Starting phenix.real_space_refine on Wed Jan 17 14:37:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ktt_5148/01_2024/3ktt_5148.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ktt_5148/01_2024/3ktt_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ktt_5148/01_2024/3ktt_5148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ktt_5148/01_2024/3ktt_5148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ktt_5148/01_2024/3ktt_5148.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ktt_5148/01_2024/3ktt_5148.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 2.76, per 1000 atoms: 0.72 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 - 3.50 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: 1.77 Conformation dependent library (CDL) restraints added in 776.4 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: 0.45 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: 1.08 Time building geometry restraints manager: 1.88 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: 91.13 - 101.59: 32 101.59 - 112.06: 1664 112.06 - 122.52: 3035 122.52 - 132.99: 514 132.99 - 143.46: 6 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 2.520 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: 0.000 Extract box with map and model: 1.910 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.900 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.060 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 32 poor density : 110 time to evaluate : 0.415 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: 0.2349 time to fit residues: 35.4350 Evaluate side-chains 82 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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: 0.0270 chunk 38 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.9244 ------------------------------------------------------------------------------- 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 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 GLN B 410 GLN B 451 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3225 moved from start: 0.5746 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= 0.328 Angle : 1.189 19.309 5251 Z= 0.616 Chirality : 0.065 0.471 630 Planarity : 0.008 0.087 676 Dihedral : 10.448 76.768 565 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 37.44 Ramachandran Plot: Outliers : 1.96 % Allowed : 8.41 % Favored : 89.63 % Rotamer: Outliers : 6.85 % Allowed : 19.32 % Favored : 73.84 % Cbeta Deviations : 0.21 % 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: -1.76 (0.35), residues: 511 helix: -0.24 (0.29), residues: 250 sheet: -0.35 (0.66), residues: 63 loop : -2.67 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP B 117 HIS 0.014 0.002 HIS B 324 PHE 0.030 0.003 PHE B 166 TYR 0.013 0.002 TYR B 395 ARG 0.006 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 117 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 89 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 VAL cc_start: 0.6914 (t) cc_final: 0.6275 (t) REVERT: B 129 LEU cc_start: 0.1458 (OUTLIER) cc_final: 0.1230 (pp) REVERT: B 147 MET cc_start: 0.0428 (mpt) cc_final: -0.0110 (mpt) REVERT: B 174 VAL cc_start: 0.4723 (OUTLIER) cc_final: 0.4475 (m) REVERT: B 211 ILE cc_start: 0.0460 (OUTLIER) cc_final: 0.0169 (mt) outliers start: 28 outliers final: 6 residues processed: 112 average time/residue: 0.1995 time to fit residues: 26.5319 Evaluate side-chains 76 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 211 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 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3424 moved from start: 0.7600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 3896 Z= 0.271 Angle : 1.051 17.278 5251 Z= 0.534 Chirality : 0.055 0.326 630 Planarity : 0.006 0.057 676 Dihedral : 8.981 73.014 556 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 31.69 Ramachandran Plot: Outliers : 1.17 % Allowed : 9.59 % Favored : 89.24 % Rotamer: Outliers : 6.11 % Allowed : 23.96 % Favored : 69.93 % 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: -2.15 (0.34), residues: 511 helix: -0.56 (0.29), residues: 251 sheet: 0.24 (0.77), residues: 51 loop : -2.97 (0.38), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 117 HIS 0.012 0.002 HIS B 324 PHE 0.018 0.003 PHE B 166 TYR 0.009 0.001 TYR B 443 ARG 0.007 0.001 ARG B 76 *********************** 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 99 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 74 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 278 ILE cc_start: 0.5659 (OUTLIER) cc_final: 0.5288 (pt) outliers start: 25 outliers final: 15 residues processed: 93 average time/residue: 0.1806 time to fit residues: 20.2835 Evaluate side-chains 79 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 146 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 402 MET Chi-restraints excluded: chain B residue 410 GLN 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 34 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 41 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 ASN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3477 moved from start: 0.8752 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= 0.236 Angle : 0.965 12.347 5251 Z= 0.485 Chirality : 0.052 0.283 630 Planarity : 0.005 0.052 676 Dihedral : 8.326 66.749 552 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 27.99 Ramachandran Plot: Outliers : 0.98 % Allowed : 10.96 % Favored : 88.06 % Rotamer: Outliers : 7.58 % Allowed : 23.47 % Favored : 68.95 % 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: -2.20 (0.34), residues: 511 helix: -0.47 (0.30), residues: 249 sheet: 0.03 (0.70), residues: 58 loop : -3.22 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 117 HIS 0.011 0.002 HIS B 272 PHE 0.018 0.003 PHE B 166 TYR 0.007 0.001 TYR B 443 ARG 0.006 0.001 ARG B 76 *********************** 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 103 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 72 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 VAL cc_start: 0.7292 (OUTLIER) cc_final: 0.6644 (t) outliers start: 31 outliers final: 20 residues processed: 92 average time/residue: 0.1963 time to fit residues: 21.5762 Evaluate side-chains 87 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 66 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 271 LYS 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 402 MET Chi-restraints excluded: chain B residue 410 GLN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 0 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3779 moved from start: 0.9950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3896 Z= 0.275 Angle : 1.002 12.058 5251 Z= 0.510 Chirality : 0.053 0.277 630 Planarity : 0.006 0.051 676 Dihedral : 8.691 60.649 552 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 31.31 Ramachandran Plot: Outliers : 1.17 % Allowed : 10.37 % Favored : 88.45 % Rotamer: Outliers : 7.09 % Allowed : 23.47 % Favored : 69.44 % 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: -2.35 (0.33), residues: 511 helix: -0.70 (0.30), residues: 248 sheet: -0.40 (0.66), residues: 65 loop : -3.08 (0.36), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 117 HIS 0.007 0.002 HIS B 324 PHE 0.021 0.003 PHE B 166 TYR 0.012 0.001 TYR B 443 ARG 0.007 0.001 ARG B 392 *********************** 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 100 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 71 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 MET cc_start: 0.4193 (tpp) cc_final: 0.3925 (tpp) REVERT: B 78 GLN cc_start: 0.6272 (tp40) cc_final: 0.5762 (tp40) REVERT: B 171 VAL cc_start: 0.3185 (OUTLIER) cc_final: 0.2972 (m) REVERT: B 214 ASN cc_start: 0.4520 (p0) cc_final: 0.4274 (p0) REVERT: B 271 LYS cc_start: 0.3661 (OUTLIER) cc_final: 0.3119 (pttm) REVERT: B 403 LEU cc_start: 0.6737 (mt) cc_final: 0.6393 (mt) outliers start: 29 outliers final: 17 residues processed: 91 average time/residue: 0.1532 time to fit residues: 17.5159 Evaluate side-chains 85 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 410 GLN 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3885 moved from start: 1.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 3896 Z= 0.308 Angle : 0.993 11.886 5251 Z= 0.507 Chirality : 0.053 0.309 630 Planarity : 0.006 0.064 676 Dihedral : 8.635 59.662 552 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 28.12 Ramachandran Plot: Outliers : 1.17 % Allowed : 9.78 % Favored : 89.04 % Rotamer: Outliers : 6.85 % Allowed : 23.47 % Favored : 69.68 % 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: -2.48 (0.33), residues: 511 helix: -0.68 (0.30), residues: 250 sheet: -0.32 (0.72), residues: 54 loop : -3.28 (0.34), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP B 117 HIS 0.008 0.002 HIS B 272 PHE 0.022 0.003 PHE B 166 TYR 0.020 0.002 TYR B 443 ARG 0.006 0.001 ARG B 392 *********************** 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 95 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 67 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: B 74 MET cc_start: 0.3987 (tpp) cc_final: 0.3732 (tpp) REVERT: B 78 GLN cc_start: 0.6282 (tp40) cc_final: 0.5793 (tp40) outliers start: 28 outliers final: 17 residues processed: 86 average time/residue: 0.1577 time to fit residues: 16.9293 Evaluate side-chains 77 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 60 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 LEU 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 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 278 ILE Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 379 ASP Chi-restraints excluded: chain B residue 410 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3907 moved from start: 1.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3896 Z= 0.248 Angle : 0.963 12.845 5251 Z= 0.487 Chirality : 0.050 0.252 630 Planarity : 0.005 0.049 676 Dihedral : 7.885 48.809 549 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 26.07 Ramachandran Plot: Outliers : 0.98 % Allowed : 9.78 % Favored : 89.24 % Rotamer: Outliers : 5.62 % Allowed : 26.89 % Favored : 67.48 % 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: -2.23 (0.34), residues: 511 helix: -0.47 (0.31), residues: 246 sheet: -0.22 (0.71), residues: 54 loop : -3.11 (0.35), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 117 HIS 0.007 0.002 HIS B 272 PHE 0.018 0.003 PHE B 166 TYR 0.014 0.001 TYR B 443 ARG 0.007 0.001 ARG B 176 *********************** 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 86 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 63 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 74 MET cc_start: 0.3993 (tpp) cc_final: 0.3690 (tpp) outliers start: 23 outliers final: 16 residues processed: 77 average time/residue: 0.1473 time to fit residues: 14.5228 Evaluate side-chains 76 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 60 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 57 ILE 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 211 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 379 ASP Chi-restraints excluded: chain B residue 410 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 GLN B 272 HIS ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3860 moved from start: 1.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3896 Z= 0.228 Angle : 0.923 11.629 5251 Z= 0.469 Chirality : 0.051 0.262 630 Planarity : 0.005 0.049 676 Dihedral : 7.446 44.054 549 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 24.41 Ramachandran Plot: Outliers : 0.98 % Allowed : 8.41 % Favored : 90.61 % Rotamer: Outliers : 6.11 % Allowed : 27.63 % 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: -2.10 (0.35), residues: 511 helix: -0.36 (0.31), residues: 248 sheet: -0.58 (0.66), residues: 65 loop : -3.05 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 117 HIS 0.009 0.001 HIS B 272 PHE 0.016 0.002 PHE B 166 TYR 0.011 0.001 TYR B 443 ARG 0.006 0.001 ARG B 176 *********************** 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 88 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 63 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 74 MET cc_start: 0.3805 (tpp) cc_final: 0.3466 (tpp) REVERT: B 76 ARG cc_start: 0.7993 (mtt90) cc_final: 0.7519 (mtt90) REVERT: B 279 ASN cc_start: 0.7030 (p0) cc_final: 0.5432 (m-40) outliers start: 25 outliers final: 19 residues processed: 81 average time/residue: 0.1626 time to fit residues: 16.6372 Evaluate side-chains 79 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 57 ILE 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 174 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 379 ASP Chi-restraints excluded: chain B residue 410 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 GLN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4101 moved from start: 1.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 3896 Z= 0.314 Angle : 1.066 11.933 5251 Z= 0.545 Chirality : 0.056 0.244 630 Planarity : 0.006 0.053 676 Dihedral : 7.989 40.768 549 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 32.59 Ramachandran Plot: Outliers : 1.17 % Allowed : 10.37 % Favored : 88.45 % Rotamer: Outliers : 6.60 % Allowed : 28.12 % Favored : 65.28 % 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: -2.43 (0.34), residues: 511 helix: -0.65 (0.31), residues: 248 sheet: -0.67 (0.63), residues: 64 loop : -3.20 (0.35), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 117 HIS 0.006 0.002 HIS B 272 PHE 0.024 0.003 PHE B 166 TYR 0.026 0.002 TYR B 443 ARG 0.010 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 96 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 69 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 MET cc_start: 0.3885 (tpp) cc_final: 0.3574 (tpp) REVERT: B 76 ARG cc_start: 0.8062 (mtt90) cc_final: 0.7660 (mtt90) REVERT: B 145 ASP cc_start: 0.7502 (t0) cc_final: 0.7004 (t0) REVERT: B 279 ASN cc_start: 0.7251 (p0) cc_final: 0.5589 (m-40) REVERT: B 431 ARG cc_start: 0.5186 (OUTLIER) cc_final: 0.4572 (tpm170) REVERT: B 467 MET cc_start: 0.2649 (OUTLIER) cc_final: 0.1063 (mtm) outliers start: 27 outliers final: 21 residues processed: 84 average time/residue: 0.1633 time to fit residues: 16.9257 Evaluate side-chains 83 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 60 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 57 ILE 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 174 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 278 ILE 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 379 ASP Chi-restraints excluded: chain B residue 410 GLN 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 467 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3960 moved from start: 1.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3896 Z= 0.234 Angle : 0.974 14.510 5251 Z= 0.485 Chirality : 0.052 0.281 630 Planarity : 0.005 0.053 676 Dihedral : 7.257 42.206 549 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 25.43 Ramachandran Plot: Outliers : 0.98 % Allowed : 8.61 % Favored : 90.41 % Rotamer: Outliers : 5.13 % Allowed : 30.56 % Favored : 64.30 % 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: -0.29 (0.32), residues: 247 sheet: 0.09 (0.68), residues: 55 loop : -3.14 (0.35), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 117 HIS 0.008 0.001 HIS B 272 PHE 0.014 0.002 PHE B 166 TYR 0.015 0.002 TYR B 286 ARG 0.006 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 87 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 66 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: B 76 ARG cc_start: 0.8024 (mtt90) cc_final: 0.7649 (mtt90) REVERT: B 145 ASP cc_start: 0.7282 (t0) cc_final: 0.6767 (t0) REVERT: B 147 MET cc_start: 0.0779 (tpt) cc_final: -0.0600 (ppp) REVERT: B 275 ASN cc_start: 0.3774 (t0) cc_final: 0.3257 (t0) REVERT: B 279 ASN cc_start: 0.7168 (p0) cc_final: 0.5620 (m-40) REVERT: B 379 ASP cc_start: 0.5978 (OUTLIER) cc_final: 0.5646 (m-30) REVERT: B 431 ARG cc_start: 0.4994 (OUTLIER) cc_final: 0.4529 (tpm170) REVERT: B 467 MET cc_start: 0.2066 (OUTLIER) cc_final: 0.1283 (mtm) outliers start: 21 outliers final: 13 residues processed: 79 average time/residue: 0.1828 time to fit residues: 17.6399 Evaluate side-chains 77 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 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 40 LEU Chi-restraints excluded: chain B residue 57 ILE 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 347 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 379 ASP Chi-restraints excluded: chain B residue 410 GLN 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 467 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 2 optimal weight: 0.2980 chunk 29 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 GLN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.203831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.196495 restraints weight = 13554.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.198148 restraints weight = 9457.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.199269 restraints weight = 6853.763| |-----------------------------------------------------------------------------| r_work (final): 0.4721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4463 moved from start: 1.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3896 Z= 0.309 Angle : 1.093 14.528 5251 Z= 0.549 Chirality : 0.056 0.288 630 Planarity : 0.006 0.054 676 Dihedral : 7.994 45.117 549 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 33.74 Ramachandran Plot: Outliers : 1.17 % Allowed : 10.57 % Favored : 88.26 % Rotamer: Outliers : 4.65 % Allowed : 30.81 % Favored : 64.55 % 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: -2.44 (0.34), residues: 511 helix: -0.61 (0.32), residues: 248 sheet: -0.81 (0.64), residues: 65 loop : -3.22 (0.36), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 117 HIS 0.007 0.002 HIS B 161 PHE 0.026 0.003 PHE B 166 TYR 0.026 0.002 TYR B 443 ARG 0.009 0.001 ARG B 176 =============================================================================== Job complete usr+sys time: 1137.13 seconds wall clock time: 21 minutes 23.18 seconds (1283.18 seconds total)