Starting phenix.real_space_refine on Tue Mar 11 15:56:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7akv_11814/03_2025/7akv_11814.cif Found real_map, /net/cci-nas-00/data/ceres_data/7akv_11814/03_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_11814/03_2025/7akv_11814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7akv_11814/03_2025/7akv_11814.map" model { file = "/net/cci-nas-00/data/ceres_data/7akv_11814/03_2025/7akv_11814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7akv_11814/03_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-5624/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: 4.15, per 1000 atoms: 0.67 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: 1.46 Conformation dependent library (CDL) restraints added in 829.6 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: 0.69 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: 2.00 Time building geometry restraints manager: 1.74 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: 1.660 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: 0.170 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.770 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.570 ------------------------------------------------------------------------------- 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 : 0.975 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: 0.1412 time to fit residues: 13.2819 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 : 0.637 ------------------------------------------------------------------------------- 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 = 0.092018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.069113 restraints weight = 15442.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.071284 restraints weight = 9462.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.072855 restraints weight = 6797.890| |-----------------------------------------------------------------------------| 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 : 0.700 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: 0.1733 time to fit residues: 13.6702 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 : 0.657 ------------------------------------------------------------------------------- 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: 0.7980 chunk 75 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 12 optimal weight: 0.0870 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 8 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3946 r_free = 0.3946 target = 0.095110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.072093 restraints weight = 15371.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.074467 restraints weight = 9148.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.076123 restraints weight = 6408.384| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6051 Z= 0.132 Angle : 0.499 4.851 8218 Z= 0.269 Chirality : 0.040 0.148 984 Planarity : 0.003 0.039 1066 Dihedral : 4.959 25.622 839 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 64.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.86 % Favored : 87.01 % Rotamer: Outliers : 0.93 % Allowed : 12.09 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.27), residues: 793 helix: 0.49 (0.46), residues: 128 sheet: -2.57 (0.32), residues: 221 loop : -3.32 (0.25), residues: 444 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 0.011 0.001 PHE A 335 TYR 0.012 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 66 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.658 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: 0.8038 (tpp) cc_final: 0.7807 (tpp) REVERT: A 245 SER cc_start: 0.9003 (m) cc_final: 0.8573 (p) REVERT: A 294 TYR cc_start: 0.8673 (p90) cc_final: 0.8373 (p90) REVERT: G 94 LEU cc_start: 0.8916 (tp) cc_final: 0.8420 (tp) outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.1265 time to fit residues: 12.2265 Evaluate side-chains 58 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 68 ILE 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: 1.9990 chunk 73 optimal weight: 0.0370 chunk 17 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- 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 G 387 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.095214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.072025 restraints weight = 15539.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.074341 restraints weight = 9313.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.076011 restraints weight = 6589.793| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6051 Z= 0.155 Angle : 0.487 4.683 8218 Z= 0.262 Chirality : 0.040 0.142 984 Planarity : 0.003 0.034 1066 Dihedral : 4.660 25.565 839 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 65.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.49 % Favored : 86.38 % Rotamer: Outliers : 1.86 % Allowed : 14.57 % Favored : 83.57 % 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: -3.40 (0.28), residues: 793 helix: 0.72 (0.46), residues: 128 sheet: -2.39 (0.33), residues: 215 loop : -3.23 (0.25), residues: 450 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 0.010 0.001 PHE A 335 TYR 0.009 0.001 TYR A 294 ARG 0.001 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 69 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.716 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: 0.8033 (tpp) cc_final: 0.7794 (tpp) REVERT: A 245 SER cc_start: 0.8954 (m) cc_final: 0.8539 (p) REVERT: A 294 TYR cc_start: 0.8678 (p90) cc_final: 0.8311 (p90) REVERT: A 310 MET cc_start: 0.8783 (mmp) cc_final: 0.8044 (mmp) REVERT: G 94 LEU cc_start: 0.8988 (tp) cc_final: 0.8526 (tp) REVERT: G 262 ASP cc_start: 0.5792 (t70) cc_final: 0.5396 (t70) REVERT: G 325 ARG cc_start: 0.7649 (ttt180) cc_final: 0.7397 (ttm-80) outliers start: 12 outliers final: 10 residues processed: 63 average time/residue: 0.1519 time to fit residues: 14.1678 Evaluate side-chains 64 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 261 LEU 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 68 ILE Chi-restraints excluded: chain G residue 199 GLN 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: 5.9990 chunk 69 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.092847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.069651 restraints weight = 15840.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.071920 restraints weight = 9570.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.073454 restraints weight = 6799.260| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6051 Z= 0.338 Angle : 0.612 6.002 8218 Z= 0.321 Chirality : 0.042 0.150 984 Planarity : 0.004 0.036 1066 Dihedral : 5.282 27.372 839 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 67.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 17.28 % Favored : 82.60 % Rotamer: Outliers : 2.95 % Allowed : 16.28 % Favored : 80.78 % 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: -3.63 (0.27), residues: 793 helix: 0.27 (0.45), residues: 128 sheet: -2.46 (0.33), residues: 206 loop : -3.34 (0.24), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 69 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.841 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: 0.8016 (tpp) cc_final: 0.7761 (tpp) REVERT: A 245 SER cc_start: 0.9084 (m) cc_final: 0.8710 (p) REVERT: G 94 LEU cc_start: 0.9137 (tp) cc_final: 0.8787 (tp) REVERT: G 236 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.7252 (pp30) REVERT: G 262 ASP cc_start: 0.5886 (t70) cc_final: 0.5558 (t70) REVERT: G 381 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8166 (tm-30) outliers start: 19 outliers final: 15 residues processed: 63 average time/residue: 0.1297 time to fit residues: 12.5707 Evaluate side-chains 65 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 325 MET 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 68 ILE 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 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: 0.9980 chunk 2 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.094005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.070953 restraints weight = 15473.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.073213 restraints weight = 9353.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.074835 restraints weight = 6649.863| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6051 Z= 0.219 Angle : 0.526 4.929 8218 Z= 0.282 Chirality : 0.040 0.146 984 Planarity : 0.003 0.040 1066 Dihedral : 4.941 26.407 839 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 65.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.01 % Favored : 84.87 % Rotamer: Outliers : 2.95 % Allowed : 17.83 % Favored : 79.22 % 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: -3.52 (0.27), residues: 793 helix: 0.48 (0.46), residues: 127 sheet: -2.39 (0.33), residues: 206 loop : -3.30 (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 0.009 0.001 TYR A 423 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: 19 poor density : 52 time to evaluate : 0.632 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: 0.8019 (tpp) cc_final: 0.7747 (tpp) REVERT: A 245 SER cc_start: 0.9031 (m) cc_final: 0.8649 (p) REVERT: A 310 MET cc_start: 0.8738 (mmp) cc_final: 0.7996 (mmp) REVERT: G 94 LEU cc_start: 0.9118 (tp) cc_final: 0.8478 (tp) REVERT: G 128 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8675 (p) REVERT: G 381 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8161 (tm-30) outliers start: 19 outliers final: 15 residues processed: 63 average time/residue: 0.1349 time to fit residues: 12.8461 Evaluate side-chains 67 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 261 LEU 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 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 258 LEU Chi-restraints excluded: chain G residue 297 THR 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: 0.7980 chunk 78 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 71 optimal weight: 0.0060 overall best weight: 1.1000 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.093165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.069812 restraints weight = 15754.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.071998 restraints weight = 9625.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.073602 restraints weight = 6905.005| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6051 Z= 0.212 Angle : 0.523 4.787 8218 Z= 0.279 Chirality : 0.040 0.144 984 Planarity : 0.003 0.038 1066 Dihedral : 4.872 26.399 839 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 66.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.26 % Favored : 84.62 % Rotamer: Outliers : 3.41 % Allowed : 17.83 % Favored : 78.76 % 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: -3.45 (0.27), residues: 793 helix: 0.52 (0.46), residues: 127 sheet: -2.31 (0.34), residues: 206 loop : -3.26 (0.25), 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 0.014 0.002 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 76 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.731 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: 0.7967 (tpp) cc_final: 0.7692 (tpp) REVERT: A 245 SER cc_start: 0.9080 (m) cc_final: 0.8707 (p) REVERT: A 310 MET cc_start: 0.8735 (mmp) cc_final: 0.8001 (mmp) REVERT: G 94 LEU cc_start: 0.9132 (tp) cc_final: 0.8578 (tp) REVERT: G 128 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8733 (p) REVERT: G 236 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.7109 (pp30) REVERT: G 361 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7372 (mt-10) REVERT: G 381 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8176 (tm-30) outliers start: 22 outliers final: 17 residues processed: 69 average time/residue: 0.1500 time to fit residues: 15.3710 Evaluate side-chains 73 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 261 LEU 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 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 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 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: 0.5980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.0980 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.0570 chunk 28 optimal weight: 5.9990 chunk 49 optimal weight: 0.0040 chunk 37 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 overall best weight: 0.3510 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.095629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.072514 restraints weight = 15453.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.074788 restraints weight = 9391.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.076394 restraints weight = 6700.995| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6051 Z= 0.113 Angle : 0.461 4.252 8218 Z= 0.246 Chirality : 0.040 0.140 984 Planarity : 0.003 0.038 1066 Dihedral : 4.303 25.105 839 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 64.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.34 % Favored : 89.53 % Rotamer: Outliers : 1.40 % Allowed : 19.69 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.28), residues: 793 helix: 0.97 (0.47), residues: 127 sheet: -1.93 (0.36), residues: 193 loop : -3.23 (0.24), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 482 HIS 0.004 0.000 HIS G 209 PHE 0.013 0.001 PHE A 335 TYR 0.007 0.001 TYR A 423 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 71 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.7873 (tpp) cc_final: 0.7663 (tpp) REVERT: A 245 SER cc_start: 0.8958 (m) cc_final: 0.8571 (p) REVERT: A 310 MET cc_start: 0.8818 (mmp) cc_final: 0.8115 (mmp) REVERT: G 94 LEU cc_start: 0.8989 (tp) cc_final: 0.8576 (tp) REVERT: G 236 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.6901 (pp30) REVERT: G 239 MET cc_start: 0.7229 (mmm) cc_final: 0.6269 (mmm) REVERT: G 325 ARG cc_start: 0.7658 (ttt180) cc_final: 0.7428 (ttm-80) REVERT: G 361 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7278 (mt-10) outliers start: 9 outliers final: 7 residues processed: 66 average time/residue: 0.1546 time to fit residues: 14.6473 Evaluate side-chains 66 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 236 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: 0.7980 chunk 59 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 77 optimal weight: 0.0570 chunk 78 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.095270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.071765 restraints weight = 15457.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.074091 restraints weight = 9358.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.075700 restraints weight = 6641.652| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6051 Z= 0.143 Angle : 0.469 4.483 8218 Z= 0.250 Chirality : 0.040 0.205 984 Planarity : 0.003 0.032 1066 Dihedral : 4.298 25.706 839 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 64.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.60 % Favored : 88.27 % Rotamer: Outliers : 1.09 % Allowed : 21.09 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.28), residues: 793 helix: 1.19 (0.47), residues: 127 sheet: -2.40 (0.33), residues: 231 loop : -2.99 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 482 HIS 0.003 0.001 HIS G 209 PHE 0.013 0.001 PHE A 335 TYR 0.014 0.001 TYR A 294 ARG 0.001 0.000 ARG G 395 *********************** 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 65 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 SER cc_start: 0.9020 (m) cc_final: 0.8644 (p) REVERT: A 310 MET cc_start: 0.8809 (mmp) cc_final: 0.8122 (mmp) REVERT: G 94 LEU cc_start: 0.9040 (tp) cc_final: 0.8652 (tp) REVERT: G 236 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.6890 (pp30) REVERT: G 325 ARG cc_start: 0.7684 (ttt180) cc_final: 0.7436 (ttm-80) REVERT: G 361 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7338 (mt-10) outliers start: 7 outliers final: 6 residues processed: 62 average time/residue: 0.1528 time to fit residues: 13.6076 Evaluate side-chains 65 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 236 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 31 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 25 optimal weight: 0.0470 chunk 55 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.095260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.071834 restraints weight = 15717.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.074099 restraints weight = 9602.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.075708 restraints weight = 6851.874| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6051 Z= 0.145 Angle : 0.468 4.394 8218 Z= 0.249 Chirality : 0.040 0.193 984 Planarity : 0.003 0.033 1066 Dihedral : 4.287 25.828 839 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 64.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.48 % Favored : 88.40 % Rotamer: Outliers : 1.09 % Allowed : 21.40 % Favored : 77.52 % 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: -3.11 (0.28), residues: 793 helix: 1.24 (0.47), residues: 127 sheet: -2.54 (0.32), residues: 243 loop : -2.89 (0.26), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 482 HIS 0.004 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 405 ********************** 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 66 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 SER cc_start: 0.8978 (m) cc_final: 0.8603 (p) REVERT: A 310 MET cc_start: 0.8819 (mmp) cc_final: 0.8147 (mmp) REVERT: A 413 MET cc_start: 0.8050 (tmm) cc_final: 0.7793 (tmm) REVERT: G 94 LEU cc_start: 0.9036 (tp) cc_final: 0.8658 (tp) REVERT: G 236 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.6838 (pp30) REVERT: G 239 MET cc_start: 0.7160 (mmm) cc_final: 0.6332 (mmm) outliers start: 7 outliers final: 6 residues processed: 63 average time/residue: 0.1606 time to fit residues: 14.4514 Evaluate side-chains 65 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 236 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 4 optimal weight: 6.9990 chunk 12 optimal weight: 0.0060 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.095139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.071816 restraints weight = 15600.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.074102 restraints weight = 9386.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.075747 restraints weight = 6660.222| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6051 Z= 0.142 Angle : 0.463 4.378 8218 Z= 0.247 Chirality : 0.040 0.187 984 Planarity : 0.003 0.036 1066 Dihedral : 4.236 25.937 839 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 64.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.48 % Favored : 88.40 % Rotamer: Outliers : 1.09 % Allowed : 21.86 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.29), residues: 793 helix: 1.30 (0.47), residues: 127 sheet: -2.47 (0.32), residues: 243 loop : -2.85 (0.26), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 405 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2439.36 seconds wall clock time: 43 minutes 20.60 seconds (2600.60 seconds total)