172 (tp) cc_final: 0.8646 (tp) REVERT: G 119 GLU cc_start: 0.8073 (pt0) cc_final: 0.7834 (pt0) REVERT: G 128 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8781 (p) REVERT: G 236 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7210 (pp30) REVERT: G 262 ASP cc_start: 0.5942 (t70) cc_final: 0.5557 (t70) REVERT: G 381 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8208 (tm-30) outliers start: 27 outliers final: 17 residues processed: 65 average time/residue: 0.1319 time to fit residues: 12.9755 Evaluate side-chains 66 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 199 GLN Chi-restraints excluded: chain G residue 236 GLN Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 302 VAL Chi-restraints excluded: chain G residue 453 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 67 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.092841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.069715 restraints weight = 15619.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.071958 restraints weight = 9475.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.073543 restraints weight = 6741.841| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6051 Z= 0.281 Angle : 0.577 5.415 8218 Z= 0.305 Chirality : 0.041 0.150 984 Planarity : 0.003 0.039 1066 Dihedral : 5.292 26.978 839 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 67.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.90 % Favored : 82.98 % Rotamer: Outliers : 3.41 % Allowed : 20.00 % Favored : 76.59 % 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: -3.71 (0.27), residues: 793 helix: 0.17 (0.45), residues: 127 sheet: -2.53 (0.33), residues: 206 loop : -3.37 (0.24), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 482 HIS 0.004 0.001 HIS G 209 PHE 0.013 0.001 PHE A 335 TYR 0.013 0.002 TYR A 294 ARG 0.002 0.000 ARG G 405 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ALA 125 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue ALA 157 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue ALA 172 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 200 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue ALA 213 is missing expected H atoms. Skipping. Residue SER 215 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue ILE 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue MET 239 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue THR 246 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue THR 249 is missing expected H atoms. Skipping. Residue THR 250 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue VAL 260 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue ALA 284 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue ALA 288 is missing expected H atoms. Skipping. Residue SER 291 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue THR 301 is missing expected H atoms. Skipping. Residue SER 306 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue ALA 326 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 340 is missing expected H atoms. Skipping. Residue ALA 341 is missing expected H atoms. Skipping. Residue MET 342 is missing expected H atoms. Skipping. Residue VAL 343 is missing expected H atoms. Skipping. Residue ALA 345 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue VAL 349 is missing expected H atoms. Skipping. Residue ALA 356 is missing expected H atoms. Skipping. Residue ALA 357 is missing expected H atoms. Skipping. Residue ALA 358 is missing expected H atoms. Skipping. Residue ALA 377 is missing expected H atoms. Skipping. Residue ALA 378 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue VAL 388 is missing expected H atoms. Skipping. Residue SER 389 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue ALA 394 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue ALA 421 is missing expected H atoms. Skipping. Residue LEU 423 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue ALA 450 is missing expected H atoms. Skipping. Residue THR 453 is missing expected H atoms. Skipping. Residue VAL 456 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue LEU 461 is missing expected H atoms. Skipping. Residue VAL 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue VAL 469 is missing expected H atoms. Skipping. Residue VAL 475 is missing expected H atoms. Skipping. Residue ALA 476 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue LYS 479 is missing expected H atoms. Skipping. Residue LEU 480 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 160 MET cc_start: 0.8031 (tpp) cc_final: 0.7738 (tpp) REVERT: A 245 SER cc_start: 0.9074 (m) cc_final: 0.8691 (p) REVERT: A 310 MET cc_start: 0.8657 (mmp) cc_final: 0.7904 (mmp) REVERT: G 94 LEU cc_start: 0.9130 (tp) cc_final: 0.8781 (tp) REVERT: G 119 GLU cc_start: 0.8034 (pt0) cc_final: 0.7798 (pt0) REVERT: G 236 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.7225 (pp30) REVERT: G 262 ASP cc_start: 0.5773 (t70) cc_final: 0.5493 (t70) REVERT: G 381 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8212 (tm-30) outliers start: 22 outliers final: 19 residues processed: 63 average time/residue: 0.2176 time to fit residues: 21.0813 Evaluate side-chains 69 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 199 GLN Chi-restraints excluded: chain G residue 236 GLN Chi-restraints excluded: chain G residue 239 MET Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 302 VAL Chi-restraints excluded: chain G residue 453 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 20 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 71 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 321 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.093500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.070225 restraints weight = 15700.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.072456 restraints weight = 9552.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.074060 restraints weight = 6811.151| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6051 Z= 0.168 Angle : 0.503 4.685 8218 Z= 0.268 Chirality : 0.040 0.145 984 Planarity : 0.003 0.036 1066 Dihedral : 4.764 25.703 839 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 66.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.38 % Favored : 85.50 % Rotamer: Outliers : 2.64 % Allowed : 20.78 % Favored : 76.59 % 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: -3.49 (0.27), residues: 793 helix: 0.59 (0.46), residues: 127 sheet: -2.41 (0.33), residues: 206 loop : -3.29 (0.25), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.004 0.001 HIS G 209 PHE 0.013 0.001 PHE A 335 TYR 0.010 0.001 TYR A 294 ARG 0.002 0.000 ARG G 405 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ALA 125 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue ALA 157 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue ALA 172 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 200 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue ALA 213 is missing expected H atoms. Skipping. Residue SER 215 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue ILE 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue MET 239 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue THR 246 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue THR 249 is missing expected H atoms. Skipping. Residue THR 250 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue VAL 260 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue ALA 284 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue ALA 288 is missing expected H atoms. Skipping. Residue SER 291 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue THR 301 is missing expected H atoms. Skipping. Residue SER 306 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue ALA 326 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 340 is missing expected H atoms. Skipping. Residue ALA 341 is missing expected H atoms. Skipping. Residue MET 342 is missing expected H atoms. Skipping. Residue VAL 343 is missing expected H atoms. Skipping. Residue ALA 345 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue VAL 349 is missing expected H atoms. Skipping. Residue ALA 356 is missing expected H atoms. Skipping. Residue ALA 357 is missing expected H atoms. Skipping. Residue ALA 358 is missing expected H atoms. Skipping. Residue ALA 377 is missing expected H atoms. Skipping. Residue ALA 378 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue VAL 388 is missing expected H atoms. Skipping. Residue SER 389 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue ALA 394 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue ALA 421 is missing expected H atoms. Skipping. Residue LEU 423 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue ALA 450 is missing expected H atoms. Skipping. Residue THR 453 is missing expected H atoms. Skipping. Residue VAL 456 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue LEU 461 is missing expected H atoms. Skipping. Residue VAL 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue VAL 469 is missing expected H atoms. Skipping. Residue VAL 475 is missing expected H atoms. Skipping. Residue ALA 476 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue LYS 479 is missing expected H atoms. Skipping. Residue LEU 480 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 160 MET cc_start: 0.8007 (tpp) cc_final: 0.7742 (tpp) REVERT: A 245 SER cc_start: 0.9069 (m) cc_final: 0.8698 (p) REVERT: A 370 MET cc_start: 0.8725 (mtm) cc_final: 0.8413 (ttm) REVERT: G 94 LEU cc_start: 0.9081 (tp) cc_final: 0.8842 (tp) REVERT: G 258 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9147 (tt) REVERT: G 325 ARG cc_start: 0.7693 (ttt180) cc_final: 0.7422 (ttm-80) outliers start: 17 outliers final: 12 residues processed: 64 average time/residue: 0.1557 time to fit residues: 14.3379 Evaluate side-chains 65 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 199 GLN Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 302 VAL Chi-restraints excluded: chain G residue 453 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 37 optimal weight: 0.0000 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.094334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.071050 restraints weight = 15562.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.073323 restraints weight = 9407.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.074940 restraints weight = 6697.078| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6051 Z= 0.145 Angle : 0.484 4.895 8218 Z= 0.258 Chirality : 0.040 0.142 984 Planarity : 0.003 0.035 1066 Dihedral : 4.559 25.642 839 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 65.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.61 % Favored : 87.26 % Rotamer: Outliers : 2.02 % Allowed : 21.86 % Favored : 76.12 % 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: -3.39 (0.28), residues: 793 helix: 0.81 (0.47), residues: 127 sheet: -2.43 (0.32), residues: 234 loop : -3.22 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.004 0.000 HIS G 209 PHE 0.013 0.001 PHE A 335 TYR 0.015 0.001 TYR A 294 ARG 0.001 0.000 ARG G 395 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ALA 125 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue ALA 157 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue ALA 172 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 200 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue ALA 213 is missing expected H atoms. Skipping. Residue SER 215 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue ILE 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue MET 239 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue THR 246 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue THR 249 is missing expected H atoms. Skipping. Residue THR 250 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue VAL 260 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue ALA 284 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue ALA 288 is missing expected H atoms. Skipping. Residue SER 291 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue THR 301 is missing expected H atoms. Skipping. Residue SER 306 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue ALA 326 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 340 is missing expected H atoms. Skipping. Residue ALA 341 is missing expected H atoms. Skipping. Residue MET 342 is missing expected H atoms. Skipping. Residue VAL 343 is missing expected H atoms. Skipping. Residue ALA 345 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue VAL 349 is missing expected H atoms. Skipping. Residue ALA 356 is missing expected H atoms. Skipping. Residue ALA 357 is missing expected H atoms. Skipping. Residue ALA 358 is missing expected H atoms. Skipping. Residue ALA 377 is missing expected H atoms. Skipping. Residue ALA 378 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue VAL 388 is missing expected H atoms. Skipping. Residue SER 389 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue ALA 394 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue ALA 421 is missing expected H atoms. Skipping. Residue LEU 423 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue ALA 450 is missing expected H atoms. Skipping. Residue THR 453 is missing expected H atoms. Skipping. Residue VAL 456 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue LEU 461 is missing expected H atoms. Skipping. Residue VAL 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue VAL 469 is missing expected H atoms. Skipping. Residue VAL 475 is missing expected H atoms. Skipping. Residue ALA 476 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue LYS 479 is missing expected H atoms. Skipping. Residue LEU 480 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 160 MET cc_start: 0.7871 (tpp) cc_final: 0.7641 (tpp) REVERT: A 245 SER cc_start: 0.9039 (m) cc_final: 0.8671 (p) REVERT: A 310 MET cc_start: 0.8794 (mmp) cc_final: 0.8096 (mmp) REVERT: A 370 MET cc_start: 0.8704 (mtm) cc_final: 0.8402 (ttm) REVERT: G 94 LEU cc_start: 0.9051 (tp) cc_final: 0.8764 (tp) REVERT: G 325 ARG cc_start: 0.7684 (ttt180) cc_final: 0.7445 (ttm-80) outliers start: 13 outliers final: 13 residues processed: 64 average time/residue: 0.1444 time to fit residues: 13.5747 Evaluate side-chains 64 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 159 GLN Chi-restraints excluded: chain G residue 199 GLN Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 302 VAL Chi-restraints excluded: chain G residue 453 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 57 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.093725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.070642 restraints weight = 15543.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.072823 restraints weight = 9575.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.074370 restraints weight = 6915.935| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6051 Z= 0.177 Angle : 0.497 4.566 8218 Z= 0.264 Chirality : 0.040 0.140 984 Planarity : 0.003 0.034 1066 Dihedral : 4.610 26.149 839 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 67.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.37 % Favored : 86.51 % Rotamer: Outliers : 3.26 % Allowed : 21.24 % Favored : 75.50 % 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: -3.30 (0.28), residues: 793 helix: 0.97 (0.47), residues: 127 sheet: -2.34 (0.33), residues: 225 loop : -3.20 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 482 HIS 0.004 0.001 HIS G 209 PHE 0.013 0.001 PHE A 335 TYR 0.009 0.001 TYR A 294 ARG 0.001 0.000 ARG G 405 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ALA 125 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue ALA 157 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue ALA 172 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 200 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue ALA 213 is missing expected H atoms. Skipping. Residue SER 215 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue ILE 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue MET 239 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue THR 246 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue THR 249 is missing expected H atoms. Skipping. Residue THR 250 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue VAL 260 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue ALA 284 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue ALA 288 is missing expected H atoms. Skipping. Residue SER 291 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue THR 301 is missing expected H atoms. Skipping. Residue SER 306 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue ALA 326 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 340 is missing expected H atoms. Skipping. Residue ALA 341 is missing expected H atoms. Skipping. Residue MET 342 is missing expected H atoms. Skipping. Residue VAL 343 is missing expected H atoms. Skipping. Residue ALA 345 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue VAL 349 is missing expected H atoms. Skipping. Residue ALA 356 is missing expected H atoms. Skipping. Residue ALA 357 is missing expected H atoms. Skipping. Residue ALA 358 is missing expected H atoms. Skipping. Residue ALA 377 is missing expected H atoms. Skipping. Residue ALA 378 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue VAL 388 is missing expected H atoms. Skipping. Residue SER 389 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue ALA 394 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue ALA 421 is missing expected H atoms. Skipping. Residue LEU 423 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue ALA 450 is missing expected H atoms. Skipping. Residue THR 453 is missing expected H atoms. Skipping. Residue VAL 456 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue LEU 461 is missing expected H atoms. Skipping. Residue VAL 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue VAL 469 is missing expected H atoms. Skipping. Residue VAL 475 is missing expected H atoms. Skipping. Residue ALA 476 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue LYS 479 is missing expected H atoms. Skipping. Residue LEU 480 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 160 MET cc_start: 0.7886 (tpp) cc_final: 0.7660 (tpp) REVERT: A 245 SER cc_start: 0.9011 (m) cc_final: 0.8628 (p) REVERT: A 310 MET cc_start: 0.8787 (mmp) cc_final: 0.8104 (mmp) REVERT: A 370 MET cc_start: 0.8705 (mtm) cc_final: 0.8353 (ttm) REVERT: G 94 LEU cc_start: 0.9100 (tp) cc_final: 0.8591 (tp) REVERT: G 128 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8730 (p) REVERT: G 236 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.6960 (pp30) REVERT: G 325 ARG cc_start: 0.7708 (ttt180) cc_final: 0.7481 (ttm-80) REVERT: G 361 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7234 (mm-30) REVERT: G 362 SER cc_start: 0.8672 (m) cc_final: 0.8265 (t) outliers start: 21 outliers final: 18 residues processed: 68 average time/residue: 0.1481 time to fit residues: 14.5403 Evaluate side-chains 74 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 199 GLN Chi-restraints excluded: chain G residue 236 GLN Chi-restraints excluded: chain G residue 239 MET Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 302 VAL Chi-restraints excluded: chain G residue 453 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 31 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 0.0370 chunk 47 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.094338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.070980 restraints weight = 15782.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.073220 restraints weight = 9521.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.074859 restraints weight = 6798.713| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6051 Z= 0.155 Angle : 0.482 4.381 8218 Z= 0.256 Chirality : 0.040 0.139 984 Planarity : 0.003 0.035 1066 Dihedral : 4.481 25.848 839 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 65.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.23 % Favored : 87.64 % Rotamer: Outliers : 2.64 % Allowed : 22.17 % Favored : 75.19 % 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: -3.13 (0.28), residues: 793 helix: 1.06 (0.47), residues: 127 sheet: -1.98 (0.35), residues: 197 loop : -3.20 (0.25), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.003 0.000 HIS G 209 PHE 0.013 0.001 PHE A 335 TYR 0.013 0.001 TYR A 294 ARG 0.001 0.000 ARG G 395 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ALA 125 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue ALA 157 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue ALA 172 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 200 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue ALA 213 is missing expected H atoms. Skipping. Residue SER 215 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue ILE 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue MET 239 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue THR 246 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue THR 249 is missing expected H atoms. Skipping. Residue THR 250 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue VAL 260 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue ALA 284 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue ALA 288 is missing expected H atoms. Skipping. Residue SER 291 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue THR 301 is missing expected H atoms. Skipping. Residue SER 306 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue ALA 326 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 340 is missing expected H atoms. Skipping. Residue ALA 341 is missing expected H atoms. Skipping. Residue MET 342 is missing expected H atoms. Skipping. Residue VAL 343 is missing expected H atoms. Skipping. Residue ALA 345 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue VAL 349 is missing expected H atoms. Skipping. Residue ALA 356 is missing expected H atoms. Skipping. Residue ALA 357 is missing expected H atoms. Skipping. Residue ALA 358 is missing expected H atoms. Skipping. Residue ALA 377 is missing expected H atoms. Skipping. Residue ALA 378 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue VAL 388 is missing expected H atoms. Skipping. Residue SER 389 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue ALA 394 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue ALA 421 is missing expected H atoms. Skipping. Residue LEU 423 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue ALA 450 is missing expected H atoms. Skipping. Residue THR 453 is missing expected H atoms. Skipping. Residue VAL 456 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue LEU 461 is missing expected H atoms. Skipping. Residue VAL 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue VAL 469 is missing expected H atoms. Skipping. Residue VAL 475 is missing expected H atoms. Skipping. Residue ALA 476 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue LYS 479 is missing expected H atoms. Skipping. Residue LEU 480 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 245 SER cc_start: 0.9023 (m) cc_final: 0.8658 (p) REVERT: A 310 MET cc_start: 0.8808 (mmp) cc_final: 0.8131 (mmp) REVERT: A 370 MET cc_start: 0.8704 (mtm) cc_final: 0.8406 (ttm) REVERT: A 413 MET cc_start: 0.8079 (tmm) cc_final: 0.7798 (tmm) REVERT: G 94 LEU cc_start: 0.9086 (tp) cc_final: 0.8558 (tp) REVERT: G 128 VAL cc_start: 0.8953 (OUTLIER) cc_final: 0.8674 (p) REVERT: G 236 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.6882 (pp30) REVERT: G 325 ARG cc_start: 0.7692 (ttt180) cc_final: 0.7456 (ttm-80) REVERT: G 362 SER cc_start: 0.8662 (m) cc_final: 0.8275 (t) outliers start: 17 outliers final: 15 residues processed: 66 average time/residue: 0.1487 time to fit residues: 14.1806 Evaluate side-chains 71 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 199 GLN Chi-restraints excluded: chain G residue 236 GLN Chi-restraints excluded: chain G residue 239 MET Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 302 VAL Chi-restraints excluded: chain G residue 453 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 4 optimal weight: 0.1980 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 0.0670 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.095115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.071928 restraints weight = 15631.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.074177 restraints weight = 9540.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.075776 restraints weight = 6827.483| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6051 Z= 0.133 Angle : 0.468 5.456 8218 Z= 0.248 Chirality : 0.040 0.137 984 Planarity : 0.003 0.035 1066 Dihedral : 4.273 25.837 839 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 64.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.98 % Favored : 87.89 % Rotamer: Outliers : 2.48 % Allowed : 22.33 % Favored : 75.19 % 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: -3.13 (0.29), residues: 793 helix: 1.29 (0.47), residues: 127 sheet: -2.56 (0.32), residues: 243 loop : -2.93 (0.27), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 482 HIS 0.003 0.000 HIS G 209 PHE 0.013 0.001 PHE A 335 TYR 0.007 0.001 TYR A 294 ARG 0.001 0.000 ARG G 395 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2301.12 seconds wall clock time: 42 minutes 23.14 seconds (2543.14 seconds total)