Starting phenix.real_space_refine on Mon Nov 13 16:59:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/11_2023/7xq1_33388_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/11_2023/7xq1_33388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/11_2023/7xq1_33388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/11_2023/7xq1_33388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/11_2023/7xq1_33388_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/11_2023/7xq1_33388_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 14 5.16 5 C 2178 2.51 5 N 548 2.21 5 O 558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 3302 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3302 Unusual residues: {'GJF': 2} Classifications: {'peptide': 400, 'undetermined': 2} Link IDs: {'PTRANS': 14, 'TRANS': 385, None: 2} Not linked: pdbres="ASP A 453 " pdbres="GJF A 601 " Not linked: pdbres="GJF A 601 " pdbres="GJF A 602 " Chain breaks: 1 Time building chain proxies: 2.46, per 1000 atoms: 0.75 Number of scatterers: 3302 At special positions: 0 Unit cell: (79, 77, 64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 4 15.00 O 558 8.00 N 548 7.00 C 2178 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: 1.39 Conformation dependent library (CDL) restraints added in 620.6 milliseconds 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 758 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 0 sheets defined 72.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 24 through 27 No H-bonds generated for 'chain 'A' and resid 24 through 27' Processing helix chain 'A' and resid 29 through 40 removed outlier: 3.604A pdb=" N PHE A 34 " --> pdb=" O CYS A 30 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE A 37 " --> pdb=" O CYS A 33 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 52 No H-bonds generated for 'chain 'A' and resid 49 through 52' Processing helix chain 'A' and resid 61 through 64 No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 69 through 78 removed outlier: 3.552A pdb=" N TYR A 74 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER A 75 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR A 76 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 removed outlier: 3.868A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 112 removed outlier: 3.601A pdb=" N LEU A 111 " --> pdb=" O TRP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 removed outlier: 3.713A pdb=" N MET A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 removed outlier: 4.127A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 175 removed outlier: 3.521A pdb=" N LEU A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 201 removed outlier: 3.811A pdb=" N VAL A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 removed outlier: 3.683A pdb=" N GLY A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 285 removed outlier: 3.615A pdb=" N LEU A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 295 Processing helix chain 'A' and resid 306 through 317 removed outlier: 3.565A pdb=" N ALA A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 335 through 355 removed outlier: 4.051A pdb=" N ALA A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 363 through 387 removed outlier: 3.764A pdb=" N PHE A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 393 through 417 removed outlier: 3.611A pdb=" N ALA A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 451 removed outlier: 3.765A pdb=" N GLN A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) 166 hydrogen bonds defined for protein. 486 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: 0.79 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.37: 1050 1.37 - 1.53: 2213 1.53 - 1.69: 120 1.69 - 1.85: 17 1.85 - 2.01: 3 Bond restraints: 3403 Sorted by residual: bond pdb=" P2 GJF A 601 " pdb=" S2 GJF A 601 " ideal model delta sigma weight residual 2.082 1.766 0.316 2.00e-02 2.50e+03 2.49e+02 bond pdb=" P1 GJF A 601 " pdb=" S1 GJF A 601 " ideal model delta sigma weight residual 2.070 1.852 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" P2 GJF A 602 " pdb=" S2 GJF A 602 " ideal model delta sigma weight residual 2.082 1.930 0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" C11 GJF A 602 " pdb=" C14 GJF A 602 " ideal model delta sigma weight residual 1.406 1.325 0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C20 GJF A 601 " pdb=" N2 GJF A 601 " ideal model delta sigma weight residual 1.322 1.402 -0.080 2.00e-02 2.50e+03 1.59e+01 ... (remaining 3398 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.07: 113 107.07 - 113.80: 1901 113.80 - 120.53: 1486 120.53 - 127.26: 1113 127.26 - 133.99: 45 Bond angle restraints: 4658 Sorted by residual: angle pdb=" N SER A 321 " pdb=" CA SER A 321 " pdb=" C SER A 321 " ideal model delta sigma weight residual 111.36 105.43 5.93 1.09e+00 8.42e-01 2.96e+01 angle pdb=" N ARG A 133 " pdb=" CA ARG A 133 " pdb=" C ARG A 133 " ideal model delta sigma weight residual 111.69 105.43 6.26 1.23e+00 6.61e-01 2.59e+01 angle pdb=" N TYR A 136 " pdb=" CA TYR A 136 " pdb=" C TYR A 136 " ideal model delta sigma weight residual 111.02 117.21 -6.19 1.22e+00 6.72e-01 2.57e+01 angle pdb=" N PRO A 381 " pdb=" CA PRO A 381 " pdb=" C PRO A 381 " ideal model delta sigma weight residual 113.53 107.04 6.49 1.39e+00 5.18e-01 2.18e+01 angle pdb=" N PHE A 103 " pdb=" CA PHE A 103 " pdb=" C PHE A 103 " ideal model delta sigma weight residual 111.36 106.30 5.06 1.09e+00 8.42e-01 2.16e+01 ... (remaining 4653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 1784 17.60 - 35.20: 101 35.20 - 52.79: 35 52.79 - 70.39: 8 70.39 - 87.99: 2 Dihedral angle restraints: 1930 sinusoidal: 751 harmonic: 1179 Sorted by residual: dihedral pdb=" C VAL A 327 " pdb=" N VAL A 327 " pdb=" CA VAL A 327 " pdb=" CB VAL A 327 " ideal model delta harmonic sigma weight residual -122.00 -133.07 11.07 0 2.50e+00 1.60e-01 1.96e+01 dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA VAL A 418 " pdb=" C VAL A 418 " pdb=" N SER A 419 " pdb=" CA SER A 419 " ideal model delta harmonic sigma weight residual -180.00 -163.75 -16.25 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 1927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 463 0.066 - 0.131: 60 0.131 - 0.196: 13 0.196 - 0.261: 5 0.261 - 0.327: 3 Chirality restraints: 544 Sorted by residual: chirality pdb=" CA VAL A 327 " pdb=" N VAL A 327 " pdb=" C VAL A 327 " pdb=" CB VAL A 327 " both_signs ideal model delta sigma weight residual False 2.44 2.11 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" C16 GJF A 601 " pdb=" C15 GJF A 601 " pdb=" C17 GJF A 601 " pdb=" O8 GJF A 601 " both_signs ideal model delta sigma weight residual False 2.40 2.71 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C16 GJF A 602 " pdb=" C15 GJF A 602 " pdb=" C17 GJF A 602 " pdb=" O8 GJF A 602 " both_signs ideal model delta sigma weight residual False 2.40 2.71 -0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 541 not shown) Planarity restraints: 549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 81 " 0.045 5.00e-02 4.00e+02 6.71e-02 7.21e+00 pdb=" N PRO A 82 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 380 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C VAL A 380 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL A 380 " 0.016 2.00e-02 2.50e+03 pdb=" N PRO A 381 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 69 " 0.038 5.00e-02 4.00e+02 5.60e-02 5.01e+00 pdb=" N PRO A 70 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " 0.032 5.00e-02 4.00e+02 ... (remaining 546 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1152 2.84 - 3.35: 3057 3.35 - 3.87: 5650 3.87 - 4.38: 6913 4.38 - 4.90: 11150 Nonbonded interactions: 27922 Sorted by model distance: nonbonded pdb=" O LYS A 411 " pdb=" OG1 THR A 415 " model vdw 2.320 2.440 nonbonded pdb=" O THR A 408 " pdb=" OG1 THR A 412 " model vdw 2.370 2.440 nonbonded pdb=" O PHE A 276 " pdb=" OH TYR A 438 " model vdw 2.382 2.440 nonbonded pdb=" N ASP A 215 " pdb=" OD1 ASP A 215 " model vdw 2.399 2.520 nonbonded pdb=" N ASP A 19 " pdb=" OD1 ASP A 19 " model vdw 2.430 2.520 ... (remaining 27917 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 6.980 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.410 Find NCS groups from input model: 0.080 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 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 : 0.010 0.316 3403 Z= 0.674 Angle : 1.051 10.484 4658 Z= 0.540 Chirality : 0.058 0.327 544 Planarity : 0.006 0.067 549 Dihedral : 13.480 87.991 1172 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.58 % Allowed : 10.72 % Favored : 88.70 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.81 (0.22), residues: 396 helix: -4.60 (0.10), residues: 316 sheet: None (None), residues: 0 loop : -2.52 (0.57), residues: 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.366 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 77 average time/residue: 0.2288 time to fit residues: 20.2810 Evaluate side-chains 60 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.380 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0348 time to fit residues: 0.5668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 277 ASN A 289 HIS A 300 ASN A 377 GLN A 431 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3403 Z= 0.238 Angle : 0.572 5.836 4658 Z= 0.289 Chirality : 0.039 0.196 544 Planarity : 0.005 0.036 549 Dihedral : 5.725 35.802 475 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.74 % Allowed : 12.75 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.33), residues: 396 helix: -2.50 (0.22), residues: 312 sheet: None (None), residues: 0 loop : -1.52 (0.63), residues: 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.380 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 71 average time/residue: 0.2152 time to fit residues: 17.8578 Evaluate side-chains 56 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.370 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0362 time to fit residues: 0.6976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 36 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3403 Z= 0.209 Angle : 0.515 7.123 4658 Z= 0.256 Chirality : 0.038 0.126 544 Planarity : 0.003 0.026 549 Dihedral : 5.013 19.559 475 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.03 % Allowed : 14.78 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.39), residues: 396 helix: -1.00 (0.27), residues: 310 sheet: None (None), residues: 0 loop : -1.29 (0.63), residues: 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.367 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 64 average time/residue: 0.2150 time to fit residues: 16.2511 Evaluate side-chains 58 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.314 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0379 time to fit residues: 0.7174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.0870 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3403 Z= 0.203 Angle : 0.503 6.171 4658 Z= 0.248 Chirality : 0.038 0.130 544 Planarity : 0.003 0.023 549 Dihedral : 4.850 19.137 475 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.74 % Allowed : 16.81 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.41), residues: 396 helix: -0.30 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -1.23 (0.66), residues: 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.367 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 60 average time/residue: 0.2108 time to fit residues: 14.9288 Evaluate side-chains 56 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.366 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0437 time to fit residues: 0.7869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 403 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3403 Z= 0.243 Angle : 0.519 6.052 4658 Z= 0.258 Chirality : 0.039 0.183 544 Planarity : 0.003 0.022 549 Dihedral : 4.988 20.260 475 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.29 % Allowed : 19.71 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.42), residues: 396 helix: -0.07 (0.29), residues: 315 sheet: None (None), residues: 0 loop : -0.95 (0.69), residues: 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.368 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.2076 time to fit residues: 13.9627 Evaluate side-chains 54 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.360 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.0980 chunk 12 optimal weight: 0.0270 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 386 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3403 Z= 0.164 Angle : 0.474 5.865 4658 Z= 0.237 Chirality : 0.037 0.121 544 Planarity : 0.003 0.022 549 Dihedral : 4.611 18.548 475 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.45 % Allowed : 19.13 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.42), residues: 396 helix: 0.31 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -1.02 (0.68), residues: 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.353 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 53 average time/residue: 0.2248 time to fit residues: 14.0415 Evaluate side-chains 54 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0406 time to fit residues: 0.7527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3403 Z= 0.212 Angle : 0.498 6.160 4658 Z= 0.246 Chirality : 0.038 0.169 544 Planarity : 0.003 0.020 549 Dihedral : 4.688 18.511 475 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.58 % Allowed : 20.00 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.43), residues: 396 helix: 0.47 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -1.01 (0.69), residues: 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.367 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 58 average time/residue: 0.2101 time to fit residues: 14.3788 Evaluate side-chains 53 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.357 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.0870 chunk 11 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3403 Z= 0.160 Angle : 0.474 5.415 4658 Z= 0.238 Chirality : 0.037 0.114 544 Planarity : 0.003 0.018 549 Dihedral : 4.510 18.475 475 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.16 % Allowed : 20.87 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.43), residues: 396 helix: 0.73 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -1.02 (0.69), residues: 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.369 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 59 average time/residue: 0.2162 time to fit residues: 15.0294 Evaluate side-chains 55 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.369 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0390 time to fit residues: 0.6697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3403 Z= 0.231 Angle : 0.524 5.511 4658 Z= 0.261 Chirality : 0.039 0.117 544 Planarity : 0.003 0.018 549 Dihedral : 4.756 19.250 475 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.58 % Allowed : 21.74 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.43), residues: 396 helix: 0.74 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -0.99 (0.69), residues: 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.331 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 55 average time/residue: 0.2124 time to fit residues: 13.7331 Evaluate side-chains 55 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.362 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0379 time to fit residues: 0.5926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 0.0570 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 0.0670 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3403 Z= 0.147 Angle : 0.488 6.024 4658 Z= 0.242 Chirality : 0.037 0.138 544 Planarity : 0.003 0.022 549 Dihedral : 4.407 18.346 475 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.29 % Allowed : 21.45 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.44), residues: 396 helix: 0.95 (0.31), residues: 314 sheet: None (None), residues: 0 loop : -1.08 (0.68), residues: 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.369 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.2227 time to fit residues: 15.0383 Evaluate side-chains 54 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.324 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 0.0050 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.136899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.120340 restraints weight = 4154.721| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.93 r_work: 0.3280 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3403 Z= 0.180 Angle : 0.494 5.422 4658 Z= 0.248 Chirality : 0.037 0.116 544 Planarity : 0.003 0.023 549 Dihedral : 4.508 18.215 475 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 21.74 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.44), residues: 396 helix: 0.98 (0.31), residues: 314 sheet: None (None), residues: 0 loop : -1.06 (0.69), residues: 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1257.84 seconds wall clock time: 23 minutes 33.31 seconds (1413.31 seconds total)