Starting phenix.real_space_refine on Tue Feb 11 02:49:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3ktt_5148/02_2025/3ktt_5148.cif Found real_map, /net/cci-nas-00/data/ceres_data/3ktt_5148/02_2025/3ktt_5148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3ktt_5148/02_2025/3ktt_5148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3ktt_5148/02_2025/3ktt_5148.map" model { file = "/net/cci-nas-00/data/ceres_data/3ktt_5148/02_2025/3ktt_5148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3ktt_5148/02_2025/3ktt_5148.cif" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 0.055 sd= 0.377 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: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 2409 2.51 5 N 679 2.21 5 O 748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3855 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3855 Classifications: {'peptide': 513} Modifications used: {'COO': 1} Link IDs: {'CIS': 7, 'PTRANS': 9, 'TRANS': 496} Time building chain proxies: 2.56, per 1000 atoms: 0.66 Number of scatterers: 3855 At special positions: 0 Unit cell: (75.6, 97.2, 94.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 748 8.00 N 679 7.00 C 2409 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 442.9 milliseconds 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB ARG B 268 " Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 6 sheets defined 55.8% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'B' and resid 7 through 29 removed outlier: 3.698A pdb=" N ALA B 11 " --> pdb=" O ARG B 7 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 19 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE B 20 " --> pdb=" O PHE B 16 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'B' and resid 53 through 61 removed outlier: 4.258A pdb=" N ILE B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 82 removed outlier: 4.343A pdb=" N SER B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG B 76 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL B 77 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 98 removed outlier: 3.564A pdb=" N LEU B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 107 Processing helix chain 'B' and resid 109 through 114 Processing helix chain 'B' and resid 114 through 128 removed outlier: 3.985A pdb=" N ARG B 118 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 157 removed outlier: 3.883A pdb=" N SER B 156 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 178 removed outlier: 3.618A pdb=" N ALA B 170 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL B 171 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU B 172 " --> pdb=" O LYS B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 273 removed outlier: 3.971A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 258 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG B 268 " --> pdb=" O GLU B 264 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 270 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 304 through 315 removed outlier: 3.508A pdb=" N GLY B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 329 Processing helix chain 'B' and resid 369 through 391 removed outlier: 4.229A pdb=" N HIS B 378 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP B 379 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 383 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 415 removed outlier: 3.671A pdb=" N GLN B 410 " --> pdb=" O HIS B 406 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B 412 " --> pdb=" O VAL B 408 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N SER B 413 " --> pdb=" O THR B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 430 removed outlier: 3.522A pdb=" N ALA B 422 " --> pdb=" O LYS B 418 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 430 " --> pdb=" O TYR B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 442 removed outlier: 3.695A pdb=" N ALA B 438 " --> pdb=" O PRO B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 459 removed outlier: 3.619A pdb=" N GLY B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 483 through 504 removed outlier: 3.657A pdb=" N LYS B 487 " --> pdb=" O SER B 483 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=B, first strand: chain 'B' and resid 37 through 40 removed outlier: 4.203A pdb=" N LYS B 37 " --> pdb=" O THR B 51 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'B' and resid 187 through 189 removed outlier: 6.856A pdb=" N HIS B 187 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU B 362 " --> pdb=" O HIS B 187 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 189 " --> pdb=" O LEU B 362 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 205 through 207 Processing sheet with id=E, first strand: chain 'B' and resid 224 through 227 removed outlier: 6.371A pdb=" N LEU B 225 " --> pdb=" O ILE B 278 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'B' and resid 463 through 466 191 hydrogen bonds defined for protein. 543 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: 1.10 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 698 1.32 - 1.44: 1280 1.44 - 1.57: 1879 1.57 - 1.70: 6 1.70 - 1.82: 33 Bond restraints: 3896 Sorted by residual: bond pdb=" C THR B 233 " pdb=" N ASP B 234 " ideal model delta sigma weight residual 1.332 1.507 -0.174 1.40e-02 5.10e+03 1.55e+02 bond pdb=" CA GLU B 260 " pdb=" CB GLU B 260 " ideal model delta sigma weight residual 1.528 1.365 0.163 1.56e-02 4.11e+03 1.09e+02 bond pdb=" CA GLU B 317 " pdb=" C GLU B 317 " ideal model delta sigma weight residual 1.523 1.436 0.087 1.34e-02 5.57e+03 4.22e+01 bond pdb=" CA GLU B 326 " pdb=" C GLU B 326 " ideal model delta sigma weight residual 1.532 1.464 0.068 1.12e-02 7.97e+03 3.70e+01 bond pdb=" CA PHE B 142 " pdb=" C PHE B 142 " ideal model delta sigma weight residual 1.523 1.447 0.076 1.34e-02 5.57e+03 3.19e+01 ... (remaining 3891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.18: 4908 5.18 - 10.36: 307 10.36 - 15.53: 27 15.53 - 20.71: 6 20.71 - 25.89: 3 Bond angle restraints: 5251 Sorted by residual: angle pdb=" N LYS B 235 " pdb=" CA LYS B 235 " pdb=" C LYS B 235 " ideal model delta sigma weight residual 111.07 136.96 -25.89 1.07e+00 8.73e-01 5.85e+02 angle pdb=" C ALA B 132 " pdb=" N VAL B 133 " pdb=" CA VAL B 133 " ideal model delta sigma weight residual 120.88 143.46 -22.58 1.22e+00 6.72e-01 3.42e+02 angle pdb=" C ILE B 211 " pdb=" CA ILE B 211 " pdb=" CB ILE B 211 " ideal model delta sigma weight residual 111.81 93.01 18.80 1.25e+00 6.40e-01 2.26e+02 angle pdb=" CA ASN B 52 " pdb=" CB ASN B 52 " pdb=" CG ASN B 52 " ideal model delta sigma weight residual 112.60 99.60 13.00 1.00e+00 1.00e+00 1.69e+02 angle pdb=" CA PHE B 322 " pdb=" CB PHE B 322 " pdb=" CG PHE B 322 " ideal model delta sigma weight residual 113.80 101.20 12.60 1.00e+00 1.00e+00 1.59e+02 ... (remaining 5246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 2199 17.85 - 35.71: 139 35.71 - 53.56: 28 53.56 - 71.42: 18 71.42 - 89.27: 11 Dihedral angle restraints: 2395 sinusoidal: 937 harmonic: 1458 Sorted by residual: dihedral pdb=" N LYS B 263 " pdb=" C LYS B 263 " pdb=" CA LYS B 263 " pdb=" CB LYS B 263 " ideal model delta harmonic sigma weight residual 122.80 166.15 -43.35 0 2.50e+00 1.60e-01 3.01e+02 dihedral pdb=" C LYS B 263 " pdb=" N LYS B 263 " pdb=" CA LYS B 263 " pdb=" CB LYS B 263 " ideal model delta harmonic sigma weight residual -122.60 -165.66 43.06 0 2.50e+00 1.60e-01 2.97e+02 dihedral pdb=" C ILE B 211 " pdb=" N ILE B 211 " pdb=" CA ILE B 211 " pdb=" CB ILE B 211 " ideal model delta harmonic sigma weight residual -122.00 -98.49 -23.51 0 2.50e+00 1.60e-01 8.84e+01 ... (remaining 2392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.523: 623 0.523 - 1.046: 5 1.046 - 1.569: 0 1.569 - 2.092: 1 2.092 - 2.616: 1 Chirality restraints: 630 Sorted by residual: chirality pdb=" CA ARG B 268 " pdb=" N ARG B 268 " pdb=" C ARG B 268 " pdb=" CB ARG B 268 " both_signs ideal model delta sigma weight residual False 2.51 -0.11 2.62 2.00e-01 2.50e+01 1.71e+02 chirality pdb=" CA LYS B 263 " pdb=" N LYS B 263 " pdb=" C LYS B 263 " pdb=" CB LYS B 263 " both_signs ideal model delta sigma weight residual False 2.51 0.62 1.89 2.00e-01 2.50e+01 8.96e+01 chirality pdb=" CA LYS B 33 " pdb=" N LYS B 33 " pdb=" C LYS B 33 " pdb=" CB LYS B 33 " both_signs ideal model delta sigma weight residual False 2.51 1.47 1.04 2.00e-01 2.50e+01 2.71e+01 ... (remaining 627 not shown) Planarity restraints: 676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 117 " 0.068 2.00e-02 2.50e+03 3.47e-02 3.02e+01 pdb=" CG TRP B 117 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP B 117 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP B 117 " -0.026 2.00e-02 2.50e+03 pdb=" NE1 TRP B 117 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 117 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 117 " -0.032 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 117 " 0.045 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 117 " -0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP B 117 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 233 " 0.023 2.00e-02 2.50e+03 5.32e-02 2.83e+01 pdb=" C THR B 233 " -0.092 2.00e-02 2.50e+03 pdb=" O THR B 233 " 0.040 2.00e-02 2.50e+03 pdb=" N ASP B 234 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 215 " 0.084 5.00e-02 4.00e+02 1.29e-01 2.66e+01 pdb=" N PRO B 216 " -0.223 5.00e-02 4.00e+02 pdb=" CA PRO B 216 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO B 216 " 0.067 5.00e-02 4.00e+02 ... (remaining 673 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 11 2.30 - 2.95: 2934 2.95 - 3.60: 6521 3.60 - 4.25: 9660 4.25 - 4.90: 14419 Nonbonded interactions: 33545 Sorted by model distance: nonbonded pdb=" NH1 ARG B 244 " pdb=" O VAL B 245 " model vdw 1.652 3.120 nonbonded pdb=" NH1 ARG B 244 " pdb=" C VAL B 245 " model vdw 2.010 3.350 nonbonded pdb=" CZ ARG B 244 " pdb=" O VAL B 245 " model vdw 2.043 3.270 nonbonded pdb=" CB PHE B 142 " pdb=" N ARG B 143 " model vdw 2.160 2.816 nonbonded pdb=" O LYS B 237 " pdb=" CD1 ILE B 238 " model vdw 2.207 3.460 ... (remaining 33540 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.470 Find NCS groups from input model: 0.030 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2994 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 : 0.020 0.174 3896 Z= 1.309 Angle : 2.863 25.890 5251 Z= 1.937 Chirality : 0.196 2.616 630 Planarity : 0.014 0.129 676 Dihedral : 15.200 89.272 1455 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 179.94 Ramachandran Plot: Outliers : 4.31 % Allowed : 6.26 % Favored : 89.43 % Rotamer: Outliers : 7.82 % Allowed : 13.20 % Favored : 78.97 % Cbeta Deviations : 4.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.39 % 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: -0.59 (0.35), residues: 511 helix: 0.98 (0.29), residues: 251 sheet: 0.07 (0.88), residues: 43 loop : -2.23 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.028 TRP B 117 HIS 0.005 0.001 HIS B 109 PHE 0.013 0.002 PHE B 322 TYR 0.022 0.003 TYR B 284 ARG 0.015 0.001 ARG B 363 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 THR cc_start: 0.5819 (m) cc_final: 0.5615 (p) REVERT: B 128 LEU cc_start: 0.6539 (mt) cc_final: 0.6049 (mt) REVERT: B 129 LEU cc_start: 0.4424 (OUTLIER) cc_final: 0.3675 (tt) REVERT: B 200 TYR cc_start: 0.5188 (m-80) cc_final: 0.4649 (m-80) REVERT: B 255 GLU cc_start: 0.4800 (tm-30) cc_final: 0.4563 (tp30) REVERT: B 296 VAL cc_start: 0.6608 (t) cc_final: 0.6304 (t) REVERT: B 465 LEU cc_start: 0.1452 (OUTLIER) cc_final: 0.0576 (mm) REVERT: B 475 MET cc_start: -0.1465 (tpp) cc_final: -0.2293 (mmm) outliers start: 32 outliers final: 7 residues processed: 130 average time/residue: 0.2285 time to fit residues: 34.3002 Evaluate side-chains 82 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 465 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 29 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN B 182 ASN B 272 HIS ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 GLN B 368 GLN B 451 GLN ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.218710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.207410 restraints weight = 12862.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.210029 restraints weight = 8786.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.211886 restraints weight = 6260.113| |-----------------------------------------------------------------------------| r_work (final): 0.4833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3600 moved from start: 0.6046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3896 Z= 0.333 Angle : 1.212 19.090 5251 Z= 0.627 Chirality : 0.067 0.433 630 Planarity : 0.008 0.075 676 Dihedral : 10.516 76.426 565 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 34.12 Ramachandran Plot: Outliers : 2.15 % Allowed : 8.22 % Favored : 89.63 % Rotamer: Outliers : 6.60 % Allowed : 20.54 % Favored : 72.86 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.39 % Twisted Proline : 0.00 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.35), residues: 511 helix: -0.31 (0.29), residues: 251 sheet: -0.30 (0.69), residues: 63 loop : -2.62 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 117 HIS 0.013 0.002 HIS B 324 PHE 0.035 0.004 PHE B 484 TYR 0.009 0.002 TYR B 443 ARG 0.007 0.001 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 VAL cc_start: 0.6922 (t) cc_final: 0.6326 (t) REVERT: B 129 LEU cc_start: 0.1427 (OUTLIER) cc_final: 0.1129 (pp) REVERT: B 147 MET cc_start: 0.0764 (mpt) cc_final: 0.0363 (mpt) REVERT: B 174 VAL cc_start: 0.5090 (OUTLIER) cc_final: 0.4763 (m) REVERT: B 278 ILE cc_start: 0.4779 (OUTLIER) cc_final: 0.4184 (mp) REVERT: B 467 MET cc_start: 0.1343 (pmm) cc_final: 0.1088 (pmm) REVERT: B 496 GLU cc_start: 0.6285 (mm-30) cc_final: 0.5804 (mm-30) outliers start: 27 outliers final: 8 residues processed: 109 average time/residue: 0.2011 time to fit residues: 26.0731 Evaluate side-chains 77 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 465 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 21 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** 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 = 0.4856 r_free = 0.4856 target = 0.213034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.202376 restraints weight = 12966.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.204757 restraints weight = 9072.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.206298 restraints weight = 6551.299| |-----------------------------------------------------------------------------| r_work (final): 0.4780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4008 moved from start: 0.7926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3896 Z= 0.304 Angle : 1.108 16.856 5251 Z= 0.564 Chirality : 0.059 0.315 630 Planarity : 0.007 0.055 676 Dihedral : 9.241 74.147 556 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 33.48 Ramachandran Plot: Outliers : 1.17 % Allowed : 9.59 % Favored : 89.24 % Rotamer: Outliers : 5.38 % Allowed : 26.41 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.39 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.34), residues: 511 helix: -0.88 (0.28), residues: 251 sheet: 0.20 (0.71), residues: 65 loop : -2.98 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 117 HIS 0.012 0.002 HIS B 324 PHE 0.019 0.003 PHE B 166 TYR 0.014 0.002 TYR B 443 ARG 0.008 0.001 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 VAL cc_start: 0.7173 (t) cc_final: 0.6656 (t) REVERT: B 129 LEU cc_start: 0.0505 (OUTLIER) cc_final: 0.0286 (pp) REVERT: B 271 LYS cc_start: 0.3997 (OUTLIER) cc_final: 0.3639 (pttm) REVERT: B 421 VAL cc_start: 0.7156 (m) cc_final: 0.6927 (p) REVERT: B 431 ARG cc_start: 0.4628 (OUTLIER) cc_final: 0.4411 (tpm170) outliers start: 22 outliers final: 13 residues processed: 91 average time/residue: 0.1862 time to fit residues: 20.4480 Evaluate side-chains 77 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 431 ARG Chi-restraints excluded: chain B residue 465 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 1 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 chunk 25 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 24 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.214193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.202652 restraints weight = 12950.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.204980 restraints weight = 9304.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.206818 restraints weight = 6926.835| |-----------------------------------------------------------------------------| r_work (final): 0.4778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3880 moved from start: 0.8800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3896 Z= 0.231 Angle : 0.974 15.566 5251 Z= 0.492 Chirality : 0.053 0.262 630 Planarity : 0.005 0.057 676 Dihedral : 8.554 69.125 556 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 24.79 Ramachandran Plot: Outliers : 0.98 % Allowed : 9.78 % Favored : 89.24 % Rotamer: Outliers : 6.85 % Allowed : 26.89 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.34), residues: 511 helix: -0.49 (0.29), residues: 251 sheet: -0.15 (0.65), residues: 75 loop : -3.40 (0.38), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 117 HIS 0.008 0.002 HIS B 324 PHE 0.018 0.002 PHE B 166 TYR 0.009 0.001 TYR B 443 ARG 0.004 0.001 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 LEU cc_start: 0.0675 (OUTLIER) cc_final: 0.0327 (pp) REVERT: B 299 ILE cc_start: 0.7129 (mp) cc_final: 0.6895 (mp) outliers start: 28 outliers final: 17 residues processed: 92 average time/residue: 0.1989 time to fit residues: 21.9599 Evaluate side-chains 80 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 431 ARG Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 502 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 32 optimal weight: 0.1980 chunk 1 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 35 optimal weight: 0.0370 chunk 6 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 14 optimal weight: 0.0770 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.215822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.204167 restraints weight = 13054.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.206704 restraints weight = 9131.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.208391 restraints weight = 6682.921| |-----------------------------------------------------------------------------| r_work (final): 0.4802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3852 moved from start: 0.9624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3896 Z= 0.217 Angle : 0.944 15.453 5251 Z= 0.468 Chirality : 0.051 0.251 630 Planarity : 0.005 0.052 676 Dihedral : 7.921 60.575 554 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 1.17 % Allowed : 9.39 % Favored : 89.43 % Rotamer: Outliers : 5.38 % Allowed : 26.89 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.35), residues: 511 helix: -0.30 (0.30), residues: 249 sheet: -0.17 (0.65), residues: 75 loop : -3.36 (0.37), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 117 HIS 0.011 0.002 HIS B 272 PHE 0.019 0.002 PHE B 166 TYR 0.005 0.001 TYR B 284 ARG 0.004 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 129 LEU cc_start: 0.0132 (OUTLIER) cc_final: -0.0178 (pp) REVERT: B 214 ASN cc_start: 0.5662 (p0) cc_final: 0.5398 (p0) REVERT: B 225 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5838 (tm) REVERT: B 269 ILE cc_start: 0.4065 (OUTLIER) cc_final: 0.3458 (mm) outliers start: 22 outliers final: 11 residues processed: 86 average time/residue: 0.1788 time to fit residues: 19.0208 Evaluate side-chains 75 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 502 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 38 optimal weight: 0.4980 chunk 41 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 GLN ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** 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 = 0.4833 r_free = 0.4833 target = 0.210466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.199798 restraints weight = 13033.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.202192 restraints weight = 8843.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.203929 restraints weight = 6380.769| |-----------------------------------------------------------------------------| r_work (final): 0.4750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4088 moved from start: 1.0456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3896 Z= 0.255 Angle : 0.991 16.016 5251 Z= 0.493 Chirality : 0.051 0.233 630 Planarity : 0.005 0.050 676 Dihedral : 7.934 52.188 554 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 23.90 Ramachandran Plot: Outliers : 1.17 % Allowed : 8.81 % Favored : 90.02 % Rotamer: Outliers : 5.62 % Allowed : 27.63 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.39 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.33), residues: 511 helix: -0.28 (0.30), residues: 249 sheet: -0.39 (0.67), residues: 62 loop : -3.09 (0.34), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 117 HIS 0.010 0.002 HIS B 272 PHE 0.020 0.002 PHE B 166 TYR 0.013 0.001 TYR B 443 ARG 0.006 0.001 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 LEU cc_start: 0.0726 (OUTLIER) cc_final: 0.0379 (pp) REVERT: B 143 ARG cc_start: 0.4468 (tpm170) cc_final: 0.4003 (tpm170) REVERT: B 403 LEU cc_start: 0.7331 (mt) cc_final: 0.6938 (mt) REVERT: B 431 ARG cc_start: 0.4515 (OUTLIER) cc_final: 0.4156 (tpm170) REVERT: B 480 ILE cc_start: -0.0626 (OUTLIER) cc_final: -0.0921 (tt) outliers start: 23 outliers final: 15 residues processed: 82 average time/residue: 0.1615 time to fit residues: 16.5127 Evaluate side-chains 81 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 431 ARG Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 480 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 42 optimal weight: 0.0980 chunk 18 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.212616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.202483 restraints weight = 13367.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.204702 restraints weight = 9288.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.206328 restraints weight = 6759.256| |-----------------------------------------------------------------------------| r_work (final): 0.4777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3922 moved from start: 1.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3896 Z= 0.218 Angle : 0.916 14.954 5251 Z= 0.455 Chirality : 0.049 0.273 630 Planarity : 0.005 0.049 676 Dihedral : 7.505 51.370 554 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 1.17 % Allowed : 9.00 % Favored : 89.82 % Rotamer: Outliers : 6.85 % Allowed : 27.63 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.35), residues: 511 helix: -0.05 (0.32), residues: 245 sheet: -0.33 (0.69), residues: 62 loop : -2.98 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 117 HIS 0.012 0.001 HIS B 272 PHE 0.015 0.002 PHE B 166 TYR 0.016 0.001 TYR B 286 ARG 0.003 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 LEU cc_start: 0.0546 (OUTLIER) cc_final: 0.0203 (pp) REVERT: B 143 ARG cc_start: 0.4401 (tpm170) cc_final: 0.4025 (tpm170) REVERT: B 225 LEU cc_start: 0.6205 (OUTLIER) cc_final: 0.5981 (tm) REVERT: B 467 MET cc_start: 0.1987 (OUTLIER) cc_final: 0.1696 (pmm) REVERT: B 480 ILE cc_start: -0.0660 (OUTLIER) cc_final: -0.0993 (tt) outliers start: 28 outliers final: 14 residues processed: 83 average time/residue: 0.1701 time to fit residues: 17.5405 Evaluate side-chains 79 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 467 MET Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 502 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 5 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 0.0970 chunk 48 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.211429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.199500 restraints weight = 12657.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.202274 restraints weight = 8582.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.204317 restraints weight = 6108.826| |-----------------------------------------------------------------------------| r_work (final): 0.4754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4084 moved from start: 1.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3896 Z= 0.226 Angle : 0.925 15.363 5251 Z= 0.462 Chirality : 0.049 0.264 630 Planarity : 0.005 0.045 676 Dihedral : 6.981 42.958 551 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.98 % Allowed : 8.22 % Favored : 90.80 % Rotamer: Outliers : 5.38 % Allowed : 27.63 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.36), residues: 511 helix: -0.05 (0.33), residues: 246 sheet: -0.08 (0.72), residues: 62 loop : -3.08 (0.36), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 117 HIS 0.009 0.001 HIS B 272 PHE 0.015 0.002 PHE B 166 TYR 0.012 0.001 TYR B 286 ARG 0.016 0.001 ARG B 431 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 LEU cc_start: 0.0753 (OUTLIER) cc_final: 0.0344 (pp) REVERT: B 143 ARG cc_start: 0.4123 (tpm170) cc_final: 0.3646 (tpm170) REVERT: B 147 MET cc_start: -0.0332 (tpt) cc_final: -0.0968 (ppp) REVERT: B 225 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.6107 (tm) REVERT: B 480 ILE cc_start: -0.0575 (OUTLIER) cc_final: -0.1136 (tt) outliers start: 22 outliers final: 16 residues processed: 80 average time/residue: 0.1472 time to fit residues: 15.0186 Evaluate side-chains 76 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 502 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.211539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.202315 restraints weight = 13790.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.204486 restraints weight = 9424.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.206089 restraints weight = 6720.523| |-----------------------------------------------------------------------------| r_work (final): 0.4759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4090 moved from start: 1.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3896 Z= 0.236 Angle : 0.926 15.313 5251 Z= 0.458 Chirality : 0.050 0.255 630 Planarity : 0.005 0.046 676 Dihedral : 6.959 43.151 551 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.98 % Allowed : 8.81 % Favored : 90.22 % Rotamer: Outliers : 5.38 % Allowed : 29.10 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.35), residues: 511 helix: -0.11 (0.33), residues: 245 sheet: 0.12 (0.75), residues: 54 loop : -3.27 (0.34), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 117 HIS 0.013 0.002 HIS B 456 PHE 0.016 0.002 PHE B 166 TYR 0.013 0.001 TYR B 443 ARG 0.005 0.001 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: B 129 LEU cc_start: 0.0836 (OUTLIER) cc_final: 0.0442 (pp) REVERT: B 143 ARG cc_start: 0.4347 (tpm170) cc_final: 0.3849 (tpm170) REVERT: B 147 MET cc_start: 0.0503 (tpt) cc_final: -0.0879 (ppp) REVERT: B 225 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.6112 (tm) REVERT: B 480 ILE cc_start: 0.0613 (OUTLIER) cc_final: -0.0185 (tt) outliers start: 22 outliers final: 15 residues processed: 74 average time/residue: 0.1627 time to fit residues: 15.0136 Evaluate side-chains 75 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 467 MET Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 502 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 7.9990 chunk 36 optimal weight: 0.0000 chunk 14 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 33 optimal weight: 0.0070 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 overall best weight: 3.2008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 ASN ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.209386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.201692 restraints weight = 13568.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.203371 restraints weight = 9483.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.204667 restraints weight = 6961.637| |-----------------------------------------------------------------------------| r_work (final): 0.4778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4225 moved from start: 1.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 3896 Z= 0.319 Angle : 1.041 16.416 5251 Z= 0.522 Chirality : 0.055 0.289 630 Planarity : 0.006 0.065 676 Dihedral : 7.607 39.423 551 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 28.63 Ramachandran Plot: Outliers : 0.98 % Allowed : 9.20 % Favored : 89.82 % Rotamer: Outliers : 4.65 % Allowed : 30.56 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.34), residues: 511 helix: -0.62 (0.31), residues: 249 sheet: 0.24 (0.76), residues: 54 loop : -3.48 (0.32), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 117 HIS 0.009 0.002 HIS B 456 PHE 0.021 0.002 PHE B 166 TYR 0.023 0.002 TYR B 443 ARG 0.009 0.001 ARG B 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.742 Fit side-chains REVERT: B 147 MET cc_start: 0.0345 (tpt) cc_final: -0.0759 (ppp) REVERT: B 402 MET cc_start: 0.6684 (ttp) cc_final: 0.6429 (tmm) REVERT: B 403 LEU cc_start: 0.7367 (mt) cc_final: 0.6468 (mt) REVERT: B 467 MET cc_start: 0.2402 (OUTLIER) cc_final: 0.1584 (mtm) REVERT: B 488 ARG cc_start: 0.4701 (mtm110) cc_final: 0.4372 (mtm180) outliers start: 19 outliers final: 15 residues processed: 84 average time/residue: 0.1515 time to fit residues: 16.5643 Evaluate side-chains 83 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 467 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 GLN ** B 386 GLN ** 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 = 0.4841 r_free = 0.4841 target = 0.209807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.202090 restraints weight = 13384.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.203754 restraints weight = 9357.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.205010 restraints weight = 6849.447| |-----------------------------------------------------------------------------| r_work (final): 0.4778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4215 moved from start: 1.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3896 Z= 0.275 Angle : 1.000 14.746 5251 Z= 0.505 Chirality : 0.052 0.281 630 Planarity : 0.006 0.050 676 Dihedral : 7.227 40.044 549 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 26.71 Ramachandran Plot: Outliers : 0.98 % Allowed : 9.59 % Favored : 89.43 % Rotamer: Outliers : 4.40 % Allowed : 28.85 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.34), residues: 511 helix: -0.48 (0.32), residues: 248 sheet: 0.35 (0.78), residues: 54 loop : -3.40 (0.32), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 117 HIS 0.009 0.002 HIS B 456 PHE 0.016 0.002 PHE B 166 TYR 0.017 0.002 TYR B 443 ARG 0.011 0.001 ARG B 176 =============================================================================== Job complete usr+sys time: 1594.32 seconds wall clock time: 29 minutes 23.81 seconds (1763.81 seconds total)