Starting phenix.real_space_refine on Wed Mar 5 21:17:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xxi_38750/03_2025/8xxi_38750_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xxi_38750/03_2025/8xxi_38750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xxi_38750/03_2025/8xxi_38750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xxi_38750/03_2025/8xxi_38750.map" model { file = "/net/cci-nas-00/data/ceres_data/8xxi_38750/03_2025/8xxi_38750_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xxi_38750/03_2025/8xxi_38750_neut.cif" } resolution = 3.04 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= 0.005 sd= 0.099 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 S 19 5.16 5 Na 1 4.78 5 C 2414 2.51 5 N 564 2.21 5 O 624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3622 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3612 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 20, 'TRANS': 444} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.91, per 1000 atoms: 0.80 Number of scatterers: 3622 At special positions: 0 Unit cell: (71.122, 83.527, 61.198, 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 19 16.00 Na 1 11.00 O 624 8.00 N 564 7.00 C 2414 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: 0.94 Conformation dependent library (CDL) restraints added in 437.3 milliseconds 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 868 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 1 sheets defined 75.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 38 through 52 removed outlier: 3.574A pdb=" N GLY A 52 " --> pdb=" O GLY A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 66 removed outlier: 3.869A pdb=" N TYR A 65 " --> pdb=" O GLY A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 98 Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.560A pdb=" N ALA A 110 " --> pdb=" O TYR A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 126 Processing helix chain 'A' and resid 126 through 144 Processing helix chain 'A' and resid 154 through 176 removed outlier: 3.572A pdb=" N TYR A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 209 removed outlier: 3.544A pdb=" N GLY A 180 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY A 209 " --> pdb=" O ARG A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 254 through 285 Proline residue: A 260 - end of helix Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'A' and resid 295 through 305 Processing helix chain 'A' and resid 310 through 341 Processing helix chain 'A' and resid 358 through 372 removed outlier: 3.670A pdb=" N TYR A 372 " --> pdb=" O MET A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 379 through 406 removed outlier: 5.452A pdb=" N PHE A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N SER A 388 " --> pdb=" O TYR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 439 Proline residue: A 435 - end of helix removed outlier: 3.627A pdb=" N ASP A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 454 Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 469 through 483 Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 352 255 hydrogen bonds defined for protein. 756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 811 1.33 - 1.45: 802 1.45 - 1.57: 2075 1.57 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 3714 Sorted by residual: bond pdb=" C HIS A 343 " pdb=" N LEU A 344 " ideal model delta sigma weight residual 1.329 1.255 0.074 3.03e-02 1.09e+03 5.93e+00 bond pdb=" C ARG A 468 " pdb=" N PRO A 469 " ideal model delta sigma weight residual 1.330 1.354 -0.024 1.19e-02 7.06e+03 3.94e+00 bond pdb=" CA GLN A 484 " pdb=" C GLN A 484 " ideal model delta sigma weight residual 1.526 1.510 0.016 9.20e-03 1.18e+04 3.22e+00 bond pdb=" CG LEU A 33 " pdb=" CD1 LEU A 33 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.88e+00 bond pdb=" N LEU A 601 " pdb=" CA LEU A 601 " ideal model delta sigma weight residual 1.458 1.428 0.030 1.90e-02 2.77e+03 2.53e+00 ... (remaining 3709 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 4878 2.02 - 4.05: 159 4.05 - 6.07: 24 6.07 - 8.09: 2 8.09 - 10.11: 1 Bond angle restraints: 5064 Sorted by residual: angle pdb=" N ALA A 347 " pdb=" CA ALA A 347 " pdb=" C ALA A 347 " ideal model delta sigma weight residual 113.89 106.97 6.92 1.58e+00 4.01e-01 1.92e+01 angle pdb=" N VAL A 296 " pdb=" CA VAL A 296 " pdb=" C VAL A 296 " ideal model delta sigma weight residual 110.42 114.15 -3.73 9.60e-01 1.09e+00 1.51e+01 angle pdb=" N VAL A 248 " pdb=" CA VAL A 248 " pdb=" C VAL A 248 " ideal model delta sigma weight residual 106.21 109.91 -3.70 1.07e+00 8.73e-01 1.20e+01 angle pdb=" N ARG A 404 " pdb=" CA ARG A 404 " pdb=" C ARG A 404 " ideal model delta sigma weight residual 111.28 107.52 3.76 1.09e+00 8.42e-01 1.19e+01 angle pdb=" N HIS A 213 " pdb=" CA HIS A 213 " pdb=" C HIS A 213 " ideal model delta sigma weight residual 113.43 109.29 4.14 1.26e+00 6.30e-01 1.08e+01 ... (remaining 5059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 1873 18.00 - 36.00: 197 36.00 - 54.00: 68 54.00 - 71.99: 11 71.99 - 89.99: 4 Dihedral angle restraints: 2153 sinusoidal: 798 harmonic: 1355 Sorted by residual: dihedral pdb=" CA CYS A 349 " pdb=" C CYS A 349 " pdb=" N MET A 350 " pdb=" CA MET A 350 " ideal model delta harmonic sigma weight residual 180.00 157.30 22.70 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ILE A 307 " pdb=" C ILE A 307 " pdb=" N PHE A 308 " pdb=" CA PHE A 308 " ideal model delta harmonic sigma weight residual -180.00 -160.72 -19.28 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA THR A 249 " pdb=" C THR A 249 " pdb=" N GLU A 250 " pdb=" CA GLU A 250 " ideal model delta harmonic sigma weight residual 180.00 161.06 18.94 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 2150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 378 0.037 - 0.075: 164 0.075 - 0.112: 43 0.112 - 0.150: 14 0.150 - 0.187: 2 Chirality restraints: 601 Sorted by residual: chirality pdb=" CB ILE A 378 " pdb=" CA ILE A 378 " pdb=" CG1 ILE A 378 " pdb=" CG2 ILE A 378 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CG LEU A 601 " pdb=" CB LEU A 601 " pdb=" CD1 LEU A 601 " pdb=" CD2 LEU A 601 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CB ILE A 126 " pdb=" CA ILE A 126 " pdb=" CG1 ILE A 126 " pdb=" CG2 ILE A 126 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 598 not shown) Planarity restraints: 619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 350 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C MET A 350 " -0.028 2.00e-02 2.50e+03 pdb=" O MET A 350 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 351 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 454 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO A 455 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 455 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 455 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 312 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO A 313 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 313 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 313 " 0.018 5.00e-02 4.00e+02 ... (remaining 616 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 267 2.72 - 3.27: 3882 3.27 - 3.81: 6429 3.81 - 4.36: 7799 4.36 - 4.90: 13312 Nonbonded interactions: 31689 Sorted by model distance: nonbonded pdb=" NH2 ARG A 288 " pdb=" OD2 ASP A 289 " model vdw 2.180 3.120 nonbonded pdb=" OE1 GLU A 92 " pdb=" NE2 GLN A 400 " model vdw 2.213 3.120 nonbonded pdb=" O SER A 58 " pdb=" OG SER A 58 " model vdw 2.215 3.040 nonbonded pdb=" O LEU A 125 " pdb=" OH TYR A 372 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR A 389 " pdb="NA NA A 602 " model vdw 2.222 2.470 ... (remaining 31684 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.540 Find NCS groups from input model: 0.040 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 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 : 0.007 0.074 3714 Z= 0.420 Angle : 0.825 10.114 5064 Z= 0.484 Chirality : 0.046 0.187 601 Planarity : 0.004 0.036 619 Dihedral : 17.377 89.992 1285 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.99 % Favored : 91.58 % Rotamer: Outliers : 10.00 % Allowed : 19.23 % Favored : 70.77 % 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: -2.27 (0.35), residues: 463 helix: -0.70 (0.26), residues: 328 sheet: None (None), residues: 0 loop : -3.40 (0.48), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 390 HIS 0.004 0.001 HIS A 352 PHE 0.017 0.002 PHE A 187 TYR 0.018 0.002 TYR A 437 ARG 0.003 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 44 time to evaluate : 0.365 Fit side-chains REVERT: A 205 ARG cc_start: 0.6475 (mmp-170) cc_final: 0.5955 (mmm-85) REVERT: A 290 ILE cc_start: 0.6985 (tt) cc_final: 0.6771 (tt) REVERT: A 410 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.5599 (ttm-80) REVERT: A 437 TYR cc_start: 0.4836 (p90) cc_final: 0.4507 (p90) REVERT: A 481 ARG cc_start: 0.6214 (tpt170) cc_final: 0.4322 (mmt180) REVERT: A 601 LEU cc_start: 0.5434 (OUTLIER) cc_final: 0.5219 (mp) outliers start: 39 outliers final: 24 residues processed: 76 average time/residue: 0.1666 time to fit residues: 15.5775 Evaluate side-chains 66 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 40 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 410 ARG Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 601 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 0.0060 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 132 GLN A 173 ASN A 246 ASN A 325 ASN A 383 ASN A 484 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.159316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.127461 restraints weight = 3706.971| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.98 r_work: 0.3382 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3714 Z= 0.214 Angle : 0.612 8.107 5064 Z= 0.320 Chirality : 0.042 0.153 601 Planarity : 0.005 0.032 619 Dihedral : 9.526 56.318 545 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.85 % Allowed : 21.79 % Favored : 74.36 % 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: -0.25 (0.39), residues: 463 helix: 0.65 (0.27), residues: 342 sheet: None (None), residues: 0 loop : -2.47 (0.56), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 390 HIS 0.001 0.000 HIS A 352 PHE 0.014 0.001 PHE A 187 TYR 0.018 0.002 TYR A 385 ARG 0.002 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.391 Fit side-chains REVERT: A 38 SER cc_start: 0.7350 (t) cc_final: 0.6893 (p) REVERT: A 68 SER cc_start: 0.8525 (t) cc_final: 0.8291 (p) REVERT: A 126 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7864 (tp) REVERT: A 205 ARG cc_start: 0.6107 (mmp-170) cc_final: 0.5407 (mmm-85) REVERT: A 287 MET cc_start: 0.7715 (tpt) cc_final: 0.7271 (tpt) REVERT: A 410 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.4807 (ttm-80) REVERT: A 481 ARG cc_start: 0.5855 (tpt170) cc_final: 0.3932 (mmt180) outliers start: 15 outliers final: 10 residues processed: 52 average time/residue: 0.1872 time to fit residues: 11.9101 Evaluate side-chains 49 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 410 ARG Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 432 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 19 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.0570 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.161181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.130200 restraints weight = 3615.940| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.93 r_work: 0.3420 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3714 Z= 0.189 Angle : 0.570 7.743 5064 Z= 0.293 Chirality : 0.041 0.141 601 Planarity : 0.004 0.031 619 Dihedral : 7.210 51.375 520 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.82 % Allowed : 22.05 % Favored : 75.13 % 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: 0.69 (0.40), residues: 463 helix: 1.43 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -2.25 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 390 HIS 0.001 0.000 HIS A 343 PHE 0.013 0.001 PHE A 187 TYR 0.014 0.002 TYR A 385 ARG 0.003 0.000 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.354 Fit side-chains REVERT: A 65 TYR cc_start: 0.8302 (m-80) cc_final: 0.8020 (m-80) REVERT: A 68 SER cc_start: 0.8467 (t) cc_final: 0.8235 (p) REVERT: A 205 ARG cc_start: 0.6037 (mmp-170) cc_final: 0.5345 (mmm-85) REVERT: A 287 MET cc_start: 0.7724 (tpt) cc_final: 0.7351 (tpt) REVERT: A 410 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.4933 (ttm-80) REVERT: A 481 ARG cc_start: 0.6108 (tpt170) cc_final: 0.4139 (mmt180) outliers start: 11 outliers final: 5 residues processed: 42 average time/residue: 0.2303 time to fit residues: 11.6473 Evaluate side-chains 39 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 410 ARG Chi-restraints excluded: chain A residue 432 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.158473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126303 restraints weight = 3699.359| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.01 r_work: 0.3374 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3714 Z= 0.236 Angle : 0.587 7.615 5064 Z= 0.303 Chirality : 0.042 0.146 601 Planarity : 0.004 0.031 619 Dihedral : 6.597 51.227 513 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.08 % Allowed : 22.31 % Favored : 74.62 % 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: 0.84 (0.40), residues: 463 helix: 1.51 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -2.09 (0.54), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 390 HIS 0.002 0.000 HIS A 352 PHE 0.015 0.001 PHE A 187 TYR 0.018 0.002 TYR A 385 ARG 0.002 0.000 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.376 Fit side-chains REVERT: A 68 SER cc_start: 0.8530 (t) cc_final: 0.8235 (p) REVERT: A 205 ARG cc_start: 0.5992 (mmp-170) cc_final: 0.5289 (mmm-85) REVERT: A 410 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.4906 (ttm-80) REVERT: A 481 ARG cc_start: 0.6098 (tpt170) cc_final: 0.4126 (mmt-90) outliers start: 12 outliers final: 7 residues processed: 45 average time/residue: 0.2199 time to fit residues: 11.9049 Evaluate side-chains 42 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 410 ARG Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 432 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 31 optimal weight: 0.0570 chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.161428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.129318 restraints weight = 3719.730| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.01 r_work: 0.3410 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3714 Z= 0.182 Angle : 0.556 8.119 5064 Z= 0.284 Chirality : 0.041 0.214 601 Planarity : 0.004 0.031 619 Dihedral : 6.369 51.703 513 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.08 % Allowed : 22.56 % Favored : 74.36 % 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: 1.14 (0.41), residues: 463 helix: 1.74 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -2.00 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 PHE 0.014 0.001 PHE A 187 TYR 0.017 0.001 TYR A 385 ARG 0.001 0.000 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.375 Fit side-chains REVERT: A 65 TYR cc_start: 0.8258 (m-80) cc_final: 0.8004 (m-80) REVERT: A 68 SER cc_start: 0.8414 (t) cc_final: 0.8180 (p) REVERT: A 205 ARG cc_start: 0.5995 (mmp-170) cc_final: 0.5305 (mmm-85) REVERT: A 410 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.5114 (ttm-80) REVERT: A 481 ARG cc_start: 0.5994 (tpt170) cc_final: 0.4057 (mmt-90) outliers start: 12 outliers final: 9 residues processed: 43 average time/residue: 0.2309 time to fit residues: 11.8714 Evaluate side-chains 43 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 410 ARG Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 432 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 30 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 41 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.147670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117709 restraints weight = 3736.406| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.79 r_work: 0.3211 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3714 Z= 0.209 Angle : 0.565 7.827 5064 Z= 0.289 Chirality : 0.042 0.187 601 Planarity : 0.004 0.030 619 Dihedral : 6.302 52.613 513 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.82 % Allowed : 22.05 % Favored : 75.13 % 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: 1.21 (0.41), residues: 463 helix: 1.77 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -1.91 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 PHE 0.015 0.001 PHE A 187 TYR 0.017 0.001 TYR A 385 ARG 0.001 0.000 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.351 Fit side-chains REVERT: A 65 TYR cc_start: 0.7805 (m-80) cc_final: 0.7535 (m-80) REVERT: A 68 SER cc_start: 0.8096 (t) cc_final: 0.7644 (p) REVERT: A 205 ARG cc_start: 0.5398 (mmp-170) cc_final: 0.4779 (mmm-85) REVERT: A 259 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6581 (tp) REVERT: A 410 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.4692 (ttm-80) REVERT: A 481 ARG cc_start: 0.5376 (tpt170) cc_final: 0.3645 (mmt-90) outliers start: 11 outliers final: 8 residues processed: 43 average time/residue: 0.2252 time to fit residues: 11.5801 Evaluate side-chains 43 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 410 ARG Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 432 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.145680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.116033 restraints weight = 3722.559| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.75 r_work: 0.3246 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3714 Z= 0.214 Angle : 0.572 8.393 5064 Z= 0.292 Chirality : 0.042 0.179 601 Planarity : 0.004 0.029 619 Dihedral : 6.291 53.818 513 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.33 % Allowed : 22.82 % Favored : 73.85 % 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: 1.25 (0.41), residues: 463 helix: 1.79 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -1.84 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 PHE 0.015 0.001 PHE A 187 TYR 0.022 0.002 TYR A 176 ARG 0.002 0.000 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.350 Fit side-chains REVERT: A 65 TYR cc_start: 0.7898 (m-80) cc_final: 0.7626 (m-80) REVERT: A 68 SER cc_start: 0.8137 (t) cc_final: 0.7698 (p) REVERT: A 205 ARG cc_start: 0.5442 (mmp-170) cc_final: 0.4823 (mmm-85) REVERT: A 259 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6641 (tp) REVERT: A 410 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.4860 (ttm-80) REVERT: A 481 ARG cc_start: 0.5453 (tpt170) cc_final: 0.3686 (mmt-90) outliers start: 13 outliers final: 10 residues processed: 45 average time/residue: 0.2138 time to fit residues: 11.5635 Evaluate side-chains 45 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 410 ARG Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 432 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 0.0870 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.148996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.119112 restraints weight = 3673.476| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.79 r_work: 0.3236 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3714 Z= 0.191 Angle : 0.567 8.370 5064 Z= 0.290 Chirality : 0.041 0.169 601 Planarity : 0.004 0.028 619 Dihedral : 6.190 54.986 513 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.08 % Allowed : 22.31 % Favored : 74.62 % 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: 1.39 (0.41), residues: 463 helix: 1.89 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -1.80 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 PHE 0.014 0.001 PHE A 187 TYR 0.018 0.001 TYR A 385 ARG 0.001 0.000 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.342 Fit side-chains REVERT: A 65 TYR cc_start: 0.7828 (m-80) cc_final: 0.7570 (m-80) REVERT: A 68 SER cc_start: 0.8069 (t) cc_final: 0.7636 (p) REVERT: A 205 ARG cc_start: 0.5320 (mmp-170) cc_final: 0.4712 (mmm-85) REVERT: A 259 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6560 (tp) REVERT: A 410 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.4792 (ttm-80) REVERT: A 481 ARG cc_start: 0.5445 (tpt170) cc_final: 0.3738 (mmt-90) outliers start: 12 outliers final: 10 residues processed: 46 average time/residue: 0.2492 time to fit residues: 13.6685 Evaluate side-chains 45 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 410 ARG Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 432 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 chunk 40 optimal weight: 0.0670 chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.153462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.124278 restraints weight = 3667.768| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.75 r_work: 0.3280 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3714 Z= 0.181 Angle : 0.559 8.259 5064 Z= 0.286 Chirality : 0.041 0.164 601 Planarity : 0.004 0.028 619 Dihedral : 6.098 55.909 513 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.82 % Allowed : 22.56 % Favored : 74.62 % 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: 1.51 (0.41), residues: 463 helix: 1.98 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -1.74 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 PHE 0.014 0.001 PHE A 187 TYR 0.017 0.001 TYR A 385 ARG 0.001 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.381 Fit side-chains REVERT: A 65 TYR cc_start: 0.7950 (m-80) cc_final: 0.7690 (m-80) REVERT: A 68 SER cc_start: 0.8147 (t) cc_final: 0.7753 (p) REVERT: A 205 ARG cc_start: 0.5487 (mmp-170) cc_final: 0.4837 (mmm-85) REVERT: A 410 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.4849 (ttm-80) REVERT: A 481 ARG cc_start: 0.5627 (tpt170) cc_final: 0.3894 (mmt-90) outliers start: 11 outliers final: 9 residues processed: 44 average time/residue: 0.2267 time to fit residues: 11.9289 Evaluate side-chains 43 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 410 ARG Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 432 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 19 optimal weight: 0.4980 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 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 = 0.3690 r_free = 0.3690 target = 0.148694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118635 restraints weight = 3674.226| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.80 r_work: 0.3228 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3714 Z= 0.200 Angle : 0.577 10.623 5064 Z= 0.292 Chirality : 0.042 0.166 601 Planarity : 0.004 0.028 619 Dihedral : 6.110 56.503 513 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.82 % Allowed : 22.82 % Favored : 74.36 % 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: 1.49 (0.41), residues: 463 helix: 1.92 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -1.65 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 PHE 0.014 0.001 PHE A 187 TYR 0.018 0.001 TYR A 385 ARG 0.002 0.000 ARG A 468 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 926 Ramachandran restraints generated. 463 Oldfield, 0 Emsley, 463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.381 Fit side-chains REVERT: A 65 TYR cc_start: 0.7912 (m-80) cc_final: 0.7652 (m-80) REVERT: A 68 SER cc_start: 0.8133 (t) cc_final: 0.7703 (p) REVERT: A 205 ARG cc_start: 0.5411 (mmp-170) cc_final: 0.4788 (mmm-85) REVERT: A 410 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.4865 (ttm-80) REVERT: A 481 ARG cc_start: 0.5444 (tpt170) cc_final: 0.3730 (mmt-90) outliers start: 11 outliers final: 10 residues processed: 43 average time/residue: 0.2278 time to fit residues: 11.6421 Evaluate side-chains 45 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 410 ARG Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 432 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 35 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 0.0060 chunk 41 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.150285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.120313 restraints weight = 3648.777| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.80 r_work: 0.3247 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3714 Z= 0.183 Angle : 0.577 12.578 5064 Z= 0.288 Chirality : 0.041 0.162 601 Planarity : 0.004 0.028 619 Dihedral : 6.043 57.090 513 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.82 % Allowed : 22.82 % Favored : 74.36 % 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: 1.55 (0.41), residues: 463 helix: 1.98 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -1.64 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 PHE 0.014 0.001 PHE A 187 TYR 0.018 0.001 TYR A 385 ARG 0.002 0.000 ARG A 468 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2186.95 seconds wall clock time: 38 minutes 14.95 seconds (2294.95 seconds total)