Starting phenix.real_space_refine on Tue Feb 11 02:12:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xxi_38750/02_2025/8xxi_38750_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xxi_38750/02_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_38750/02_2025/8xxi_38750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xxi_38750/02_2025/8xxi_38750.map" model { file = "/net/cci-nas-00/data/ceres_data/8xxi_38750/02_2025/8xxi_38750_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xxi_38750/02_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-5592/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: 3.33, per 1000 atoms: 0.92 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: 1.06 Conformation dependent library (CDL) restraints added in 509.5 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: 0.34 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: 1.20 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: 1.410 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 13.890 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.450 ------------------------------------------------------------------------------- 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 : 0.384 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: 0.1694 time to fit residues: 15.8495 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 : 0.386 ------------------------------------------------------------------------------- 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 = 0.159253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.127424 restraints weight = 3708.992| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.99 r_work: 0.3381 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3714 Z= 0.213 Angle : 0.612 8.150 5064 Z= 0.319 Chirality : 0.042 0.154 601 Planarity : 0.005 0.032 619 Dihedral : 9.565 56.674 545 Min Nonbonded Distance : 2.309 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: -0.26 (0.39), residues: 463 helix: 0.64 (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 : 0.409 Fit side-chains REVERT: A 38 SER cc_start: 0.7332 (t) cc_final: 0.6881 (p) REVERT: A 68 SER cc_start: 0.8534 (t) cc_final: 0.8299 (p) REVERT: A 126 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7874 (tp) REVERT: A 205 ARG cc_start: 0.6119 (mmp-170) cc_final: 0.5418 (mmm-85) REVERT: A 287 MET cc_start: 0.7722 (tpt) cc_final: 0.7282 (tpt) REVERT: A 410 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.4832 (ttm-80) REVERT: A 481 ARG cc_start: 0.5864 (tpt170) cc_final: 0.3941 (mmt180) outliers start: 15 outliers final: 10 residues processed: 52 average time/residue: 0.1953 time to fit residues: 12.5136 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 : 0.395 ------------------------------------------------------------------------------- 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: 1.9990 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.157112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126137 restraints weight = 3650.393| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.93 r_work: 0.3366 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3714 Z= 0.237 Angle : 0.603 8.652 5064 Z= 0.311 Chirality : 0.042 0.149 601 Planarity : 0.004 0.033 619 Dihedral : 7.560 52.141 520 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.59 % Allowed : 21.54 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.40), residues: 463 helix: 1.25 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -2.26 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 390 HIS 0.001 0.001 HIS A 352 PHE 0.015 0.001 PHE A 187 TYR 0.016 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 48 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.363 Fit side-chains REVERT: A 68 SER cc_start: 0.8542 (t) cc_final: 0.8257 (p) REVERT: A 205 ARG cc_start: 0.6069 (mmp-170) cc_final: 0.5354 (mmm-85) REVERT: A 287 MET cc_start: 0.7737 (tpt) cc_final: 0.7400 (tpt) REVERT: A 410 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.4839 (ttm-80) REVERT: A 481 ARG cc_start: 0.6146 (tpt170) cc_final: 0.4175 (mmt180) outliers start: 14 outliers final: 7 residues processed: 47 average time/residue: 0.2097 time to fit residues: 11.8412 Evaluate side-chains 41 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 161 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 14 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 0.0970 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 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 = 0.3928 r_free = 0.3928 target = 0.162148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.129916 restraints weight = 3672.056| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.00 r_work: 0.3416 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2039 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= 0.183 Angle : 0.555 7.296 5064 Z= 0.286 Chirality : 0.041 0.144 601 Planarity : 0.004 0.031 619 Dihedral : 6.689 51.675 515 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.31 % Allowed : 23.08 % 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: 0.92 (0.41), residues: 463 helix: 1.59 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -2.14 (0.54), 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 343 PHE 0.013 0.001 PHE A 187 TYR 0.014 0.001 TYR A 385 ARG 0.001 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 44 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.406 Fit side-chains REVERT: A 65 TYR cc_start: 0.8275 (m-80) cc_final: 0.8006 (m-80) REVERT: A 68 SER cc_start: 0.8444 (t) cc_final: 0.8231 (p) REVERT: A 205 ARG cc_start: 0.6045 (mmp-170) cc_final: 0.5352 (mmm-85) REVERT: A 287 MET cc_start: 0.7700 (tpt) cc_final: 0.7395 (tpt) REVERT: A 410 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.5102 (ttm-80) REVERT: A 481 ARG cc_start: 0.6059 (tpt170) cc_final: 0.4129 (mmt-90) outliers start: 9 outliers final: 7 residues processed: 44 average time/residue: 0.2274 time to fit residues: 12.0356 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 : 0.364 ------------------------------------------------------------------------------- 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 273 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 0.0070 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.159707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.127088 restraints weight = 3735.496| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.03 r_work: 0.3379 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3714 Z= 0.218 Angle : 0.573 8.023 5064 Z= 0.293 Chirality : 0.042 0.211 601 Planarity : 0.004 0.031 619 Dihedral : 6.404 52.016 513 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % 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: 1.07 (0.41), residues: 463 helix: 1.69 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -2.03 (0.55), 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 352 PHE 0.015 0.001 PHE A 187 TYR 0.018 0.001 TYR A 385 ARG 0.002 0.000 ARG A 468 *********************** 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 : 0.450 Fit side-chains REVERT: A 65 TYR cc_start: 0.8301 (m-80) cc_final: 0.8026 (m-80) REVERT: A 68 SER cc_start: 0.8494 (t) cc_final: 0.8206 (p) REVERT: A 205 ARG cc_start: 0.6032 (mmp-170) cc_final: 0.5330 (mmm-85) REVERT: A 410 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.5073 (ttm-80) REVERT: A 481 ARG cc_start: 0.5986 (tpt170) cc_final: 0.4077 (mmt-90) outliers start: 12 outliers final: 10 residues processed: 44 average time/residue: 0.2245 time to fit residues: 11.8015 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 : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU 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 319 SER Chi-restraints excluded: chain A residue 339 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 40 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.160499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.128967 restraints weight = 3767.980| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.99 r_work: 0.3400 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2159 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= 0.196 Angle : 0.556 7.854 5064 Z= 0.284 Chirality : 0.041 0.183 601 Planarity : 0.004 0.029 619 Dihedral : 6.294 53.903 513 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.59 % Allowed : 22.31 % Favored : 74.10 % 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: 1.20 (0.41), residues: 463 helix: 1.79 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -1.99 (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 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 47 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.398 Fit side-chains REVERT: A 65 TYR cc_start: 0.8299 (m-80) cc_final: 0.8047 (m-80) REVERT: A 68 SER cc_start: 0.8424 (t) cc_final: 0.8191 (p) REVERT: A 205 ARG cc_start: 0.6026 (mmp-170) cc_final: 0.5311 (mmm-85) REVERT: A 259 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7196 (tp) REVERT: A 410 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.5100 (ttm-80) REVERT: A 481 ARG cc_start: 0.5981 (tpt170) cc_final: 0.4078 (mmt-90) outliers start: 14 outliers final: 11 residues processed: 46 average time/residue: 0.2176 time to fit residues: 12.0918 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 : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 84 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.146352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.116220 restraints weight = 3703.514| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.79 r_work: 0.3213 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3714 Z= 0.238 Angle : 0.580 8.538 5064 Z= 0.297 Chirality : 0.042 0.178 601 Planarity : 0.004 0.029 619 Dihedral : 6.365 55.518 513 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 4.36 % Allowed : 21.28 % 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: 1.15 (0.41), residues: 463 helix: 1.75 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -1.96 (0.55), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 0.001 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 50 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 33 time to evaluate : 0.369 Fit side-chains REVERT: A 65 TYR cc_start: 0.7959 (m-80) cc_final: 0.7667 (m-80) REVERT: A 68 SER cc_start: 0.8201 (t) cc_final: 0.7747 (p) REVERT: A 205 ARG cc_start: 0.5460 (mmp-170) cc_final: 0.4798 (mmm-85) REVERT: A 259 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6747 (tp) REVERT: A 410 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.4919 (ttm-80) REVERT: A 481 ARG cc_start: 0.5438 (tpt170) cc_final: 0.3659 (mmt-90) outliers start: 17 outliers final: 11 residues processed: 49 average time/residue: 0.2301 time to fit residues: 13.4295 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 : 0.384 ------------------------------------------------------------------------------- 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 84 VAL 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 319 SER Chi-restraints excluded: chain A residue 339 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 0.0370 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.148641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.118975 restraints weight = 3666.684| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.77 r_work: 0.3200 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2130 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= 0.224 Angle : 0.584 8.640 5064 Z= 0.299 Chirality : 0.042 0.174 601 Planarity : 0.004 0.029 619 Dihedral : 6.341 56.110 513 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.85 % Allowed : 21.54 % 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: 1.21 (0.41), residues: 463 helix: 1.78 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -1.90 (0.56), residues: 129 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 0.019 0.002 TYR A 385 ARG 0.002 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 49 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.387 Fit side-chains REVERT: A 65 TYR cc_start: 0.7954 (m-80) cc_final: 0.7663 (m-80) REVERT: A 68 SER cc_start: 0.8201 (t) cc_final: 0.7779 (p) REVERT: A 205 ARG cc_start: 0.5465 (mmp-170) cc_final: 0.4809 (mmm-85) REVERT: A 259 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6730 (tp) REVERT: A 410 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.4825 (ttm-80) REVERT: A 481 ARG cc_start: 0.5504 (tpt170) cc_final: 0.3719 (mmt-90) outliers start: 15 outliers final: 12 residues processed: 48 average time/residue: 0.2166 time to fit residues: 12.5323 Evaluate side-chains 47 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 84 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 12 optimal weight: 0.0010 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 40 optimal weight: 0.0670 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.4724 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.149974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.119861 restraints weight = 3621.950| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.79 r_work: 0.3270 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3714 Z= 0.180 Angle : 0.553 8.248 5064 Z= 0.282 Chirality : 0.041 0.162 601 Planarity : 0.004 0.028 619 Dihedral : 6.149 57.486 513 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.56 % Allowed : 22.56 % Favored : 74.87 % 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: 1.46 (0.41), residues: 463 helix: 1.95 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -1.77 (0.56), residues: 129 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 119 *********************** 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 44 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.406 Fit side-chains REVERT: A 65 TYR cc_start: 0.7844 (m-80) cc_final: 0.7563 (m-80) REVERT: A 68 SER cc_start: 0.8068 (t) cc_final: 0.7698 (p) REVERT: A 205 ARG cc_start: 0.5394 (mmp-170) cc_final: 0.4799 (mmm-85) REVERT: A 287 MET cc_start: 0.7108 (tpt) cc_final: 0.6809 (tpt) REVERT: A 355 ARG cc_start: 0.7055 (mtt90) cc_final: 0.6784 (mtt-85) REVERT: A 410 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.5001 (ttm-80) REVERT: A 481 ARG cc_start: 0.5427 (tpt170) cc_final: 0.3738 (mmt-90) outliers start: 10 outliers final: 8 residues processed: 43 average time/residue: 0.2507 time to fit residues: 12.8706 Evaluate side-chains 42 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 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: 0.0970 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.148340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118009 restraints weight = 3675.249| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.80 r_work: 0.3246 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2335 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= 0.202 Angle : 0.575 10.501 5064 Z= 0.291 Chirality : 0.041 0.165 601 Planarity : 0.004 0.028 619 Dihedral : 6.147 57.972 513 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % 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: 1.46 (0.41), residues: 463 helix: 1.92 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -1.68 (0.57), 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 0.018 0.001 TYR A 385 ARG 0.001 0.000 ARG A 481 ********************** 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 46 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.373 Fit side-chains REVERT: A 65 TYR cc_start: 0.7829 (m-80) cc_final: 0.7548 (m-80) REVERT: A 68 SER cc_start: 0.8103 (t) cc_final: 0.7668 (p) REVERT: A 205 ARG cc_start: 0.5412 (mmp-170) cc_final: 0.4791 (mmm-85) REVERT: A 259 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6608 (tp) REVERT: A 355 ARG cc_start: 0.7026 (mtt90) cc_final: 0.6745 (mtt-85) REVERT: A 410 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.4912 (ttm-80) REVERT: A 481 ARG cc_start: 0.5405 (tpt170) cc_final: 0.3665 (mmt-90) outliers start: 12 outliers final: 10 residues processed: 45 average time/residue: 0.2254 time to fit residues: 12.3193 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 : 0.373 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 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 = 0.3650 r_free = 0.3650 target = 0.145379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.115097 restraints weight = 3696.852| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.79 r_work: 0.3204 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3714 Z= 0.218 Angle : 0.596 12.808 5064 Z= 0.299 Chirality : 0.042 0.169 601 Planarity : 0.004 0.028 619 Dihedral : 6.217 59.124 513 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % 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: 1.40 (0.41), residues: 463 helix: 1.88 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -1.76 (0.57), 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 0.015 0.001 PHE A 187 TYR 0.019 0.001 TYR A 385 ARG 0.003 0.000 ARG A 468 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2142.51 seconds wall clock time: 38 minutes 48.71 seconds (2328.71 seconds total)