Starting phenix.real_space_refine on Mon Sep 23 14:12:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/09_2024/7xq1_33388.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/09_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_33388/09_2024/7xq1_33388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/09_2024/7xq1_33388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/09_2024/7xq1_33388.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq1_33388/09_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. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 3.24, per 1000 atoms: 0.98 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 - 3.00 Amino acid : True - 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: 0.83 Conformation dependent library (CDL) restraints added in 375.3 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: 0.31 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: 0.83 Time building geometry restraints manager: 0.93 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: 0.00 - 2.10: 4455 2.10 - 4.19: 134 4.19 - 6.29: 48 6.29 - 8.39: 15 8.39 - 10.48: 6 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 3.040 nonbonded pdb=" O THR A 408 " pdb=" OG1 THR A 412 " model vdw 2.370 3.040 nonbonded pdb=" O PHE A 276 " pdb=" OH TYR A 438 " model vdw 2.382 3.040 nonbonded pdb=" N ASP A 215 " pdb=" OD1 ASP A 215 " model vdw 2.399 3.120 nonbonded pdb=" N ASP A 19 " pdb=" OD1 ASP A 19 " model vdw 2.430 3.120 ... (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: 1.570 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.360 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.000 ------------------------------------------------------------------------------- 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 : 0.379 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: 0.2408 time to fit residues: 21.3567 Evaluate side-chains 61 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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: 0.7980 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.0670 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 289 HIS A 300 ASN A 377 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3403 Z= 0.203 Angle : 0.576 6.391 4658 Z= 0.295 Chirality : 0.039 0.174 544 Planarity : 0.005 0.037 549 Dihedral : 6.598 35.884 572 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.16 % Allowed : 13.33 % 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: -3.77 (0.33), residues: 396 helix: -2.41 (0.22), residues: 317 sheet: None (None), residues: 0 loop : -1.73 (0.64), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.000 HIS A 289 PHE 0.010 0.001 PHE A 432 TYR 0.017 0.001 TYR A 446 ARG 0.005 0.000 ARG A 373 *********************** 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 73 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.346 Fit side-chains REVERT: A 23 ARG cc_start: 0.7312 (ttt180) cc_final: 0.6921 (ttm170) REVERT: A 67 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7532 (mt-10) REVERT: A 296 ASP cc_start: 0.8317 (t0) cc_final: 0.7952 (t70) REVERT: A 351 PHE cc_start: 0.7269 (t80) cc_final: 0.6904 (t80) REVERT: A 394 GLU cc_start: 0.7871 (mp0) cc_final: 0.7640 (mp0) outliers start: 4 outliers final: 2 residues processed: 73 average time/residue: 0.2081 time to fit residues: 17.6950 Evaluate side-chains 59 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 174 LEU 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: 0.5980 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 0.0270 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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: 0.7492 moved from start: 0.2840 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= 0.187 Angle : 0.523 6.608 4658 Z= 0.263 Chirality : 0.038 0.137 544 Planarity : 0.003 0.028 549 Dihedral : 5.693 23.883 571 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.74 % Allowed : 15.94 % Favored : 82.32 % 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: -1.84 (0.39), residues: 396 helix: -0.97 (0.27), residues: 315 sheet: None (None), residues: 0 loop : -1.48 (0.66), residues: 81 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 432 TYR 0.009 0.001 TYR A 35 ARG 0.006 0.000 ARG A 373 *********************** 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 65 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.349 Fit side-chains REVERT: A 23 ARG cc_start: 0.7129 (ttt180) cc_final: 0.6820 (ttm170) REVERT: A 67 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7587 (mt-10) REVERT: A 190 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7357 (tt) REVERT: A 296 ASP cc_start: 0.8341 (t0) cc_final: 0.7956 (t70) REVERT: A 351 PHE cc_start: 0.7407 (t80) cc_final: 0.6966 (t80) REVERT: A 394 GLU cc_start: 0.7665 (mp0) cc_final: 0.7421 (mp0) outliers start: 6 outliers final: 4 residues processed: 63 average time/residue: 0.1904 time to fit residues: 14.2547 Evaluate side-chains 61 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 190 LEU Chi-restraints excluded: chain A residue 398 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 0.0970 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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: 0.3006 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= 0.203 Angle : 0.511 5.767 4658 Z= 0.257 Chirality : 0.038 0.131 544 Planarity : 0.003 0.024 549 Dihedral : 5.684 24.728 571 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.74 % Allowed : 17.97 % Favored : 80.29 % 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: -0.89 (0.41), residues: 396 helix: -0.26 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -1.34 (0.66), residues: 80 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 0.014 0.001 PHE A 322 TYR 0.016 0.001 TYR A 438 ARG 0.005 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: 6 poor density : 58 time to evaluate : 0.373 Fit side-chains REVERT: A 23 ARG cc_start: 0.7118 (ttt180) cc_final: 0.6819 (ttm170) REVERT: A 67 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7620 (mt-10) REVERT: A 74 TYR cc_start: 0.8861 (m-10) cc_final: 0.8070 (m-80) REVERT: A 80 LEU cc_start: 0.7878 (tp) cc_final: 0.7643 (tp) REVERT: A 296 ASP cc_start: 0.8265 (t0) cc_final: 0.7914 (t70) REVERT: A 351 PHE cc_start: 0.7531 (t80) cc_final: 0.7058 (t80) REVERT: A 394 GLU cc_start: 0.7709 (mp0) cc_final: 0.7380 (mp0) REVERT: A 447 PHE cc_start: 0.7632 (t80) cc_final: 0.7343 (t80) outliers start: 6 outliers final: 4 residues processed: 63 average time/residue: 0.2003 time to fit residues: 14.8878 Evaluate side-chains 60 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 189 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7535 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3403 Z= 0.270 Angle : 0.546 5.510 4658 Z= 0.273 Chirality : 0.040 0.123 544 Planarity : 0.003 0.037 549 Dihedral : 5.922 24.546 571 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.03 % Allowed : 18.55 % 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: -0.52 (0.41), residues: 396 helix: -0.01 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -1.16 (0.67), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.001 0.000 HIS A 289 PHE 0.007 0.001 PHE A 369 TYR 0.013 0.001 TYR A 438 ARG 0.008 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 68 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.344 Fit side-chains REVERT: A 67 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7585 (mt-10) REVERT: A 74 TYR cc_start: 0.8859 (m-10) cc_final: 0.8122 (m-80) REVERT: A 80 LEU cc_start: 0.7892 (tp) cc_final: 0.7638 (tp) REVERT: A 85 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8113 (mp) REVERT: A 202 PHE cc_start: 0.8028 (m-80) cc_final: 0.7690 (m-10) REVERT: A 296 ASP cc_start: 0.8316 (t0) cc_final: 0.7938 (t70) REVERT: A 393 LYS cc_start: 0.7861 (mmmt) cc_final: 0.7613 (tptp) REVERT: A 447 PHE cc_start: 0.7675 (t80) cc_final: 0.7455 (t80) outliers start: 7 outliers final: 6 residues processed: 65 average time/residue: 0.2086 time to fit residues: 15.9950 Evaluate side-chains 64 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 189 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 398 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7510 moved from start: 0.3276 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= 0.208 Angle : 0.508 5.665 4658 Z= 0.256 Chirality : 0.038 0.116 544 Planarity : 0.003 0.027 549 Dihedral : 5.730 24.847 571 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.61 % Allowed : 18.84 % Favored : 78.55 % 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: -0.12 (0.42), residues: 396 helix: 0.28 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -1.11 (0.68), residues: 79 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 0.009 0.001 PHE A 211 TYR 0.013 0.001 TYR A 438 ARG 0.007 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 69 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.382 Fit side-chains REVERT: A 67 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7538 (mt-10) REVERT: A 74 TYR cc_start: 0.8854 (m-10) cc_final: 0.8164 (m-80) REVERT: A 80 LEU cc_start: 0.7866 (tp) cc_final: 0.7584 (tp) REVERT: A 85 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8083 (mp) REVERT: A 296 ASP cc_start: 0.8273 (t0) cc_final: 0.7915 (t70) REVERT: A 393 LYS cc_start: 0.7929 (mmmt) cc_final: 0.7700 (tptp) REVERT: A 447 PHE cc_start: 0.7665 (t80) cc_final: 0.7434 (t80) outliers start: 9 outliers final: 7 residues processed: 66 average time/residue: 0.2028 time to fit residues: 15.7948 Evaluate side-chains 66 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 189 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 0.0470 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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: 0.7495 moved from start: 0.3364 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= 0.187 Angle : 0.501 5.404 4658 Z= 0.254 Chirality : 0.038 0.114 544 Planarity : 0.003 0.023 549 Dihedral : 5.626 24.973 571 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.19 % Allowed : 17.68 % 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: 0.23 (0.42), residues: 396 helix: 0.50 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.91 (0.69), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 331 HIS 0.001 0.000 HIS A 289 PHE 0.016 0.001 PHE A 322 TYR 0.013 0.001 TYR A 438 ARG 0.006 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 68 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.353 Fit side-chains REVERT: A 67 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7552 (mt-10) REVERT: A 74 TYR cc_start: 0.8844 (m-10) cc_final: 0.8131 (m-80) REVERT: A 80 LEU cc_start: 0.7932 (tp) cc_final: 0.7696 (tp) REVERT: A 85 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8067 (mp) REVERT: A 296 ASP cc_start: 0.8273 (t0) cc_final: 0.7929 (t70) REVERT: A 351 PHE cc_start: 0.7559 (t80) cc_final: 0.7257 (t80) outliers start: 11 outliers final: 8 residues processed: 64 average time/residue: 0.1789 time to fit residues: 13.8823 Evaluate side-chains 65 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 189 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.0980 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7498 moved from start: 0.3412 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= 0.197 Angle : 0.506 5.348 4658 Z= 0.257 Chirality : 0.038 0.113 544 Planarity : 0.003 0.022 549 Dihedral : 5.601 25.832 571 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.03 % Allowed : 19.42 % Favored : 78.55 % 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 (0.42), residues: 396 helix: 0.67 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.85 (0.69), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 331 HIS 0.001 0.000 HIS A 289 PHE 0.010 0.001 PHE A 211 TYR 0.012 0.001 TYR A 438 ARG 0.005 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 68 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.344 Fit side-chains REVERT: A 67 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7555 (mt-10) REVERT: A 74 TYR cc_start: 0.8844 (m-10) cc_final: 0.8134 (m-80) REVERT: A 80 LEU cc_start: 0.7927 (tp) cc_final: 0.7699 (tp) REVERT: A 85 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8064 (mp) REVERT: A 202 PHE cc_start: 0.8049 (m-80) cc_final: 0.7766 (m-10) REVERT: A 296 ASP cc_start: 0.8265 (t0) cc_final: 0.7915 (t70) REVERT: A 351 PHE cc_start: 0.7606 (t80) cc_final: 0.7272 (t80) outliers start: 7 outliers final: 6 residues processed: 66 average time/residue: 0.1784 time to fit residues: 14.0954 Evaluate side-chains 65 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 189 SER Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7495 moved from start: 0.3478 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= 0.199 Angle : 0.518 5.337 4658 Z= 0.262 Chirality : 0.038 0.113 544 Planarity : 0.003 0.022 549 Dihedral : 5.596 25.800 571 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.74 % Allowed : 20.58 % 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: 0.59 (0.43), residues: 396 helix: 0.79 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -0.96 (0.69), residues: 77 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 0.018 0.001 PHE A 322 TYR 0.012 0.001 TYR A 438 ARG 0.005 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: 6 poor density : 55 time to evaluate : 0.356 Fit side-chains REVERT: A 67 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7554 (mt-10) REVERT: A 74 TYR cc_start: 0.8819 (m-10) cc_final: 0.8175 (m-80) REVERT: A 85 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8104 (mp) REVERT: A 202 PHE cc_start: 0.8068 (m-80) cc_final: 0.7805 (m-10) REVERT: A 296 ASP cc_start: 0.8248 (t0) cc_final: 0.7910 (t70) REVERT: A 351 PHE cc_start: 0.7604 (t80) cc_final: 0.7261 (t80) outliers start: 6 outliers final: 5 residues processed: 60 average time/residue: 0.1906 time to fit residues: 13.7283 Evaluate side-chains 60 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 189 SER Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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: 0.7497 moved from start: 0.3512 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= 0.203 Angle : 0.519 5.821 4658 Z= 0.262 Chirality : 0.039 0.113 544 Planarity : 0.003 0.022 549 Dihedral : 5.599 25.976 571 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.45 % Allowed : 21.16 % Favored : 77.39 % 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: 0.64 (0.42), residues: 396 helix: 0.85 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.06 (0.68), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 331 HIS 0.001 0.000 HIS A 289 PHE 0.021 0.001 PHE A 84 TYR 0.011 0.001 TYR A 438 ARG 0.005 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 59 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.343 Fit side-chains REVERT: A 67 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7562 (mt-10) REVERT: A 74 TYR cc_start: 0.8828 (m-10) cc_final: 0.8184 (m-80) REVERT: A 202 PHE cc_start: 0.8079 (m-80) cc_final: 0.7821 (m-10) REVERT: A 296 ASP cc_start: 0.8264 (t0) cc_final: 0.7909 (t70) REVERT: A 326 PHE cc_start: 0.7688 (m-10) cc_final: 0.7403 (m-10) REVERT: A 351 PHE cc_start: 0.7632 (t80) cc_final: 0.7289 (t80) outliers start: 5 outliers final: 5 residues processed: 59 average time/residue: 0.1813 time to fit residues: 12.9452 Evaluate side-chains 60 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 189 SER Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.128224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.112501 restraints weight = 4122.036| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.80 r_work: 0.3180 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3507 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= 0.199 Angle : 0.517 5.827 4658 Z= 0.263 Chirality : 0.039 0.112 544 Planarity : 0.003 0.022 549 Dihedral : 5.570 26.169 571 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.74 % Allowed : 20.87 % Favored : 77.39 % 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: 0.76 (0.43), residues: 396 helix: 0.95 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -1.11 (0.68), residues: 77 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 0.011 0.001 TYR A 438 ARG 0.005 0.000 ARG A 373 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1194.86 seconds wall clock time: 21 minutes 48.94 seconds (1308.94 seconds total)