Starting phenix.real_space_refine (version: dev) on Mon Apr 4 12:08:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ktt_5148/04_2022/3ktt_5148.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ktt_5148/04_2022/3ktt_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_5148/04_2022/3ktt_5148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ktt_5148/04_2022/3ktt_5148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ktt_5148/04_2022/3ktt_5148.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ktt_5148/04_2022/3ktt_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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: {'PTRANS': 9, 'CIS': 7, 'TRANS': 496} Time building chain proxies: 2.52, per 1000 atoms: 0.65 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: 1.78 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.24 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: 1.13 Time building geometry restraints manager: 1.89 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 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. 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: 0.460 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: 0.070 Convert atoms to be neutral: 0.030 Process input model: 15.470 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.860 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: 0.2842 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 : 2.861 25.890 5251 Z= 1.934 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 : 0.453 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: 8 residues processed: 130 average time/residue: 0.2195 time to fit residues: 33.1970 Evaluate side-chains 78 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.455 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1191 time to fit residues: 1.8766 ------------------------------------------------------------------------------- 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: 7.9990 chunk 38 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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: 0.3188 moved from start: 0.5958 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= 0.331 Angle : 1.235 19.572 5251 Z= 0.617 Chirality : 0.065 0.484 630 Planarity : 0.008 0.085 676 Dihedral : 8.862 77.704 543 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 39.23 Ramachandran Plot: Outliers : 2.15 % Allowed : 8.22 % Favored : 89.63 % Rotamer Outliers : 5.38 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.39 % Twisted Proline : 0.00 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.35), residues: 511 helix: -0.27 (0.29), residues: 253 sheet: -0.11 (0.68), residues: 63 loop : -2.93 (0.41), residues: 195 *********************** 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 108 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 86 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 101 average time/residue: 0.1863 time to fit residues: 22.8258 Evaluate side-chains 75 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.537 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0456 time to fit residues: 1.4187 ------------------------------------------------------------------------------- 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: 0.9990 chunk 14 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 31 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 50 optimal weight: 0.4980 chunk 41 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN ** 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: 0.3306 moved from start: 0.7773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 3896 Z= 0.258 Angle : 1.071 18.715 5251 Z= 0.519 Chirality : 0.054 0.322 630 Planarity : 0.006 0.058 676 Dihedral : 7.969 74.355 543 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 29.52 Ramachandran Plot: Outliers : 1.17 % Allowed : 9.98 % 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: -2.11 (0.35), residues: 511 helix: -0.64 (0.29), residues: 253 sheet: 0.57 (0.77), residues: 55 loop : -2.97 (0.39), residues: 203 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 93 average time/residue: 0.1768 time to fit residues: 19.9098 Evaluate side-chains 68 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.452 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0406 time to fit residues: 1.2230 ------------------------------------------------------------------------------- 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: 4.9990 chunk 24 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 410 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: 0.3517 moved from start: 0.9221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.087 3896 Z= 0.272 Angle : 1.107 18.130 5251 Z= 0.533 Chirality : 0.054 0.239 630 Planarity : 0.006 0.067 676 Dihedral : 7.896 70.465 543 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 29.90 Ramachandran Plot: Outliers : 0.98 % Allowed : 10.37 % Favored : 88.65 % Rotamer Outliers : 5.13 % 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: -2.33 (0.34), residues: 511 helix: -0.73 (0.30), residues: 253 sheet: -0.20 (0.68), residues: 64 loop : -3.13 (0.38), residues: 194 *********************** 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 92 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 71 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 86 average time/residue: 0.1596 time to fit residues: 17.0907 Evaluate side-chains 71 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 0.410 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0486 time to fit residues: 1.5434 ------------------------------------------------------------------------------- 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: 20.0000 chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 42 optimal weight: 30.0000 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 410 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: 0.3582 moved from start: 1.0157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 3896 Z= 0.233 Angle : 1.016 18.795 5251 Z= 0.492 Chirality : 0.049 0.253 630 Planarity : 0.007 0.116 676 Dihedral : 7.440 65.781 543 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 26.45 Ramachandran Plot: Outliers : 1.17 % Allowed : 9.78 % Favored : 89.04 % Rotamer Outliers : 3.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.01 (0.35), residues: 511 helix: -0.36 (0.31), residues: 249 sheet: -0.24 (0.67), residues: 62 loop : -2.98 (0.37), residues: 200 *********************** 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 83 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 67 time to evaluate : 0.447 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 78 average time/residue: 0.1612 time to fit residues: 15.7412 Evaluate side-chains 66 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.443 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1216 time to fit residues: 1.3975 ------------------------------------------------------------------------------- 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: 9.9990 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3512 moved from start: 1.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.090 3896 Z= 0.210 Angle : 0.992 18.572 5251 Z= 0.476 Chirality : 0.047 0.270 630 Planarity : 0.007 0.126 676 Dihedral : 6.836 57.660 543 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 1.17 % Allowed : 8.41 % Favored : 90.41 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.34), residues: 511 helix: -0.29 (0.31), residues: 248 sheet: -0.30 (0.66), residues: 64 loop : -2.85 (0.38), residues: 199 *********************** 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 82 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.464 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 75 average time/residue: 0.1628 time to fit residues: 15.3377 Evaluate side-chains 66 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.449 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0382 time to fit residues: 0.8515 ------------------------------------------------------------------------------- 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: 0.9990 chunk 41 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.3515 moved from start: 1.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.099 3896 Z= 0.216 Angle : 0.975 18.374 5251 Z= 0.472 Chirality : 0.048 0.273 630 Planarity : 0.007 0.130 676 Dihedral : 6.564 47.886 543 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 22.49 Ramachandran Plot: Outliers : 1.17 % Allowed : 7.63 % Favored : 91.19 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.35), residues: 511 helix: -0.24 (0.32), residues: 248 sheet: -0.38 (0.66), residues: 64 loop : -2.81 (0.38), residues: 199 *********************** 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 77 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 72 average time/residue: 0.1499 time to fit residues: 13.7456 Evaluate side-chains 69 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.447 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0445 time to fit residues: 1.0042 ------------------------------------------------------------------------------- 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: 8.9990 chunk 4 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 0.0670 chunk 47 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 35 optimal weight: 0.4980 chunk 14 optimal weight: 8.9990 overall best weight: 2.1124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN ** 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: 0.3696 moved from start: 1.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.131 3896 Z= 0.251 Angle : 1.037 17.668 5251 Z= 0.512 Chirality : 0.049 0.280 630 Planarity : 0.008 0.141 676 Dihedral : 6.786 39.642 543 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 28.12 Ramachandran Plot: Outliers : 1.17 % Allowed : 9.39 % Favored : 89.43 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.35), residues: 511 helix: -0.31 (0.32), residues: 250 sheet: -0.53 (0.63), residues: 62 loop : -2.87 (0.37), residues: 199 *********************** 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 76 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.459 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 73 average time/residue: 0.1525 time to fit residues: 14.2382 Evaluate side-chains 63 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.460 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0405 time to fit residues: 0.9442 ------------------------------------------------------------------------------- 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: 5.9990 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.3758 moved from start: 1.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.236 3896 Z= 0.273 Angle : 1.082 17.528 5251 Z= 0.548 Chirality : 0.049 0.305 630 Planarity : 0.009 0.155 676 Dihedral : 6.919 40.050 543 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 28.88 Ramachandran Plot: Outliers : 1.17 % Allowed : 8.02 % Favored : 90.80 % Rotamer Outliers : 1.22 % 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: -2.13 (0.34), residues: 511 helix: -0.38 (0.31), residues: 254 sheet: -0.42 (0.64), residues: 63 loop : -3.18 (0.36), residues: 194 *********************** 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 71 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 68 average time/residue: 0.1498 time to fit residues: 13.0937 Evaluate side-chains 64 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.465 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0451 time to fit residues: 0.9008 ------------------------------------------------------------------------------- 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: 6.9990 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 215 GLN ** 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: 0.3764 moved from start: 1.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.179 3896 Z= 0.258 Angle : 1.080 20.858 5251 Z= 0.556 Chirality : 0.048 0.279 630 Planarity : 0.009 0.179 676 Dihedral : 6.624 31.303 543 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 26.58 Ramachandran Plot: Outliers : 1.17 % Allowed : 8.41 % Favored : 90.41 % 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: -1.92 (0.35), residues: 511 helix: -0.22 (0.32), residues: 249 sheet: -0.29 (0.65), residues: 63 loop : -3.01 (0.36), residues: 199 ********************** 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 69 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.512 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 69 average time/residue: 0.1654 time to fit residues: 14.3674 Evaluate side-chains 61 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.459 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0390 time to fit residues: 0.7350 ------------------------------------------------------------------------------- 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: 8.9990 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 2 optimal weight: 0.3980 chunk 29 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 GLN B 165 HIS ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.202601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.195712 restraints weight = 13468.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.197558 restraints weight = 9189.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.198838 restraints weight = 6396.391| |-----------------------------------------------------------------------------| r_work (final): 0.4724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4252 moved from start: 1.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.155 3896 Z= 0.332 Angle : 1.221 20.619 5251 Z= 0.627 Chirality : 0.056 0.306 630 Planarity : 0.010 0.177 676 Dihedral : 7.596 29.722 543 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 37.19 Ramachandran Plot: Outliers : 1.17 % Allowed : 10.18 % Favored : 88.65 % Rotamer Outliers : 1.22 % 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: -2.54 (0.34), residues: 511 helix: -0.77 (0.32), residues: 249 sheet: -0.79 (0.62), residues: 65 loop : -3.19 (0.35), residues: 197 =============================================================================== Job complete usr+sys time: 1100.62 seconds wall clock time: 20 minutes 47.25 seconds (1247.25 seconds total)