Starting phenix.real_space_refine on Thu Jul 18 19:37:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/07_2024/7xq1_33388.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/07_2024/7xq1_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_33388/07_2024/7xq1_33388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/07_2024/7xq1_33388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/07_2024/7xq1_33388.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/07_2024/7xq1_33388.cif" } 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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3302 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3214 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 14, 'TRANS': 385} Chain breaks: 1 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'GJF': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.16, per 1000 atoms: 0.96 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: 1.31 Conformation dependent library (CDL) restraints added in 560.0 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... Secondary structure from input PDB file: 23 helices and 0 sheets defined 82.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 28 through 39 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) Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 71 through 79 removed outlier: 4.066A pdb=" N LEU A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 removed outlier: 3.868A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 113 removed outlier: 3.601A pdb=" N LEU A 111 " --> pdb=" O TRP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 132 removed outlier: 3.713A pdb=" N MET A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 removed outlier: 4.297A pdb=" N TYR A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) 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 148 through 176 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 181 through 202 removed outlier: 3.811A pdb=" N VAL A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 262 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 264 through 286 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 287 through 296 Processing helix chain 'A' and resid 307 through 318 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 318 through 323 removed outlier: 3.556A pdb=" N PHE A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 removed outlier: 4.170A pdb=" N VAL A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 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 358 through 361 Processing helix chain 'A' and resid 362 through 388 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 392 through 418 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 427 through 452 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) removed outlier: 3.572A pdb=" N LEU A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) 198 hydrogen bonds defined for protein. 591 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: 0.84 Time building geometry restraints manager: 1.37 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: 1858 17.60 - 35.20: 123 35.20 - 52.79: 35 52.79 - 70.39: 8 70.39 - 87.99: 2 Dihedral angle restraints: 2026 sinusoidal: 847 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 2023 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: 1147 2.84 - 3.35: 3035 3.35 - 3.87: 5616 3.87 - 4.38: 6854 4.38 - 4.90: 11142 Nonbonded interactions: 27794 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 27789 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.990 Find NCS groups from input model: 0.030 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.410 ------------------------------------------------------------------------------- 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= 0.563 Angle : 1.051 10.484 4658 Z= 0.540 Chirality : 0.058 0.327 544 Planarity : 0.006 0.067 549 Dihedral : 13.483 87.991 1268 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 107 HIS 0.002 0.001 HIS A 289 PHE 0.009 0.001 PHE A 37 TYR 0.012 0.001 TYR A 139 ARG 0.002 0.000 ARG A 179 *********************** 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 : 0.367 Fit side-chains REVERT: A 23 ARG cc_start: 0.7629 (ttt180) cc_final: 0.6992 (ttt180) REVERT: A 26 ARG cc_start: 0.7432 (mmt90) cc_final: 0.7190 (mmm-85) REVERT: A 74 TYR cc_start: 0.8759 (m-10) cc_final: 0.7903 (m-80) REVERT: A 277 ASN cc_start: 0.8658 (t0) cc_final: 0.8262 (t0) outliers start: 2 outliers final: 1 residues processed: 77 average time/residue: 0.2358 time to fit residues: 20.8389 Evaluate side-chains 61 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 0.0070 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.0980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2419 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= 0.184 Angle : 0.556 6.231 4658 Z= 0.286 Chirality : 0.038 0.182 544 Planarity : 0.005 0.037 549 Dihedral : 6.026 29.929 572 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.74 % Allowed : 13.33 % Favored : 84.93 % 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: -3.84 (0.33), residues: 396 helix: -2.44 (0.22), residues: 317 sheet: None (None), residues: 0 loop : -1.86 (0.64), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.003 0.000 HIS A 289 PHE 0.010 0.001 PHE A 432 TYR 0.015 0.001 TYR A 446 ARG 0.005 0.000 ARG A 422 *********************** 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 76 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.359 Fit side-chains REVERT: A 23 ARG cc_start: 0.7315 (ttt180) cc_final: 0.6921 (ttm170) REVERT: A 26 ARG cc_start: 0.7471 (mmt90) cc_final: 0.7231 (mmm-85) REVERT: A 67 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7591 (mt-10) REVERT: A 296 ASP cc_start: 0.8337 (t0) cc_final: 0.7967 (t70) REVERT: A 351 PHE cc_start: 0.7249 (t80) cc_final: 0.6887 (t80) REVERT: A 394 GLU cc_start: 0.7900 (mp0) cc_final: 0.7532 (mp0) outliers start: 6 outliers final: 3 residues processed: 76 average time/residue: 0.2063 time to fit residues: 18.1897 Evaluate side-chains 62 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 198 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 0.0470 chunk 18 optimal weight: 0.0570 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2841 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= 0.158 Angle : 0.495 6.673 4658 Z= 0.248 Chirality : 0.037 0.132 544 Planarity : 0.003 0.027 549 Dihedral : 5.428 22.512 571 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.74 % Allowed : 16.23 % Favored : 82.03 % 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: -1.57 (0.39), residues: 396 helix: -0.84 (0.27), residues: 310 sheet: None (None), residues: 0 loop : -1.08 (0.63), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 331 HIS 0.001 0.000 HIS A 289 PHE 0.008 0.001 PHE A 385 TYR 0.009 0.001 TYR A 35 ARG 0.004 0.000 ARG A 422 *********************** 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 64 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.495 Fit side-chains REVERT: A 23 ARG cc_start: 0.7141 (ttt180) cc_final: 0.6824 (ttm170) REVERT: A 67 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7581 (mt-10) REVERT: A 351 PHE cc_start: 0.7339 (t80) cc_final: 0.6904 (t80) REVERT: A 394 GLU cc_start: 0.7668 (mp0) cc_final: 0.7383 (mp0) REVERT: A 422 ARG cc_start: 0.7866 (mtm-85) cc_final: 0.7664 (mtm110) outliers start: 6 outliers final: 4 residues processed: 63 average time/residue: 0.2024 time to fit residues: 15.1040 Evaluate side-chains 58 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 215 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.7544 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3403 Z= 0.287 Angle : 0.554 5.347 4658 Z= 0.277 Chirality : 0.040 0.132 544 Planarity : 0.003 0.023 549 Dihedral : 6.028 22.534 571 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.32 % Allowed : 17.97 % Favored : 79.71 % 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: -0.90 (0.40), residues: 396 helix: -0.32 (0.28), residues: 312 sheet: None (None), residues: 0 loop : -1.12 (0.65), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.002 0.000 HIS A 289 PHE 0.015 0.001 PHE A 322 TYR 0.011 0.001 TYR A 35 ARG 0.003 0.000 ARG A 373 *********************** 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 64 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.369 Fit side-chains REVERT: A 23 ARG cc_start: 0.7114 (ttt180) cc_final: 0.6577 (tmt170) REVERT: A 74 TYR cc_start: 0.8888 (m-10) cc_final: 0.8183 (m-80) REVERT: A 296 ASP cc_start: 0.8357 (t0) cc_final: 0.7953 (t70) REVERT: A 394 GLU cc_start: 0.7682 (mp0) cc_final: 0.7381 (mp0) REVERT: A 447 PHE cc_start: 0.7698 (t80) cc_final: 0.7377 (t80) outliers start: 8 outliers final: 3 residues processed: 62 average time/residue: 0.2050 time to fit residues: 14.9479 Evaluate side-chains 58 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.0570 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.0020 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 overall best weight: 0.4106 ------------------------------------------------------------------------------- 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: 0.7488 moved from start: 0.3235 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 : 0.480 5.862 4658 Z= 0.242 Chirality : 0.037 0.120 544 Planarity : 0.003 0.022 549 Dihedral : 5.436 22.968 571 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.74 % Allowed : 18.55 % Favored : 79.71 % 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: -0.28 (0.41), residues: 396 helix: 0.10 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -0.83 (0.65), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 331 HIS 0.001 0.000 HIS A 289 PHE 0.008 0.001 PHE A 326 TYR 0.017 0.001 TYR A 438 ARG 0.002 0.000 ARG A 373 *********************** 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 61 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.359 Fit side-chains REVERT: A 23 ARG cc_start: 0.7155 (ttt180) cc_final: 0.6598 (tmt170) REVERT: A 67 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7702 (mt-10) REVERT: A 74 TYR cc_start: 0.8861 (m-10) cc_final: 0.8133 (m-80) REVERT: A 296 ASP cc_start: 0.8345 (t0) cc_final: 0.7958 (t70) REVERT: A 351 PHE cc_start: 0.7568 (t80) cc_final: 0.7293 (t80) REVERT: A 394 GLU cc_start: 0.7643 (mp0) cc_final: 0.7378 (mp0) REVERT: A 447 PHE cc_start: 0.7641 (t80) cc_final: 0.7394 (t80) outliers start: 6 outliers final: 5 residues processed: 60 average time/residue: 0.2172 time to fit residues: 15.2150 Evaluate side-chains 56 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 215 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3403 Z= 0.202 Angle : 0.496 5.463 4658 Z= 0.248 Chirality : 0.038 0.115 544 Planarity : 0.003 0.022 549 Dihedral : 5.517 22.908 571 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.03 % Allowed : 18.26 % Favored : 79.71 % 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: 0.04 (0.42), residues: 396 helix: 0.34 (0.29), residues: 315 sheet: None (None), residues: 0 loop : -0.74 (0.66), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.000 HIS A 289 PHE 0.015 0.001 PHE A 322 TYR 0.015 0.001 TYR A 438 ARG 0.004 0.000 ARG A 373 *********************** 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 59 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.391 Fit side-chains REVERT: A 23 ARG cc_start: 0.7126 (ttt180) cc_final: 0.6560 (tmt170) REVERT: A 67 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7696 (mt-10) REVERT: A 74 TYR cc_start: 0.8873 (m-10) cc_final: 0.8207 (m-80) REVERT: A 296 ASP cc_start: 0.8284 (t0) cc_final: 0.7906 (t70) REVERT: A 351 PHE cc_start: 0.7591 (t80) cc_final: 0.7306 (t80) REVERT: A 394 GLU cc_start: 0.7588 (mp0) cc_final: 0.7335 (mp0) outliers start: 7 outliers final: 6 residues processed: 58 average time/residue: 0.2435 time to fit residues: 16.2903 Evaluate side-chains 57 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 398 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7523 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3403 Z= 0.246 Angle : 0.520 5.342 4658 Z= 0.260 Chirality : 0.039 0.113 544 Planarity : 0.003 0.022 549 Dihedral : 5.753 23.016 571 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.61 % Allowed : 17.97 % 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: 0.19 (0.42), residues: 396 helix: 0.46 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -0.78 (0.65), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 331 HIS 0.002 0.000 HIS A 289 PHE 0.014 0.001 PHE A 211 TYR 0.015 0.001 TYR A 438 ARG 0.004 0.000 ARG A 373 *********************** 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 65 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.357 Fit side-chains REVERT: A 23 ARG cc_start: 0.7129 (ttt180) cc_final: 0.6555 (tmt170) REVERT: A 67 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7700 (mt-10) REVERT: A 74 TYR cc_start: 0.8888 (m-10) cc_final: 0.8215 (m-80) REVERT: A 85 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8087 (mp) REVERT: A 296 ASP cc_start: 0.8253 (t0) cc_final: 0.7902 (t70) REVERT: A 351 PHE cc_start: 0.7664 (t80) cc_final: 0.7339 (t80) REVERT: A 394 GLU cc_start: 0.7610 (mp0) cc_final: 0.7314 (mp0) outliers start: 9 outliers final: 7 residues processed: 62 average time/residue: 0.2259 time to fit residues: 16.3283 Evaluate side-chains 61 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 398 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 0.1980 chunk 36 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.7494 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3403 Z= 0.182 Angle : 0.490 5.416 4658 Z= 0.247 Chirality : 0.038 0.110 544 Planarity : 0.003 0.022 549 Dihedral : 5.484 23.011 571 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.90 % Allowed : 17.97 % Favored : 79.13 % 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 (0.42), residues: 396 helix: 0.67 (0.29), residues: 315 sheet: None (None), residues: 0 loop : -0.69 (0.67), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 331 HIS 0.001 0.000 HIS A 289 PHE 0.016 0.001 PHE A 322 TYR 0.014 0.001 TYR A 438 ARG 0.003 0.000 ARG A 373 *********************** 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 63 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.451 Fit side-chains REVERT: A 23 ARG cc_start: 0.7117 (ttt180) cc_final: 0.6532 (tmt170) REVERT: A 67 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7678 (mt-10) REVERT: A 74 TYR cc_start: 0.8870 (m-10) cc_final: 0.8176 (m-80) REVERT: A 85 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8054 (mp) REVERT: A 296 ASP cc_start: 0.8275 (t0) cc_final: 0.7928 (t70) REVERT: A 351 PHE cc_start: 0.7640 (t80) cc_final: 0.7321 (t80) REVERT: A 394 GLU cc_start: 0.7615 (mp0) cc_final: 0.7335 (mp0) outliers start: 10 outliers final: 7 residues processed: 60 average time/residue: 0.2420 time to fit residues: 16.9150 Evaluate side-chains 58 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 398 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.7496 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3403 Z= 0.192 Angle : 0.504 5.345 4658 Z= 0.253 Chirality : 0.038 0.110 544 Planarity : 0.003 0.021 549 Dihedral : 5.494 23.057 571 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.61 % Allowed : 19.13 % 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: 0.67 (0.43), residues: 396 helix: 0.82 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -0.71 (0.67), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 331 HIS 0.001 0.000 HIS A 289 PHE 0.014 0.001 PHE A 211 TYR 0.014 0.001 TYR A 438 ARG 0.004 0.000 ARG A 373 *********************** 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 61 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.363 Fit side-chains REVERT: A 23 ARG cc_start: 0.7113 (ttt180) cc_final: 0.6528 (tmt170) REVERT: A 67 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7685 (mt-10) REVERT: A 74 TYR cc_start: 0.8869 (m-10) cc_final: 0.8180 (m-80) REVERT: A 85 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8056 (mp) REVERT: A 296 ASP cc_start: 0.8276 (t0) cc_final: 0.7919 (t70) REVERT: A 351 PHE cc_start: 0.7659 (t80) cc_final: 0.7342 (t80) REVERT: A 394 GLU cc_start: 0.7579 (mp0) cc_final: 0.7328 (mp0) outliers start: 9 outliers final: 6 residues processed: 58 average time/residue: 0.2327 time to fit residues: 15.7733 Evaluate side-chains 57 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 398 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7504 moved from start: 0.3469 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= 0.217 Angle : 0.520 5.376 4658 Z= 0.261 Chirality : 0.039 0.111 544 Planarity : 0.003 0.021 549 Dihedral : 5.603 23.145 571 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.32 % Allowed : 19.71 % 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: 0.71 (0.43), residues: 396 helix: 0.86 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -0.77 (0.67), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 331 HIS 0.001 0.000 HIS A 289 PHE 0.017 0.001 PHE A 211 TYR 0.014 0.001 TYR A 438 ARG 0.004 0.000 ARG A 373 ********************** 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 60 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.367 Fit side-chains REVERT: A 23 ARG cc_start: 0.7108 (ttt180) cc_final: 0.6521 (tmt170) REVERT: A 67 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7699 (mt-10) REVERT: A 74 TYR cc_start: 0.8875 (m-10) cc_final: 0.8197 (m-80) REVERT: A 85 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8052 (mp) REVERT: A 296 ASP cc_start: 0.8225 (t0) cc_final: 0.7902 (t70) REVERT: A 351 PHE cc_start: 0.7637 (t80) cc_final: 0.7339 (t80) REVERT: A 394 GLU cc_start: 0.7555 (mp0) cc_final: 0.7305 (mp0) outliers start: 8 outliers final: 7 residues processed: 57 average time/residue: 0.2054 time to fit residues: 13.7900 Evaluate side-chains 58 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 398 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 0.0970 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 0.0050 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.130570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115251 restraints weight = 4191.485| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.83 r_work: 0.3179 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3403 Z= 0.178 Angle : 0.504 5.343 4658 Z= 0.253 Chirality : 0.038 0.109 544 Planarity : 0.003 0.021 549 Dihedral : 5.393 23.145 571 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.32 % Allowed : 20.00 % 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: 0.91 (0.43), residues: 396 helix: 1.00 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -0.72 (0.67), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 331 HIS 0.001 0.000 HIS A 289 PHE 0.015 0.001 PHE A 211 TYR 0.013 0.001 TYR A 438 ARG 0.004 0.000 ARG A 373 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1239.41 seconds wall clock time: 23 minutes 13.59 seconds (1393.59 seconds total)