Starting phenix.real_space_refine on Tue Feb 13 12:40:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7akv_11814/02_2024/7akv_11814.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7akv_11814/02_2024/7akv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7akv_11814/02_2024/7akv_11814.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7akv_11814/02_2024/7akv_11814.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7akv_11814/02_2024/7akv_11814.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7akv_11814/02_2024/7akv_11814.pdb" } 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 Residue "A TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 55": "OD1" <-> "OD2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 212": "OD1" <-> "OD2" Residue "G GLU 229": "OE1" <-> "OE2" Residue "G ASP 262": "OD1" <-> "OD2" Residue "G ASP 310": "OD1" <-> "OD2" Residue "G ASP 368": "OD1" <-> "OD2" Residue "G ASP 419": "OD1" <-> "OD2" Residue "G GLU 435": "OE1" <-> "OE2" Residue "G ASP 445": "OD1" <-> "OD2" Residue "G GLU 477": "OE1" <-> "OE2" Residue "G GLU 481": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 4.01, per 1000 atoms: 0.65 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 0.65 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: 1.78 Time building geometry restraints manager: 2.85 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: 99.54 - 106.43: 152 106.43 - 113.31: 3517 113.31 - 120.20: 2151 120.20 - 127.09: 2830 127.09 - 133.98: 58 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 1.850 nonbonded pdb=" O ILE G 223 " pdb=" H THR G 249 " model vdw 1.691 1.850 nonbonded pdb=" O ILE G 118 " pdb=" H THR G 120 " model vdw 1.694 1.850 nonbonded pdb=" H LEU G 461 " pdb=" O LYS G 479 " model vdw 1.732 1.850 nonbonded pdb=" H ILE G 84 " pdb=" O ILE G 117 " model vdw 1.774 1.850 ... (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 ========== 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: 1.950 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: 7.280 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.800 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.450 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. revert: 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: 0.1469 time to fit residues: 13.7410 Evaluate side-chains 51 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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: 2.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 HIS G 364 HIS ** G 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 6051 Z= 0.518 Angle : 0.780 7.224 8218 Z= 0.407 Chirality : 0.046 0.159 984 Planarity : 0.005 0.048 1066 Dihedral : 6.364 32.780 841 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 79.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 24.09 % Favored : 75.79 % Rotamer: Outliers : 2.48 % Allowed : 11.94 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.27), residues: 793 helix: -0.63 (0.47), residues: 127 sheet: -2.87 (0.33), residues: 214 loop : -3.58 (0.24), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 186 HIS 0.006 0.001 HIS G 209 PHE 0.015 0.002 PHE A 335 TYR 0.013 0.002 TYR A 294 ARG 0.003 0.001 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 62 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 46 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 310 MET cc_start: 0.8601 (mmp) cc_final: 0.7873 (mmp) REVERT: A 324 MET cc_start: 0.7999 (mtp) cc_final: 0.7730 (mtt) REVERT: G 94 LEU cc_start: 0.9128 (tp) cc_final: 0.8719 (tp) outliers start: 16 outliers final: 13 residues processed: 56 average time/residue: 0.1485 time to fit residues: 12.3814 Evaluate side-chains 58 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 45 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 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 130 VAL Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 199 GLN Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 426 ASP 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 39 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 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 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 GLN G 314 HIS G 364 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6051 Z= 0.180 Angle : 0.530 5.191 8218 Z= 0.285 Chirality : 0.040 0.151 984 Planarity : 0.004 0.043 1066 Dihedral : 5.268 29.077 841 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 71.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.01 % Favored : 84.87 % Rotamer: Outliers : 1.24 % Allowed : 15.04 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.27), residues: 793 helix: 0.19 (0.47), residues: 128 sheet: -2.60 (0.33), residues: 222 loop : -3.40 (0.25), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.004 0.001 HIS G 209 PHE 0.012 0.001 PHE A 335 TYR 0.014 0.002 TYR A 294 ARG 0.002 0.000 ARG G 95 *********************** 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 61 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.8096 (tpp) cc_final: 0.7838 (tpp) REVERT: A 245 SER cc_start: 0.9009 (m) cc_final: 0.8584 (p) REVERT: A 310 MET cc_start: 0.8658 (mmp) cc_final: 0.7921 (mmp) REVERT: G 94 LEU cc_start: 0.8982 (tp) cc_final: 0.8475 (tp) outliers start: 8 outliers final: 8 residues processed: 56 average time/residue: 0.1423 time to fit residues: 11.8611 Evaluate side-chains 59 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 68 ILE Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 426 ASP 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 37 optimal weight: 0.0030 chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.9594 ------------------------------------------------------------------------------- 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 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 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6051 Z= 0.348 Angle : 0.621 5.847 8218 Z= 0.328 Chirality : 0.042 0.150 984 Planarity : 0.004 0.039 1066 Dihedral : 5.506 26.781 839 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 73.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 20.81 % Favored : 79.07 % Rotamer: Outliers : 2.95 % Allowed : 19.07 % Favored : 77.98 % 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: -3.79 (0.27), residues: 793 helix: 0.04 (0.46), residues: 127 sheet: -2.57 (0.34), residues: 212 loop : -3.40 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP G 186 HIS 0.005 0.001 HIS G 209 PHE 0.012 0.001 PHE A 335 TYR 0.007 0.002 TYR A 244 ARG 0.002 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue VAL 111 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue ALA 125 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue VAL 130 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue MET 143 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue ALA 157 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 161 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LEU 168 is missing expected H atoms. Skipping. Residue VAL 171 is missing expected H atoms. Skipping. Residue ALA 172 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue ALA 193 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue VAL 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue VAL 200 is missing expected H atoms. Skipping. Residue ALA 207 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue ALA 213 is missing expected H atoms. Skipping. Residue SER 215 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue ILE 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue MET 239 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue THR 246 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue THR 249 is missing expected H atoms. Skipping. Residue THR 250 is missing expected H atoms. Skipping. Residue ALA 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue VAL 260 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue THR 265 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue ALA 283 is missing expected H atoms. Skipping. Residue ALA 284 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue LEU 287 is missing expected H atoms. Skipping. Residue ALA 288 is missing expected H atoms. Skipping. Residue SER 291 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue THR 301 is missing expected H atoms. Skipping. Residue SER 306 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue ALA 312 is missing expected H atoms. Skipping. Residue ALA 313 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue ALA 326 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue VAL 335 is missing expected H atoms. Skipping. Residue VAL 336 is missing expected H atoms. Skipping. Residue THR 337 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 340 is missing expected H atoms. Skipping. Residue ALA 341 is missing expected H atoms. Skipping. Residue MET 342 is missing expected H atoms. Skipping. Residue VAL 343 is missing expected H atoms. Skipping. Residue ALA 345 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue VAL 349 is missing expected H atoms. Skipping. Residue ALA 356 is missing expected H atoms. Skipping. Residue ALA 357 is missing expected H atoms. Skipping. Residue ALA 358 is missing expected H atoms. Skipping. Residue ALA 377 is missing expected H atoms. Skipping. Residue ALA 378 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Residue VAL 388 is missing expected H atoms. Skipping. Residue SER 389 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 391 is missing expected H atoms. Skipping. Residue ALA 394 is missing expected H atoms. Skipping. Residue LEU 396 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue ALA 421 is missing expected H atoms. Skipping. Residue LEU 423 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue ALA 450 is missing expected H atoms. Skipping. Residue THR 453 is missing expected H atoms. Skipping. Residue VAL 456 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 459 is missing expected H atoms. Skipping. Residue LEU 461 is missing expected H atoms. Skipping. Residue VAL 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue VAL 469 is missing expected H atoms. Skipping. Residue VAL 475 is missing expected H atoms. Skipping. Residue ALA 476 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue LYS 479 is missing expected H atoms. Skipping. Residue LEU 480 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 47 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.8129 (tpp) cc_final: 0.7840 (tpp) REVERT: A 245 SER cc_start: 0.9103 (m) cc_final: 0.8721 (p) REVERT: A 310 MET cc_start: 0.8667 (mmp) cc_final: 0.7903 (mmp) REVERT: G 94 LEU cc_start: 0.9148 (tp) cc_final: 0.8774 (tp) REVERT: G 236 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.7241 (pp30) REVERT: G 381 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8222 (tm-30) outliers start: 19 outliers final: 16 residues processed: 60 average time/residue: 0.1460 time to fit residues: 13.0494 Evaluate side-chains 63 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 46 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 199 GLN Chi-restraints excluded: chain G residue 236 GLN Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 302 VAL Chi-restraints excluded: chain G residue 426 ASP 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 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.0970 chunk 65 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 68 optimal weight: 0.0050 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 overall best weight: 1.5396 ------------------------------------------------------------------------------- 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 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 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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 : 0.004 0.026 6051 Z= 0.281 Angle : 0.575 5.657 8218 Z= 0.306 Chirality : 0.041 0.148 984 Planarity : 0.004 0.043 1066 Dihedral : 5.338 26.144 839 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 72.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 17.40 % Favored : 82.47 % Rotamer: Outliers : 4.34 % Allowed : 20.47 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.27), residues: 793 helix: 0.18 (0.46), residues: 128 sheet: -2.53 (0.34), residues: 213 loop : -3.37 (0.25), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 482 HIS 0.004 0.001 HIS G 209 PHE 0.014 0.001 PHE A 335 TYR 0.009 0.001 TYR A 294 ARG 0.002 0.000 ARG A 233 *********************** 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 76 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 48 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 160 MET cc_start: 0.8102 (tpp) cc_final: 0.7818 (tpp) REVERT: A 245 SER cc_start: 0.9053 (m) cc_final: 0.8659 (p) REVERT: A 310 MET cc_start: 0.8677 (mmp) cc_final: 0.7959 (mmp) REVERT: G 94 LEU cc_start: 0.9118 (tp) cc_final: 0.8535 (tp) REVERT: G 128 VAL cc_start: 0.9019 (OUTLIER) cc_final: 0.8712 (p) REVERT: G 381 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8264 (tm-30) outliers start: 28 outliers final: 24 residues processed: 67 average time/residue: 0.1384 time to fit residues: 13.9994 Evaluate side-chains 73 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 48 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 326 ASN Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain G residue 60 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 175 THR Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 302 VAL Chi-restraints excluded: chain G residue 426 ASP 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 18 optimal weight: 0.4980 chunk 76 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 43 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 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 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1483 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= 0.215 Angle : 0.531 5.194 8218 Z= 0.282 Chirality : 0.040 0.146 984 Planarity : 0.003 0.040 1066 Dihedral : 4.984 25.492 839 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 70.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 18.03 % Favored : 81.84 % Rotamer: Outliers : 4.50 % Allowed : 21.40 % Favored : 74.11 % 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: -3.57 (0.28), residues: 793 helix: 0.48 (0.47), residues: 128 sheet: -2.46 (0.33), residues: 226 loop : -3.33 (0.25), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 482 HIS 0.003 0.001 HIS G 209 PHE 0.014 0.001 PHE A 335 TYR 0.013 0.001 TYR A 294 ARG 0.002 0.000 ARG G 438 *********************** 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 78 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 49 time to evaluate : 0.695 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: 0.8101 (tpp) cc_final: 0.7825 (tpp) REVERT: A 245 SER cc_start: 0.9007 (m) cc_final: 0.8622 (p) REVERT: A 310 MET cc_start: 0.8676 (mmp) cc_final: 0.7951 (mmp) REVERT: G 94 LEU cc_start: 0.9095 (tp) cc_final: 0.8515 (tp) REVERT: G 128 VAL cc_start: 0.8977 (OUTLIER) cc_final: 0.8711 (p) REVERT: G 236 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7186 (pp30) REVERT: G 262 ASP cc_start: 0.5933 (t70) cc_final: 0.5526 (t70) REVERT: G 381 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8245 (tm-30) outliers start: 29 outliers final: 23 residues processed: 69 average time/residue: 0.1361 time to fit residues: 13.9046 Evaluate side-chains 72 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 47 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 325 MET Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain G residue 60 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 276 THR Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 302 VAL Chi-restraints excluded: chain G residue 426 ASP 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 43 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 45 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1629 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= 0.192 Angle : 0.510 4.893 8218 Z= 0.271 Chirality : 0.039 0.145 984 Planarity : 0.003 0.040 1066 Dihedral : 4.778 25.324 839 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 71.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.76 % Favored : 84.11 % Rotamer: Outliers : 4.50 % Allowed : 21.40 % Favored : 74.11 % 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: -3.42 (0.28), residues: 793 helix: 0.58 (0.48), residues: 128 sheet: -2.27 (0.35), residues: 211 loop : -3.28 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.004 0.001 HIS G 209 PHE 0.013 0.001 PHE A 335 TYR 0.010 0.001 TYR A 294 ARG 0.002 0.000 ARG G 438 *********************** 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 77 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 48 time to evaluate : 0.763 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: 0.8086 (tpp) cc_final: 0.7825 (tpp) REVERT: A 245 SER cc_start: 0.8988 (m) cc_final: 0.8612 (p) REVERT: A 310 MET cc_start: 0.8701 (mmp) cc_final: 0.7986 (mmp) REVERT: G 94 LEU cc_start: 0.9063 (tp) cc_final: 0.8454 (tp) REVERT: G 128 VAL cc_start: 0.8974 (OUTLIER) cc_final: 0.8611 (p) REVERT: G 236 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7172 (pp30) REVERT: G 262 ASP cc_start: 0.5808 (t70) cc_final: 0.5473 (t70) REVERT: G 381 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8276 (tm-30) outliers start: 29 outliers final: 24 residues processed: 69 average time/residue: 0.1479 time to fit residues: 14.7399 Evaluate side-chains 76 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 50 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain G residue 60 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 175 THR 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 276 THR Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 302 VAL Chi-restraints excluded: chain G residue 426 ASP 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 14 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 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 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6051 Z= 0.171 Angle : 0.494 4.630 8218 Z= 0.262 Chirality : 0.039 0.142 984 Planarity : 0.003 0.039 1066 Dihedral : 4.602 24.932 839 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 72.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.38 % Favored : 84.49 % Rotamer: Outliers : 3.88 % Allowed : 22.64 % Favored : 73.49 % 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: -3.31 (0.28), residues: 793 helix: 0.69 (0.48), residues: 128 sheet: -2.17 (0.35), residues: 211 loop : -3.24 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.004 0.001 HIS G 209 PHE 0.013 0.001 PHE A 335 TYR 0.014 0.001 TYR A 294 ARG 0.001 0.000 ARG G 438 *********************** 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 75 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 50 time to evaluate : 0.873 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: 0.8072 (tpp) cc_final: 0.7819 (tpp) REVERT: A 245 SER cc_start: 0.8963 (m) cc_final: 0.8587 (p) REVERT: A 310 MET cc_start: 0.8735 (mmp) cc_final: 0.8034 (mmp) REVERT: G 94 LEU cc_start: 0.9064 (tp) cc_final: 0.8666 (tp) REVERT: G 236 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7184 (pp30) REVERT: G 262 ASP cc_start: 0.5835 (t70) cc_final: 0.5583 (t70) REVERT: G 325 ARG cc_start: 0.7655 (ttt180) cc_final: 0.7400 (ttm-80) outliers start: 25 outliers final: 23 residues processed: 69 average time/residue: 0.1587 time to fit residues: 15.9239 Evaluate side-chains 73 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 49 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 256 ASP 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 347 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 175 THR 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 276 THR Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 426 ASP 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 30 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6051 Z= 0.258 Angle : 0.547 5.077 8218 Z= 0.289 Chirality : 0.040 0.145 984 Planarity : 0.003 0.038 1066 Dihedral : 4.895 25.234 839 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 72.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 17.53 % Favored : 82.35 % Rotamer: Outliers : 4.50 % Allowed : 22.17 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.28), residues: 793 helix: 0.45 (0.47), residues: 127 sheet: -2.18 (0.35), residues: 213 loop : -3.25 (0.25), residues: 453 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 294 ARG 0.002 0.000 ARG A 233 *********************** 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 76 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 47 time to evaluate : 0.700 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: 0.8018 (tpp) cc_final: 0.7757 (tpp) REVERT: A 245 SER cc_start: 0.9010 (m) cc_final: 0.8633 (p) REVERT: A 310 MET cc_start: 0.8694 (mmp) cc_final: 0.8041 (mmp) REVERT: G 94 LEU cc_start: 0.9121 (tp) cc_final: 0.8571 (tp) REVERT: G 128 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8786 (p) REVERT: G 236 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7600 (pt0) REVERT: G 262 ASP cc_start: 0.5902 (t70) cc_final: 0.5632 (t70) REVERT: G 381 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8228 (tm-30) outliers start: 29 outliers final: 25 residues processed: 69 average time/residue: 0.1375 time to fit residues: 14.1791 Evaluate side-chains 74 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 47 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain G residue 60 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 175 THR Chi-restraints excluded: chain G residue 199 GLN Chi-restraints excluded: chain G residue 236 GLN Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 302 VAL Chi-restraints excluded: chain G residue 426 ASP 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 78 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 HIS ** 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 ** G 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 6051 Z= 0.472 Angle : 0.716 7.226 8218 Z= 0.374 Chirality : 0.044 0.164 984 Planarity : 0.004 0.039 1066 Dihedral : 5.786 27.324 839 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 79.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 21.31 % Favored : 78.56 % Rotamer: Outliers : 4.65 % Allowed : 21.86 % Favored : 73.49 % 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: -3.72 (0.27), residues: 793 helix: -0.27 (0.46), residues: 128 sheet: -2.23 (0.36), residues: 194 loop : -3.39 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 186 HIS 0.005 0.001 HIS G 209 PHE 0.014 0.002 PHE A 335 TYR 0.011 0.002 TYR A 294 ARG 0.003 0.001 ARG G 438 ********************** 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 76 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 46 time to evaluate : 0.754 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: 0.8157 (tpp) cc_final: 0.7833 (tpp) REVERT: A 245 SER cc_start: 0.9132 (m) cc_final: 0.8786 (p) REVERT: A 310 MET cc_start: 0.8630 (mmp) cc_final: 0.8259 (mmp) REVERT: G 94 LEU cc_start: 0.9216 (tp) cc_final: 0.8947 (tp) REVERT: G 236 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7705 (pt0) REVERT: G 262 ASP cc_start: 0.6177 (t70) cc_final: 0.5705 (t70) REVERT: G 381 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8150 (tm-30) outliers start: 30 outliers final: 27 residues processed: 67 average time/residue: 0.1373 time to fit residues: 13.6718 Evaluate side-chains 73 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 45 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 256 ASP Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain G residue 60 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 175 THR Chi-restraints excluded: chain G residue 199 GLN Chi-restraints excluded: chain G residue 236 GLN Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 302 VAL Chi-restraints excluded: chain G residue 426 ASP 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 17 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 GLN ** G 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.093286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.070394 restraints weight = 15617.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.072638 restraints weight = 9488.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.074198 restraints weight = 6745.171| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1760 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= 0.156 Angle : 0.498 4.803 8218 Z= 0.267 Chirality : 0.040 0.146 984 Planarity : 0.003 0.041 1066 Dihedral : 4.834 25.026 839 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 69.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.00 % Favored : 85.88 % Rotamer: Outliers : 3.26 % Allowed : 23.57 % Favored : 73.18 % 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: -3.41 (0.28), residues: 793 helix: 0.36 (0.47), residues: 127 sheet: -2.20 (0.35), residues: 206 loop : -3.23 (0.25), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.004 0.001 HIS G 209 PHE 0.013 0.001 PHE A 335 TYR 0.010 0.001 TYR A 294 ARG 0.001 0.000 ARG G 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1664.75 seconds wall clock time: 31 minutes 7.05 seconds (1867.05 seconds total)