Starting phenix.real_space_refine on Wed Jul 1 22:41:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xxi_38750/07_2026/8xxi_38750_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xxi_38750/07_2026/8xxi_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xxi_38750/07_2026/8xxi_38750_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xxi_38750/07_2026/8xxi_38750_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xxi_38750/07_2026/8xxi_38750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xxi_38750/07_2026/8xxi_38750.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Time building chain proxies: 0.99, per 1000 atoms: 0.27 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: 0.32 Conformation dependent library (CDL) restraints added in 147.6 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: 0.09 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: 0.56 Time building geometry restraints manager: 0.42 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 3.210 ... (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: 1.230 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.190 Find NCS groups from input model: 0.020 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 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= 0.294 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.000 ARG A 473 TYR 0.018 0.002 TYR A 437 PHE 0.017 0.002 PHE A 187 TRP 0.015 0.002 TRP A 390 HIS 0.004 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.29 ( 3714) covalent geometry : angle 0.82512 / 0.48 ( 5064) hydrogen bonds : bond 0.12831 / 8.89 ( 255) hydrogen bonds : angle 6.46758 / 4.48 ( 756) *********************** 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 : 0.122 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: 0.4837 (p90) cc_final: 0.4507 (p90) REVERT: A 481 ARG cc_start: 0.6214 (tpt170) cc_final: 0.4321 (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: 0.0576 time to fit residues: 5.5297 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 : 0.120 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.0070 chunk 2 optimal weight: 0.0770 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.0060 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.2572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3951 r_free = 0.3951 target = 0.164049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.131740 restraints weight = 3712.736| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.02 r_work: 0.3432 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3714 Z= 0.134 Angle : 0.595 7.605 5064 Z= 0.310 Chirality : 0.041 0.157 601 Planarity : 0.004 0.032 619 Dihedral : 9.165 55.648 545 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.39), residues: 463 helix: 0.82 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -2.55 (0.54), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 355 TYR 0.017 0.002 TYR A 385 PHE 0.013 0.001 PHE A 187 TRP 0.010 0.002 TRP A 121 HIS 0.001 0.000 HIS A 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 3714) covalent geometry : angle 0.59537 / 0.31 ( 5064) hydrogen bonds : bond 0.04259 / 2.81 ( 255) hydrogen bonds : angle 4.39528 / 3.21 ( 756) *********************** 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 50 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.072 Fit side-chains REVERT: A 38 SER cc_start: 0.7352 (t) cc_final: 0.6889 (p) REVERT: A 65 TYR cc_start: 0.8282 (m-80) cc_final: 0.8009 (m-80) REVERT: A 126 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7790 (tp) REVERT: A 205 ARG cc_start: 0.6051 (mmp-170) cc_final: 0.5375 (mmm-85) REVERT: A 410 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.4794 (ttm-80) REVERT: A 481 ARG cc_start: 0.5793 (tpt170) cc_final: 0.3996 (mmt-90) outliers start: 15 outliers final: 9 residues processed: 50 average time/residue: 0.0778 time to fit residues: 4.6612 Evaluate side-chains 46 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 18 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.160980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.128544 restraints weight = 3719.893| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.02 r_work: 0.3397 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3714 Z= 0.145 Angle : 0.578 7.450 5064 Z= 0.299 Chirality : 0.042 0.145 601 Planarity : 0.004 0.032 619 Dihedral : 7.163 50.738 518 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.08 % Allowed : 21.03 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.40), residues: 463 helix: 1.39 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -2.23 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 119 TYR 0.016 0.001 TYR A 385 PHE 0.014 0.001 PHE A 187 TRP 0.012 0.001 TRP A 390 HIS 0.002 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 3714) covalent geometry : angle 0.57801 / 0.30 ( 5064) hydrogen bonds : bond 0.04349 / 2.91 ( 255) hydrogen bonds : angle 4.22099 / 3.08 ( 756) *********************** 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 45 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.112 Fit side-chains REVERT: A 65 TYR cc_start: 0.8301 (m-80) cc_final: 0.8016 (m-80) REVERT: A 92 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6962 (tm-30) REVERT: A 205 ARG cc_start: 0.6019 (mmp-170) cc_final: 0.5325 (mmm-85) REVERT: A 410 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.4942 (ttm-80) REVERT: A 481 ARG cc_start: 0.6093 (tpt170) cc_final: 0.4145 (mmt-90) outliers start: 12 outliers final: 6 residues processed: 44 average time/residue: 0.0703 time to fit residues: 3.7449 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 : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 232 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 6 optimal weight: 0.4980 chunk 44 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.158996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.127957 restraints weight = 3705.298| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.94 r_work: 0.3382 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3714 Z= 0.152 Angle : 0.579 8.143 5064 Z= 0.298 Chirality : 0.042 0.153 601 Planarity : 0.004 0.031 619 Dihedral : 6.628 50.909 514 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.59 % Allowed : 20.51 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.41), residues: 463 helix: 1.56 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -2.08 (0.54), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 119 TYR 0.017 0.001 TYR A 385 PHE 0.014 0.001 PHE A 187 TRP 0.012 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 3714) covalent geometry : angle 0.57894 / 0.30 ( 5064) hydrogen bonds : bond 0.04361 / 2.92 ( 255) hydrogen bonds : angle 4.16527 / 3.03 ( 756) *********************** 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: 14 poor density : 32 time to evaluate : 0.116 Fit side-chains REVERT: A 65 TYR cc_start: 0.8337 (m-80) cc_final: 0.8044 (m-80) REVERT: A 92 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: A 205 ARG cc_start: 0.6009 (mmp-170) cc_final: 0.5315 (mmm-85) REVERT: A 410 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.5099 (ttm-80) REVERT: A 481 ARG cc_start: 0.6123 (tpt170) cc_final: 0.4223 (mmt-90) outliers start: 14 outliers final: 9 residues processed: 45 average time/residue: 0.0881 time to fit residues: 4.6781 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 : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 92 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.158768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.127475 restraints weight = 3710.575| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.94 r_work: 0.3377 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3714 Z= 0.149 Angle : 0.574 8.051 5064 Z= 0.294 Chirality : 0.042 0.217 601 Planarity : 0.004 0.031 619 Dihedral : 6.431 52.191 513 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.41), residues: 463 helix: 1.66 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -2.01 (0.54), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 119 TYR 0.018 0.001 TYR A 385 PHE 0.015 0.001 PHE A 187 TRP 0.012 0.001 TRP A 390 HIS 0.002 0.000 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 3714) covalent geometry : angle 0.57442 / 0.29 ( 5064) hydrogen bonds : bond 0.04307 / 2.88 ( 255) hydrogen bonds : angle 4.12955 / 3.01 ( 756) *********************** 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 44 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.072 Fit side-chains REVERT: A 65 TYR cc_start: 0.8335 (m-80) cc_final: 0.8061 (m-80) REVERT: A 92 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7038 (tm-30) REVERT: A 205 ARG cc_start: 0.5997 (mmp-170) cc_final: 0.5286 (mmm-85) REVERT: A 410 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.5026 (ttm-80) REVERT: A 481 ARG cc_start: 0.6108 (tpt170) cc_final: 0.4281 (mmt-90) outliers start: 11 outliers final: 9 residues processed: 43 average time/residue: 0.0890 time to fit residues: 4.4767 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 : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 92 GLU 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 5 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 0.0870 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.159097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.128351 restraints weight = 3736.238| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.93 r_work: 0.3390 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2129 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= 0.144 Angle : 0.565 8.090 5064 Z= 0.290 Chirality : 0.042 0.188 601 Planarity : 0.004 0.031 619 Dihedral : 6.342 54.293 513 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.85 % Allowed : 21.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.41), residues: 463 helix: 1.73 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -1.93 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 119 TYR 0.017 0.001 TYR A 385 PHE 0.014 0.001 PHE A 187 TRP 0.012 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 3714) covalent geometry : angle 0.56533 / 0.29 ( 5064) hydrogen bonds : bond 0.04221 / 2.82 ( 255) hydrogen bonds : angle 4.11409 / 3.00 ( 756) *********************** 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 48 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 33 time to evaluate : 0.119 Fit side-chains REVERT: A 65 TYR cc_start: 0.8355 (m-80) cc_final: 0.8101 (m-80) REVERT: A 92 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: A 205 ARG cc_start: 0.6089 (mmp-170) cc_final: 0.5333 (mmm-85) REVERT: A 410 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.5202 (ttm-80) REVERT: A 481 ARG cc_start: 0.6250 (tpt170) cc_final: 0.4364 (mmt-90) outliers start: 15 outliers final: 10 residues processed: 47 average time/residue: 0.0825 time to fit residues: 4.6950 Evaluate side-chains 44 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 92 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 15 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.148573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.118414 restraints weight = 3800.491| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.82 r_work: 0.3236 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3714 Z= 0.145 Angle : 0.572 8.291 5064 Z= 0.293 Chirality : 0.042 0.172 601 Planarity : 0.004 0.030 619 Dihedral : 6.290 55.460 513 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.10 % Allowed : 20.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.41), residues: 463 helix: 1.78 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -1.85 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 119 TYR 0.018 0.001 TYR A 385 PHE 0.014 0.001 PHE A 187 TRP 0.012 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 3714) covalent geometry : angle 0.57197 / 0.29 ( 5064) hydrogen bonds : bond 0.04216 / 2.81 ( 255) hydrogen bonds : angle 4.09931 / 3.00 ( 756) *********************** 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: 16 poor density : 34 time to evaluate : 0.100 Fit side-chains REVERT: A 65 TYR cc_start: 0.7893 (m-80) cc_final: 0.7627 (m-80) REVERT: A 92 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6185 (tm-30) REVERT: A 205 ARG cc_start: 0.5404 (mmp-170) cc_final: 0.4778 (mmm-85) REVERT: A 410 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.4817 (ttm-80) REVERT: A 481 ARG cc_start: 0.5526 (tpt170) cc_final: 0.3821 (mmt-90) outliers start: 16 outliers final: 14 residues processed: 47 average time/residue: 0.0844 time to fit residues: 4.8218 Evaluate side-chains 49 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 33 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 103 SER 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 237 PHE Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 288 ARG 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 44 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 19 optimal weight: 0.0270 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.148080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117776 restraints weight = 3749.123| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.82 r_work: 0.3200 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3714 Z= 0.150 Angle : 0.574 8.109 5064 Z= 0.295 Chirality : 0.042 0.170 601 Planarity : 0.004 0.030 619 Dihedral : 6.292 56.362 513 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 4.10 % Allowed : 20.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.41), residues: 463 helix: 1.79 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -1.82 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 119 TYR 0.019 0.001 TYR A 385 PHE 0.014 0.001 PHE A 187 TRP 0.012 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 3714) covalent geometry : angle 0.57403 / 0.29 ( 5064) hydrogen bonds : bond 0.04275 / 2.85 ( 255) hydrogen bonds : angle 4.08610 / 2.99 ( 756) *********************** 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 48 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 32 time to evaluate : 0.101 Fit side-chains REVERT: A 65 TYR cc_start: 0.7887 (m-80) cc_final: 0.7621 (m-80) REVERT: A 92 GLU cc_start: 0.6565 (OUTLIER) cc_final: 0.6137 (tm-30) REVERT: A 205 ARG cc_start: 0.5325 (mmp-170) cc_final: 0.4705 (mmm-85) REVERT: A 259 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6622 (tp) REVERT: A 410 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.4890 (ttm-80) REVERT: A 481 ARG cc_start: 0.5477 (tpt170) cc_final: 0.3777 (mmt-90) outliers start: 16 outliers final: 10 residues processed: 46 average time/residue: 0.0739 time to fit residues: 4.1467 Evaluate side-chains 45 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 92 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.149473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119664 restraints weight = 3656.338| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.77 r_work: 0.3212 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3714 Z= 0.146 Angle : 0.567 7.859 5064 Z= 0.291 Chirality : 0.042 0.168 601 Planarity : 0.004 0.030 619 Dihedral : 6.250 57.015 513 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.36 % Allowed : 20.26 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.41), residues: 463 helix: 1.85 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -1.83 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 119 TYR 0.019 0.001 TYR A 385 PHE 0.014 0.001 PHE A 187 TRP 0.011 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 3714) covalent geometry : angle 0.56719 / 0.29 ( 5064) hydrogen bonds : bond 0.04217 / 2.81 ( 255) hydrogen bonds : angle 4.05660 / 2.98 ( 756) *********************** 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 49 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 32 time to evaluate : 0.150 Fit side-chains REVERT: A 65 TYR cc_start: 0.7852 (m-80) cc_final: 0.7589 (m-80) REVERT: A 92 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.6159 (tm-30) REVERT: A 205 ARG cc_start: 0.5322 (mmp-170) cc_final: 0.4701 (mmm-85) REVERT: A 259 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6611 (tp) REVERT: A 410 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.4883 (ttm-80) REVERT: A 481 ARG cc_start: 0.5475 (tpt170) cc_final: 0.3781 (mmt-90) outliers start: 17 outliers final: 13 residues processed: 46 average time/residue: 0.0873 time to fit residues: 4.7774 Evaluate side-chains 48 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 32 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 103 SER 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.147170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.116968 restraints weight = 3743.655| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.79 r_work: 0.3205 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2253 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= 0.148 Angle : 0.571 8.185 5064 Z= 0.293 Chirality : 0.042 0.166 601 Planarity : 0.004 0.030 619 Dihedral : 6.230 57.583 513 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.36 % Allowed : 20.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.41), residues: 463 helix: 1.86 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -1.79 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 119 TYR 0.019 0.001 TYR A 385 PHE 0.014 0.001 PHE A 187 TRP 0.012 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 3714) covalent geometry : angle 0.57051 / 0.29 ( 5064) hydrogen bonds : bond 0.04248 / 2.83 ( 255) hydrogen bonds : angle 4.06543 / 2.99 ( 756) ********************** 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 49 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 32 time to evaluate : 0.120 Fit side-chains REVERT: A 65 TYR cc_start: 0.7912 (m-80) cc_final: 0.7647 (m-80) REVERT: A 92 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6289 (tm-30) REVERT: A 205 ARG cc_start: 0.5440 (mmp-170) cc_final: 0.4804 (mmm-85) REVERT: A 259 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6702 (tp) REVERT: A 410 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.4850 (ttm-80) REVERT: A 481 ARG cc_start: 0.5594 (tpt170) cc_final: 0.3850 (mmt-90) outliers start: 17 outliers final: 13 residues processed: 46 average time/residue: 0.0808 time to fit residues: 4.4843 Evaluate side-chains 48 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 32 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 103 SER 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 27 optimal weight: 0.2980 chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.147650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.117764 restraints weight = 3652.715| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.76 r_work: 0.3214 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3714 Z= 0.144 Angle : 0.567 8.291 5064 Z= 0.291 Chirality : 0.042 0.168 601 Planarity : 0.004 0.030 619 Dihedral : 6.199 57.971 513 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.36 % Allowed : 21.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.41), residues: 463 helix: 1.90 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -1.76 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 468 TYR 0.019 0.001 TYR A 385 PHE 0.014 0.001 PHE A 187 TRP 0.011 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 3714) covalent geometry : angle 0.56672 / 0.29 ( 5064) hydrogen bonds : bond 0.04196 / 2.80 ( 255) hydrogen bonds : angle 4.04444 / 2.97 ( 756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 984.72 seconds wall clock time: 17 minutes 31.10 seconds (1051.10 seconds total)