Starting phenix.real_space_refine on Mon Feb 10 23:48:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xq1_33388/02_2025/7xq1_33388.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xq1_33388/02_2025/7xq1_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/cci-nas-00/data/ceres_data/7xq1_33388/02_2025/7xq1_33388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xq1_33388/02_2025/7xq1_33388.map" model { file = "/net/cci-nas-00/data/ceres_data/7xq1_33388/02_2025/7xq1_33388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xq1_33388/02_2025/7xq1_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-5592/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: 3.22, 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: 0.97 Conformation dependent library (CDL) restraints added in 407.9 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: 0.84 Time building geometry restraints manager: 1.02 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: 1.710 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: 0.030 Set scattering table: 0.030 Process input model: 13.220 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.060 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.368 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: 0.2324 time to fit residues: 20.6368 Evaluate side-chains 61 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.136498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.120020 restraints weight = 4126.692| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.97 r_work: 0.3273 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.379 Fit side-chains REVERT: A 23 ARG cc_start: 0.7726 (ttt180) cc_final: 0.7329 (ttm170) REVERT: A 67 GLU cc_start: 0.8233 (mt-10) cc_final: 0.8012 (mt-10) REVERT: A 296 ASP cc_start: 0.8648 (t0) cc_final: 0.8279 (t70) REVERT: A 351 PHE cc_start: 0.7634 (t80) cc_final: 0.7291 (t80) outliers start: 4 outliers final: 2 residues processed: 73 average time/residue: 0.2126 time to fit residues: 18.2306 Evaluate side-chains 59 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 29 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 11 optimal weight: 0.0040 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.129139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113475 restraints weight = 4017.445| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.81 r_work: 0.3190 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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= 0.180 Angle : 0.517 6.623 4658 Z= 0.260 Chirality : 0.038 0.136 544 Planarity : 0.003 0.028 549 Dihedral : 5.686 23.587 571 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.45 % Allowed : 16.52 % 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: -1.88 (0.39), residues: 396 helix: -1.03 (0.27), residues: 317 sheet: None (None), residues: 0 loop : -1.36 (0.67), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.400 Fit side-chains REVERT: A 23 ARG cc_start: 0.7394 (ttt180) cc_final: 0.7048 (ttm170) REVERT: A 67 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7987 (mt-10) REVERT: A 296 ASP cc_start: 0.8629 (t0) cc_final: 0.8246 (t70) REVERT: A 351 PHE cc_start: 0.7674 (t80) cc_final: 0.7242 (t80) outliers start: 5 outliers final: 4 residues processed: 64 average time/residue: 0.2003 time to fit residues: 15.1879 Evaluate side-chains 63 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 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 Chi-restraints excluded: chain A residue 190 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3463 r_free = 0.3463 target = 0.127319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111549 restraints weight = 4110.593| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.82 r_work: 0.3164 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2985 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= 0.215 Angle : 0.518 5.707 4658 Z= 0.260 Chirality : 0.038 0.131 544 Planarity : 0.003 0.024 549 Dihedral : 5.735 24.991 571 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: -0.91 (0.41), residues: 396 helix: -0.29 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -1.30 (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 0.006 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 65 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.298 Fit side-chains REVERT: A 23 ARG cc_start: 0.7354 (ttt180) cc_final: 0.7017 (ttm170) REVERT: A 67 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7992 (mt-10) REVERT: A 74 TYR cc_start: 0.9039 (m-10) cc_final: 0.8253 (m-80) REVERT: A 296 ASP cc_start: 0.8569 (t0) cc_final: 0.8211 (t70) REVERT: A 351 PHE cc_start: 0.7823 (t80) cc_final: 0.7379 (t80) REVERT: A 393 LYS cc_start: 0.7762 (mmmt) cc_final: 0.7475 (tptp) outliers start: 7 outliers final: 6 residues processed: 63 average time/residue: 0.2099 time to fit residues: 15.5106 Evaluate side-chains 62 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 190 LEU Chi-restraints excluded: chain A residue 398 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 0.0770 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.135779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.119445 restraints weight = 4053.476| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.86 r_work: 0.3265 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3171 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= 0.212 Angle : 0.513 5.836 4658 Z= 0.258 Chirality : 0.038 0.121 544 Planarity : 0.003 0.036 549 Dihedral : 5.684 24.785 571 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.32 % Allowed : 18.55 % 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: -0.44 (0.41), residues: 396 helix: 0.04 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -1.14 (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 0.010 0.001 PHE A 211 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 69 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.375 Fit side-chains REVERT: A 67 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7967 (mt-10) REVERT: A 74 TYR cc_start: 0.9069 (m-10) cc_final: 0.8330 (m-80) REVERT: A 85 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8427 (mp) REVERT: A 202 PHE cc_start: 0.8200 (m-80) cc_final: 0.7898 (m-10) REVERT: A 296 ASP cc_start: 0.8610 (t0) cc_final: 0.8244 (t70) REVERT: A 393 LYS cc_start: 0.7878 (mmmt) cc_final: 0.7619 (tptp) outliers start: 8 outliers final: 6 residues processed: 66 average time/residue: 0.1844 time to fit residues: 14.5578 Evaluate side-chains 65 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 30 optimal weight: 0.0370 chunk 34 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 2 optimal weight: 0.1980 chunk 14 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 overall best weight: 0.3058 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.138517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122135 restraints weight = 4218.262| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.93 r_work: 0.3301 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3403 Z= 0.140 Angle : 0.475 5.814 4658 Z= 0.241 Chirality : 0.036 0.115 544 Planarity : 0.003 0.027 549 Dihedral : 5.381 25.126 571 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.31 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: 0.11 (0.42), residues: 396 helix: 0.41 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.93 (0.68), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 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 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 67 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.370 Fit side-chains REVERT: A 74 TYR cc_start: 0.9031 (m-10) cc_final: 0.8307 (m-80) REVERT: A 85 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8374 (mp) REVERT: A 256 ARG cc_start: 0.7510 (mpt180) cc_final: 0.7308 (mmt-90) REVERT: A 296 ASP cc_start: 0.8557 (t0) cc_final: 0.8233 (t70) REVERT: A 351 PHE cc_start: 0.7713 (t80) cc_final: 0.7189 (t80) outliers start: 8 outliers final: 6 residues processed: 64 average time/residue: 0.2187 time to fit residues: 16.3122 Evaluate side-chains 64 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.119019 restraints weight = 4135.212| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.89 r_work: 0.3259 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3347 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= 0.217 Angle : 0.513 5.315 4658 Z= 0.258 Chirality : 0.039 0.115 544 Planarity : 0.003 0.023 549 Dihedral : 5.649 24.918 571 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.61 % Allowed : 19.71 % 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: 0.28 (0.42), residues: 396 helix: 0.54 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.90 (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 0.008 0.001 PHE A 211 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 69 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.477 Fit side-chains REVERT: A 74 TYR cc_start: 0.9053 (m-10) cc_final: 0.8365 (m-80) REVERT: A 85 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8380 (mp) REVERT: A 202 PHE cc_start: 0.8216 (m-80) cc_final: 0.7939 (m-10) REVERT: A 296 ASP cc_start: 0.8593 (t0) cc_final: 0.8244 (t70) REVERT: A 351 PHE cc_start: 0.7911 (t80) cc_final: 0.7619 (t80) REVERT: A 393 LYS cc_start: 0.7874 (mmmt) cc_final: 0.7588 (tptp) outliers start: 9 outliers final: 6 residues processed: 66 average time/residue: 0.2040 time to fit residues: 16.0635 Evaluate side-chains 66 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 398 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 28 optimal weight: 0.0770 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.136382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.120016 restraints weight = 4089.937| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.88 r_work: 0.3269 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3423 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 : 0.505 5.295 4658 Z= 0.256 Chirality : 0.038 0.113 544 Planarity : 0.003 0.026 549 Dihedral : 5.609 25.036 571 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.61 % Allowed : 19.42 % 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: 0.46 (0.42), residues: 396 helix: 0.68 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.91 (0.68), 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 0.017 0.001 PHE A 322 TYR 0.013 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 66 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.378 Fit side-chains REVERT: A 74 TYR cc_start: 0.9044 (m-10) cc_final: 0.8409 (m-80) REVERT: A 85 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8404 (mp) REVERT: A 202 PHE cc_start: 0.8225 (m-80) cc_final: 0.7967 (m-10) REVERT: A 296 ASP cc_start: 0.8598 (t0) cc_final: 0.8235 (t70) REVERT: A 351 PHE cc_start: 0.7933 (t80) cc_final: 0.7627 (t80) outliers start: 9 outliers final: 8 residues processed: 62 average time/residue: 0.1901 time to fit residues: 14.2814 Evaluate side-chains 66 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.141338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124489 restraints weight = 4315.411| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.92 r_work: 0.3251 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3428 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= 0.245 Angle : 0.542 5.376 4658 Z= 0.273 Chirality : 0.040 0.114 544 Planarity : 0.003 0.026 549 Dihedral : 5.766 26.040 571 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.90 % Allowed : 19.71 % 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: 0.42 (0.43), residues: 396 helix: 0.71 (0.30), residues: 317 sheet: None (None), residues: 0 loop : -1.16 (0.68), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 331 HIS 0.001 0.000 HIS A 289 PHE 0.008 0.001 PHE A 447 TYR 0.013 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 65 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.343 Fit side-chains REVERT: A 74 TYR cc_start: 0.9046 (m-10) cc_final: 0.8423 (m-80) REVERT: A 85 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8360 (mp) REVERT: A 202 PHE cc_start: 0.8226 (m-80) cc_final: 0.7974 (m-10) REVERT: A 296 ASP cc_start: 0.8552 (t0) cc_final: 0.8214 (t70) outliers start: 10 outliers final: 8 residues processed: 62 average time/residue: 0.1893 time to fit residues: 14.0142 Evaluate side-chains 62 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 3 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.135625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.119410 restraints weight = 4096.479| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.88 r_work: 0.3261 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3499 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= 0.220 Angle : 0.531 5.901 4658 Z= 0.268 Chirality : 0.039 0.111 544 Planarity : 0.003 0.022 549 Dihedral : 5.705 25.814 571 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.19 % Allowed : 19.42 % 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: 0.49 (0.43), residues: 396 helix: 0.77 (0.30), residues: 317 sheet: None (None), residues: 0 loop : -1.24 (0.67), residues: 79 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 0.022 0.001 PHE A 84 TYR 0.013 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 66 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.372 Fit side-chains REVERT: A 74 TYR cc_start: 0.9037 (m-10) cc_final: 0.8427 (m-80) REVERT: A 85 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8354 (mp) REVERT: A 202 PHE cc_start: 0.8176 (m-80) cc_final: 0.7931 (m-10) REVERT: A 296 ASP cc_start: 0.8581 (t0) cc_final: 0.8251 (t70) REVERT: A 351 PHE cc_start: 0.7885 (t80) cc_final: 0.7559 (t80) REVERT: A 393 LYS cc_start: 0.7993 (mmmt) cc_final: 0.7576 (tptp) outliers start: 11 outliers final: 10 residues processed: 62 average time/residue: 0.1915 time to fit residues: 14.2468 Evaluate side-chains 65 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL 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 190 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 12 optimal weight: 0.0970 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.137186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.120891 restraints weight = 4200.828| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.91 r_work: 0.3277 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3508 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= 0.186 Angle : 0.515 5.707 4658 Z= 0.261 Chirality : 0.038 0.111 544 Planarity : 0.003 0.022 549 Dihedral : 5.556 25.568 571 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.90 % Allowed : 20.00 % Favored : 77.10 % 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: 0.61 (0.43), residues: 396 helix: 0.85 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -1.18 (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 0.017 0.001 PHE A 322 TYR 0.013 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: 1866.41 seconds wall clock time: 34 minutes 9.07 seconds (2049.07 seconds total)