Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 19:28:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ktt_5148/07_2023/3ktt_5148.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ktt_5148/07_2023/3ktt_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_5148/07_2023/3ktt_5148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ktt_5148/07_2023/3ktt_5148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ktt_5148/07_2023/3ktt_5148.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ktt_5148/07_2023/3ktt_5148.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 2.15, per 1000 atoms: 0.56 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: 1.89 Conformation dependent library (CDL) restraints added in 521.2 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: 0.25 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: 0.98 Time building geometry restraints manager: 1.99 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: 0.360 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: 2.050 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.320 Find NCS groups from input model: 0.090 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.900 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 7 residues processed: 130 average time/residue: 0.2317 time to fit residues: 34.9652 Evaluate side-chains 77 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.413 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1214 time to fit residues: 1.6850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3331 moved from start: 0.6037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 3896 Z= 0.332 Angle : 1.199 16.399 5251 Z= 0.623 Chirality : 0.064 0.439 630 Planarity : 0.008 0.085 676 Dihedral : 8.912 77.338 543 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 37.57 Ramachandran Plot: Outliers : 2.15 % Allowed : 8.22 % Favored : 89.63 % Rotamer Outliers : 5.13 % Cbeta Deviations : 0.21 % 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: -1.93 (0.35), residues: 511 helix: -0.37 (0.29), residues: 254 sheet: -0.13 (0.69), residues: 63 loop : -2.93 (0.41), residues: 194 *********************** 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 106 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 6 residues processed: 100 average time/residue: 0.1867 time to fit residues: 22.5539 Evaluate side-chains 73 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.417 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0419 time to fit residues: 1.0505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.0980 chunk 38 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 410 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: 0.3426 moved from start: 0.7780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 3896 Z= 0.263 Angle : 1.006 11.922 5251 Z= 0.518 Chirality : 0.053 0.338 630 Planarity : 0.006 0.059 676 Dihedral : 7.990 73.585 543 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 28.50 Ramachandran Plot: Outliers : 1.17 % Allowed : 9.98 % Favored : 88.85 % Rotamer Outliers : 3.67 % 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 (0.35), residues: 511 helix: -0.62 (0.29), residues: 254 sheet: 0.09 (0.71), residues: 63 loop : -3.06 (0.40), residues: 194 *********************** 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 91 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 87 average time/residue: 0.1835 time to fit residues: 19.3218 Evaluate side-chains 75 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.371 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0397 time to fit residues: 1.3149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3729 moved from start: 0.9306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 3896 Z= 0.300 Angle : 1.028 11.163 5251 Z= 0.525 Chirality : 0.054 0.220 630 Planarity : 0.006 0.052 676 Dihedral : 7.992 68.739 543 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 31.05 Ramachandran Plot: Outliers : 0.98 % Allowed : 10.18 % Favored : 88.85 % Rotamer Outliers : 3.91 % 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: -2.18 (0.35), residues: 511 helix: -0.61 (0.30), residues: 256 sheet: 0.04 (0.70), residues: 65 loop : -3.16 (0.39), residues: 190 *********************** 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 87 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 71 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 82 average time/residue: 0.1838 time to fit residues: 18.5556 Evaluate side-chains 71 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0432 time to fit residues: 1.0530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 20 optimal weight: 0.0870 chunk 42 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 386 GLN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3847 moved from start: 1.0473 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= 0.261 Angle : 0.964 11.215 5251 Z= 0.494 Chirality : 0.052 0.249 630 Planarity : 0.006 0.077 676 Dihedral : 7.739 64.315 543 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 29.14 Ramachandran Plot: Outliers : 1.17 % Allowed : 9.78 % Favored : 89.04 % Rotamer Outliers : 3.42 % 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: -0.50 (0.30), residues: 256 sheet: -0.13 (0.71), residues: 60 loop : -3.23 (0.37), residues: 195 *********************** 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 88 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 84 average time/residue: 0.1600 time to fit residues: 16.8652 Evaluate side-chains 74 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0864 time to fit residues: 1.3112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 GLN ** 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: 0.3913 moved from start: 1.1429 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= 0.248 Angle : 0.963 10.756 5251 Z= 0.494 Chirality : 0.051 0.301 630 Planarity : 0.006 0.063 676 Dihedral : 7.564 57.033 543 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 29.52 Ramachandran Plot: Outliers : 1.17 % Allowed : 11.15 % Favored : 87.67 % Rotamer Outliers : 4.16 % 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: -2.20 (0.34), residues: 511 helix: -0.50 (0.31), residues: 252 sheet: -0.44 (0.75), residues: 57 loop : -3.04 (0.36), residues: 202 *********************** 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 fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 0.396 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 80 average time/residue: 0.1471 time to fit residues: 15.0536 Evaluate side-chains 76 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0390 time to fit residues: 1.1658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 8.9990 chunk 41 optimal weight: 0.0270 chunk 49 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 ASN ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3920 moved from start: 1.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3896 Z= 0.223 Angle : 0.947 10.788 5251 Z= 0.474 Chirality : 0.048 0.263 630 Planarity : 0.005 0.059 676 Dihedral : 7.317 51.069 543 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 26.96 Ramachandran Plot: Outliers : 0.98 % Allowed : 10.18 % Favored : 88.85 % Rotamer Outliers : 1.47 % 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: -2.11 (0.34), residues: 511 helix: -0.37 (0.31), residues: 249 sheet: -0.18 (0.73), residues: 54 loop : -3.07 (0.35), residues: 208 *********************** 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 75 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.365 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 72 average time/residue: 0.1629 time to fit residues: 14.7919 Evaluate side-chains 66 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.424 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0405 time to fit residues: 0.6718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 0.0070 chunk 4 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- 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 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3929 moved from start: 1.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3896 Z= 0.220 Angle : 0.951 15.645 5251 Z= 0.471 Chirality : 0.048 0.226 630 Planarity : 0.005 0.058 676 Dihedral : 6.969 41.794 543 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 26.45 Ramachandran Plot: Outliers : 0.98 % Allowed : 9.59 % Favored : 89.43 % Rotamer Outliers : 1.96 % 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: -2.14 (0.34), residues: 511 helix: -0.34 (0.31), residues: 255 sheet: -0.08 (0.73), residues: 54 loop : -3.28 (0.34), residues: 202 *********************** 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 79 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.436 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 77 average time/residue: 0.1555 time to fit residues: 15.2644 Evaluate side-chains 70 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.425 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0470 time to fit residues: 0.7776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 20.0000 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 46 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 272 HIS ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4050 moved from start: 1.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 3896 Z= 0.247 Angle : 0.976 14.117 5251 Z= 0.483 Chirality : 0.050 0.277 630 Planarity : 0.005 0.051 676 Dihedral : 7.057 28.247 543 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 30.67 Ramachandran Plot: Outliers : 0.98 % Allowed : 11.15 % Favored : 87.87 % Rotamer Outliers : 0.98 % 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: -2.27 (0.34), residues: 511 helix: -0.52 (0.31), residues: 253 sheet: -0.30 (0.72), residues: 54 loop : -3.16 (0.34), residues: 204 *********************** 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 75 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.383 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 73 average time/residue: 0.1457 time to fit residues: 13.6456 Evaluate side-chains 71 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.434 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0406 time to fit residues: 0.8254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 5 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 165 HIS ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4076 moved from start: 1.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 3896 Z= 0.241 Angle : 0.985 13.923 5251 Z= 0.489 Chirality : 0.049 0.237 630 Planarity : 0.006 0.051 676 Dihedral : 6.848 25.329 543 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 29.27 Ramachandran Plot: Outliers : 0.98 % Allowed : 10.96 % Favored : 88.06 % Rotamer Outliers : 0.49 % 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: -0.44 (0.31), residues: 251 sheet: 0.10 (0.76), residues: 47 loop : -3.20 (0.34), residues: 213 ********************** 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 74 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.468 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 74 average time/residue: 0.1458 time to fit residues: 13.9659 Evaluate side-chains 70 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.453 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0405 time to fit residues: 0.7169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 0.8980 chunk 5 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 2 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS ** B 410 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 = 0.4770 r_free = 0.4770 target = 0.202850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.196102 restraints weight = 13364.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.197788 restraints weight = 9059.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.199055 restraints weight = 6346.469| |-----------------------------------------------------------------------------| r_work (final): 0.4725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4540 moved from start: 1.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 3896 Z= 0.320 Angle : 1.107 14.478 5251 Z= 0.555 Chirality : 0.054 0.287 630 Planarity : 0.006 0.058 676 Dihedral : 8.031 60.853 543 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 34.63 Ramachandran Plot: Outliers : 1.17 % Allowed : 11.55 % Favored : 87.28 % Rotamer Outliers : 0.24 % 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: -2.51 (0.34), residues: 511 helix: -0.81 (0.31), residues: 252 sheet: 0.09 (0.74), residues: 49 loop : -3.22 (0.34), residues: 210 =============================================================================== Job complete usr+sys time: 1070.53 seconds wall clock time: 20 minutes 17.99 seconds (1217.99 seconds total)