Starting phenix.real_space_refine on Wed Sep 17 04:01:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xxi_38750/09_2025/8xxi_38750_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xxi_38750/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xxi_38750/09_2025/8xxi_38750_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xxi_38750/09_2025/8xxi_38750_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xxi_38750/09_2025/8xxi_38750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xxi_38750/09_2025/8xxi_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-2.0-5805/lib/python3.9/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, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.28, per 1000 atoms: 0.35 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: 0.34 Conformation dependent library (CDL) restraints added in 173.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.11 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: 0.62 Time building geometry restraints manager: 0.47 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: 1.560 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.940 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.030 ------------------------------------------------------------------------------- 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= 0.294 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 aren 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 covalent geometry : bond 0.00684 ( 3714) covalent geometry : angle 0.82512 ( 5064) hydrogen bonds : bond 0.12831 ( 255) hydrogen bonds : angle 6.46758 ( 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 : 0.129 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: 0.0771 time to fit residues: 7.2050 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 : 0.142 ------------------------------------------------------------------------------- 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... 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 = 0.3944 r_free = 0.3944 target = 0.163478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.131019 restraints weight = 3710.865| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.01 r_work: 0.3422 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3714 Z= 0.136 Angle : 0.595 7.872 5064 Z= 0.310 Chirality : 0.042 0.156 601 Planarity : 0.004 0.032 619 Dihedral : 9.279 56.075 545 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.99 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 aren not related in a simple way. whole: -0.10 (0.39), residues: 463 helix: 0.81 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -2.53 (0.54), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 355 TYR 0.016 0.002 TYR A 385 PHE 0.013 0.001 PHE A 187 TRP 0.011 0.002 TRP A 390 HIS 0.001 0.000 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3714) covalent geometry : angle 0.59468 ( 5064) hydrogen bonds : bond 0.04285 ( 255) hydrogen bonds : angle 4.40964 ( 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 : 0.131 Fit side-chains REVERT: A 38 SER cc_start: 0.7332 (t) cc_final: 0.6863 (p) REVERT: A 65 TYR cc_start: 0.8292 (m-80) cc_final: 0.8024 (m-80) REVERT: A 68 SER cc_start: 0.8466 (t) cc_final: 0.8254 (p) REVERT: A 126 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7820 (tp) REVERT: A 205 ARG cc_start: 0.6075 (mmp-170) cc_final: 0.5394 (mmm-85) REVERT: A 410 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.4829 (ttm-80) REVERT: A 481 ARG cc_start: 0.5818 (tpt170) cc_final: 0.4015 (mmt-90) outliers start: 15 outliers final: 9 residues processed: 50 average time/residue: 0.0910 time to fit residues: 5.5816 Evaluate side-chains 47 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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: 0.5980 chunk 31 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 40 optimal weight: 0.0670 chunk 23 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.161505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.130851 restraints weight = 3711.190| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.89 r_work: 0.3427 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3714 Z= 0.135 Angle : 0.564 7.169 5064 Z= 0.291 Chirality : 0.041 0.139 601 Planarity : 0.004 0.032 619 Dihedral : 6.995 50.583 518 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.82 % Allowed : 21.28 % 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 aren not related in a simple way. whole: 0.80 (0.40), residues: 463 helix: 1.55 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -2.28 (0.53), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 481 TYR 0.014 0.001 TYR A 385 PHE 0.014 0.001 PHE A 187 TRP 0.013 0.001 TRP A 390 HIS 0.002 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 3714) covalent geometry : angle 0.56362 ( 5064) hydrogen bonds : bond 0.04169 ( 255) hydrogen bonds : angle 4.15978 ( 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: 11 poor density : 34 time to evaluate : 0.138 Fit side-chains REVERT: A 65 TYR cc_start: 0.8317 (m-80) cc_final: 0.8042 (m-80) REVERT: A 68 SER cc_start: 0.8464 (t) cc_final: 0.8228 (p) REVERT: A 92 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7046 (tm-30) REVERT: A 205 ARG cc_start: 0.6084 (mmp-170) cc_final: 0.5383 (mmm-85) REVERT: A 410 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.4952 (ttm-80) REVERT: A 481 ARG cc_start: 0.6126 (tpt170) cc_final: 0.4228 (mmt-90) outliers start: 11 outliers final: 6 residues processed: 44 average time/residue: 0.1079 time to fit residues: 5.6636 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 : 0.122 ------------------------------------------------------------------------------- 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 273 ILE Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 410 ARG Chi-restraints excluded: chain A residue 432 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.157446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126025 restraints weight = 3706.424| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.97 r_work: 0.3360 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3714 Z= 0.168 Angle : 0.602 9.883 5064 Z= 0.309 Chirality : 0.043 0.157 601 Planarity : 0.004 0.032 619 Dihedral : 6.587 51.151 513 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % 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 aren not related in a simple way. whole: 0.84 (0.40), residues: 463 helix: 1.52 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -2.12 (0.54), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 119 TYR 0.018 0.002 TYR A 385 PHE 0.015 0.001 PHE A 424 TRP 0.013 0.001 TRP A 390 HIS 0.002 0.000 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 3714) covalent geometry : angle 0.60194 ( 5064) hydrogen bonds : bond 0.04558 ( 255) hydrogen bonds : angle 4.22824 ( 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 47 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.132 Fit side-chains REVERT: A 68 SER cc_start: 0.8544 (t) cc_final: 0.8257 (p) REVERT: A 92 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7011 (tm-30) REVERT: A 205 ARG cc_start: 0.6052 (mmp-170) cc_final: 0.5338 (mmm-85) REVERT: A 410 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.4978 (ttm-80) REVERT: A 481 ARG cc_start: 0.6113 (tpt170) cc_final: 0.4213 (mmt-90) outliers start: 14 outliers final: 7 residues processed: 46 average time/residue: 0.1067 time to fit residues: 5.7504 Evaluate side-chains 43 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 34 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 38 optimal weight: 0.0770 chunk 0 optimal weight: 3.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.162282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.131510 restraints weight = 3677.487| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.88 r_work: 0.3428 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3714 Z= 0.125 Angle : 0.551 8.592 5064 Z= 0.281 Chirality : 0.041 0.217 601 Planarity : 0.004 0.031 619 Dihedral : 6.278 51.825 513 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 2.82 % Allowed : 22.56 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.41), residues: 463 helix: 1.80 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -2.05 (0.54), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 355 TYR 0.016 0.001 TYR A 385 PHE 0.013 0.001 PHE A 187 TRP 0.011 0.001 TRP A 390 HIS 0.001 0.000 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 3714) covalent geometry : angle 0.55078 ( 5064) hydrogen bonds : bond 0.03979 ( 255) hydrogen bonds : angle 4.05672 ( 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 45 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.143 Fit side-chains REVERT: A 65 TYR cc_start: 0.8295 (m-80) cc_final: 0.8041 (m-80) REVERT: A 205 ARG cc_start: 0.6037 (mmp-170) cc_final: 0.5334 (mmm-85) REVERT: A 410 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.5253 (ttm-80) REVERT: A 481 ARG cc_start: 0.6006 (tpt170) cc_final: 0.4196 (mmt-90) outliers start: 11 outliers final: 9 residues processed: 42 average time/residue: 0.1078 time to fit residues: 5.3609 Evaluate side-chains 42 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.106 ------------------------------------------------------------------------------- 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 288 ARG 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: 0.1980 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.3888 r_free = 0.3888 target = 0.158867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.127766 restraints weight = 3741.624| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.94 r_work: 0.3380 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2136 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= 0.149 Angle : 0.582 11.066 5064 Z= 0.295 Chirality : 0.042 0.189 601 Planarity : 0.004 0.031 619 Dihedral : 6.303 53.419 513 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.85 % Allowed : 20.26 % 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 aren not related in a simple way. whole: 1.20 (0.41), residues: 463 helix: 1.74 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.92 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 119 TYR 0.018 0.001 TYR A 385 PHE 0.015 0.001 PHE A 187 TRP 0.013 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 3714) covalent geometry : angle 0.58204 ( 5064) hydrogen bonds : bond 0.04261 ( 255) hydrogen bonds : angle 4.11102 ( 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 47 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 32 time to evaluate : 0.132 Fit side-chains REVERT: A 65 TYR cc_start: 0.8338 (m-80) cc_final: 0.8067 (m-80) REVERT: A 92 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7235 (tm-30) REVERT: A 205 ARG cc_start: 0.6035 (mmp-170) cc_final: 0.5300 (mmm-85) REVERT: A 410 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.5110 (ttm-80) REVERT: A 481 ARG cc_start: 0.6024 (tpt170) cc_final: 0.4125 (mmt-90) outliers start: 15 outliers final: 10 residues processed: 45 average time/residue: 0.0967 time to fit residues: 5.2162 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 : 0.130 ------------------------------------------------------------------------------- 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 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 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 15 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.148714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118793 restraints weight = 3755.055| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.80 r_work: 0.3224 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3714 Z= 0.139 Angle : 0.557 5.803 5064 Z= 0.288 Chirality : 0.041 0.174 601 Planarity : 0.004 0.030 619 Dihedral : 6.241 54.930 513 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.59 % Allowed : 21.03 % 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 aren not related in a simple way. whole: 1.30 (0.41), residues: 463 helix: 1.81 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.85 (0.56), residues: 125 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 covalent geometry : bond 0.00324 ( 3714) covalent geometry : angle 0.55693 ( 5064) hydrogen bonds : bond 0.04120 ( 255) hydrogen bonds : angle 4.08479 ( 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 48 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.130 Fit side-chains REVERT: A 65 TYR cc_start: 0.7907 (m-80) cc_final: 0.7634 (m-80) REVERT: A 92 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.6419 (tm-30) REVERT: A 205 ARG cc_start: 0.5447 (mmp-170) cc_final: 0.4800 (mmm-85) REVERT: A 410 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.4864 (ttm-80) REVERT: A 481 ARG cc_start: 0.5514 (tpt170) cc_final: 0.3756 (mmt-90) outliers start: 14 outliers final: 9 residues processed: 46 average time/residue: 0.1060 time to fit residues: 5.7604 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 : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 1.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 chunk 34 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.154861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.125210 restraints weight = 3726.367| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.82 r_work: 0.3289 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3714 Z= 0.121 Angle : 0.552 9.944 5064 Z= 0.279 Chirality : 0.040 0.160 601 Planarity : 0.004 0.028 619 Dihedral : 6.057 56.067 513 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.33 % Allowed : 20.77 % 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 aren not related in a simple way. whole: 1.51 (0.41), residues: 463 helix: 1.95 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.75 (0.57), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 481 TYR 0.016 0.001 TYR A 385 PHE 0.013 0.001 PHE A 187 TRP 0.010 0.001 TRP A 390 HIS 0.001 0.000 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 3714) covalent geometry : angle 0.55150 ( 5064) hydrogen bonds : bond 0.03824 ( 255) hydrogen bonds : angle 3.95720 ( 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 46 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.112 Fit side-chains REVERT: A 65 TYR cc_start: 0.7838 (m-80) cc_final: 0.7578 (m-80) REVERT: A 205 ARG cc_start: 0.5364 (mmp-170) cc_final: 0.4766 (mmm-85) REVERT: A 410 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.5116 (ttm-80) REVERT: A 481 ARG cc_start: 0.5439 (tpt170) cc_final: 0.3823 (mpt180) outliers start: 13 outliers final: 11 residues processed: 44 average time/residue: 0.1099 time to fit residues: 5.6878 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 : 0.138 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 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 = 0.3682 r_free = 0.3682 target = 0.147520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117615 restraints weight = 3684.500| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.78 r_work: 0.3212 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2303 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= 0.155 Angle : 0.578 9.340 5064 Z= 0.295 Chirality : 0.042 0.171 601 Planarity : 0.004 0.028 619 Dihedral : 6.180 56.527 513 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.08 % Allowed : 21.28 % Favored : 75.64 % 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 aren not related in a simple way. whole: 1.41 (0.41), residues: 463 helix: 1.88 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -1.77 (0.57), residues: 126 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 0.015 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 covalent geometry : bond 0.00375 ( 3714) covalent geometry : angle 0.57813 ( 5064) hydrogen bonds : bond 0.04245 ( 255) hydrogen bonds : angle 4.04549 ( 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 44 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.133 Fit side-chains REVERT: A 65 TYR cc_start: 0.7892 (m-80) cc_final: 0.7625 (m-80) REVERT: A 205 ARG cc_start: 0.5429 (mmp-170) cc_final: 0.4781 (mmm-85) REVERT: A 410 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.4886 (ttm-80) REVERT: A 481 ARG cc_start: 0.5493 (tpt170) cc_final: 0.3760 (mmt-90) outliers start: 12 outliers final: 9 residues processed: 42 average time/residue: 0.1115 time to fit residues: 5.4781 Evaluate side-chains 41 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.134 ------------------------------------------------------------------------------- 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 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 34 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 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: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.145082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.114820 restraints weight = 3781.363| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.78 r_work: 0.3228 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2278 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= 0.154 Angle : 0.583 9.443 5064 Z= 0.298 Chirality : 0.042 0.177 601 Planarity : 0.004 0.028 619 Dihedral : 6.245 57.762 513 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.08 % Allowed : 21.28 % Favored : 75.64 % 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 aren not related in a simple way. whole: 1.37 (0.41), residues: 463 helix: 1.81 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.68 (0.57), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 119 TYR 0.020 0.001 TYR A 385 PHE 0.015 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 covalent geometry : bond 0.00368 ( 3714) covalent geometry : angle 0.58318 ( 5064) hydrogen bonds : bond 0.04281 ( 255) hydrogen bonds : angle 4.08083 ( 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 43 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.141 Fit side-chains REVERT: A 65 TYR cc_start: 0.7903 (m-80) cc_final: 0.7638 (m-80) REVERT: A 205 ARG cc_start: 0.5431 (mmp-170) cc_final: 0.4768 (mmm-85) REVERT: A 410 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.4916 (ttm-80) REVERT: A 481 ARG cc_start: 0.5450 (tpt170) cc_final: 0.3721 (mmt-90) outliers start: 12 outliers final: 10 residues processed: 41 average time/residue: 0.1132 time to fit residues: 5.4616 Evaluate side-chains 42 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 0.0010 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 0.0470 chunk 22 optimal weight: 4.9990 overall best weight: 0.4684 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.151462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122080 restraints weight = 3707.283| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.74 r_work: 0.3250 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3714 Z= 0.126 Angle : 0.550 8.037 5064 Z= 0.281 Chirality : 0.041 0.164 601 Planarity : 0.004 0.029 619 Dihedral : 6.114 59.117 513 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.56 % Allowed : 22.05 % 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 aren not related in a simple way. whole: 1.59 (0.41), residues: 463 helix: 1.95 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.55 (0.58), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 468 TYR 0.017 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 covalent geometry : bond 0.00286 ( 3714) covalent geometry : angle 0.54985 ( 5064) hydrogen bonds : bond 0.03938 ( 255) hydrogen bonds : angle 3.97749 ( 756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1167.20 seconds wall clock time: 20 minutes 41.72 seconds (1241.72 seconds total)