Starting phenix.real_space_refine on Tue Mar 3 14:50:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wu0_21901/03_2026/6wu0_21901.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wu0_21901/03_2026/6wu0_21901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wu0_21901/03_2026/6wu0_21901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wu0_21901/03_2026/6wu0_21901.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wu0_21901/03_2026/6wu0_21901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wu0_21901/03_2026/6wu0_21901.map" } resolution = 3.59 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.648 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: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 4090 2.51 5 N 1097 2.21 5 O 1133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6340 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 6340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 854, 6340 Classifications: {'peptide': 854} Link IDs: {'PTRANS': 52, 'TRANS': 801} Chain breaks: 1 Time building chain proxies: 1.74, per 1000 atoms: 0.27 Number of scatterers: 6340 At special positions: 0 Unit cell: (89.64, 70.2, 131.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1133 8.00 N 1097 7.00 C 4090 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: 0.81 Conformation dependent library (CDL) restraints added in 174.3 milliseconds 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1596 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 1 sheets defined 74.9% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'B' and resid 1 through 15 Processing helix chain 'B' and resid 18 through 38 Processing helix chain 'B' and resid 52 through 66 removed outlier: 3.538A pdb=" N LEU B 58 " --> pdb=" O LYS B 54 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 70 removed outlier: 3.711A pdb=" N ASN B 70 " --> pdb=" O PRO B 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 67 through 70' Processing helix chain 'B' and resid 81 through 102 removed outlier: 4.036A pdb=" N ALA B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 126 through 140 Processing helix chain 'B' and resid 140 through 149 Processing helix chain 'B' and resid 152 through 171 removed outlier: 4.107A pdb=" N VAL B 166 " --> pdb=" O THR B 162 " (cutoff:3.500A) Proline residue: B 167 - end of helix removed outlier: 3.682A pdb=" N GLY B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 178 through 194 Processing helix chain 'B' and resid 233 through 247 removed outlier: 4.156A pdb=" N ARG B 241 " --> pdb=" O SER B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 253 Processing helix chain 'B' and resid 261 through 276 removed outlier: 3.713A pdb=" N GLY B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 296 Processing helix chain 'B' and resid 298 through 324 removed outlier: 3.543A pdb=" N ILE B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 303 " --> pdb=" O LYS B 299 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER B 304 " --> pdb=" O ARG B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 333 through 342 removed outlier: 4.315A pdb=" N VAL B 339 " --> pdb=" O MET B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 360 removed outlier: 4.239A pdb=" N ALA B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 374 Processing helix chain 'B' and resid 375 through 391 Processing helix chain 'B' and resid 397 through 429 removed outlier: 3.500A pdb=" N SER B 401 " --> pdb=" O TYR B 397 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU B 422 " --> pdb=" O THR B 418 " (cutoff:3.500A) Proline residue: B 423 - end of helix Processing helix chain 'B' and resid 443 through 450 removed outlier: 3.805A pdb=" N TYR B 449 " --> pdb=" O PRO B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 467 removed outlier: 3.721A pdb=" N LEU B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLY B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 473 removed outlier: 3.563A pdb=" N LEU B 471 " --> pdb=" O ALA B 468 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B 473 " --> pdb=" O PRO B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 485 removed outlier: 3.521A pdb=" N HIS B 483 " --> pdb=" O ASN B 480 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 485 " --> pdb=" O LEU B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 498 removed outlier: 4.491A pdb=" N LEU B 495 " --> pdb=" O SER B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 528 Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 545 through 561 removed outlier: 3.719A pdb=" N LYS B 549 " --> pdb=" O ALA B 545 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 559 " --> pdb=" O ALA B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 564 No H-bonds generated for 'chain 'B' and resid 562 through 564' Processing helix chain 'B' and resid 573 through 595 Processing helix chain 'B' and resid 599 through 614 removed outlier: 3.539A pdb=" N ALA B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 644 removed outlier: 3.538A pdb=" N GLU B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL B 630 " --> pdb=" O HIS B 626 " (cutoff:3.500A) Proline residue: B 631 - end of helix removed outlier: 3.831A pdb=" N GLN B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 653 Processing helix chain 'B' and resid 654 through 662 removed outlier: 3.511A pdb=" N VAL B 658 " --> pdb=" O PRO B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 699 removed outlier: 3.671A pdb=" N LEU B 688 " --> pdb=" O ASP B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 708 Processing helix chain 'B' and resid 709 through 739 removed outlier: 3.586A pdb=" N ALA B 713 " --> pdb=" O ILE B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 767 removed outlier: 4.126A pdb=" N VAL B 745 " --> pdb=" O ARG B 741 " (cutoff:3.500A) Proline residue: B 751 - end of helix Processing helix chain 'B' and resid 776 through 796 removed outlier: 3.887A pdb=" N MET B 794 " --> pdb=" O VAL B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 799 No H-bonds generated for 'chain 'B' and resid 797 through 799' Processing helix chain 'B' and resid 809 through 828 Processing helix chain 'B' and resid 831 through 854 removed outlier: 4.311A pdb=" N MET B 837 " --> pdb=" O GLY B 833 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE B 850 " --> pdb=" O SER B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 859 Processing sheet with id=AA1, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.715A pdb=" N ALA B 215 " --> pdb=" O ALA B 79 " (cutoff:3.500A) 436 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2079 1.34 - 1.46: 748 1.46 - 1.57: 3601 1.57 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 6466 Sorted by residual: bond pdb=" C VAL B 858 " pdb=" O VAL B 858 " ideal model delta sigma weight residual 1.236 1.224 0.012 1.19e-02 7.06e+03 1.05e+00 bond pdb=" CA VAL B 670 " pdb=" CB VAL B 670 " ideal model delta sigma weight residual 1.533 1.545 -0.012 1.26e-02 6.30e+03 8.78e-01 bond pdb=" CA VAL B 858 " pdb=" C VAL B 858 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.27e-02 6.20e+03 6.54e-01 bond pdb=" C GLU B 213 " pdb=" N PRO B 214 " ideal model delta sigma weight residual 1.334 1.352 -0.018 2.34e-02 1.83e+03 5.68e-01 bond pdb=" C THR B 260 " pdb=" N GLY B 261 " ideal model delta sigma weight residual 1.331 1.320 0.011 1.46e-02 4.69e+03 5.56e-01 ... (remaining 6461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 8607 1.71 - 3.42: 177 3.42 - 5.14: 34 5.14 - 6.85: 10 6.85 - 8.56: 2 Bond angle restraints: 8830 Sorted by residual: angle pdb=" C ASP B 665 " pdb=" N GLY B 666 " pdb=" CA GLY B 666 " ideal model delta sigma weight residual 121.41 127.46 -6.05 1.96e+00 2.60e-01 9.51e+00 angle pdb=" C VAL B 750 " pdb=" CA VAL B 750 " pdb=" CB VAL B 750 " ideal model delta sigma weight residual 113.70 110.92 2.78 9.50e-01 1.11e+00 8.54e+00 angle pdb=" C LEU B 749 " pdb=" N VAL B 750 " pdb=" CA VAL B 750 " ideal model delta sigma weight residual 120.43 123.12 -2.69 9.60e-01 1.09e+00 7.83e+00 angle pdb=" CA LEU B 498 " pdb=" CB LEU B 498 " pdb=" CG LEU B 498 " ideal model delta sigma weight residual 116.30 124.86 -8.56 3.50e+00 8.16e-02 5.98e+00 angle pdb=" N ARG B 740 " pdb=" CA ARG B 740 " pdb=" C ARG B 740 " ideal model delta sigma weight residual 110.80 115.94 -5.14 2.13e+00 2.20e-01 5.83e+00 ... (remaining 8825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 3480 16.09 - 32.18: 328 32.18 - 48.27: 80 48.27 - 64.36: 13 64.36 - 80.45: 3 Dihedral angle restraints: 3904 sinusoidal: 1447 harmonic: 2457 Sorted by residual: dihedral pdb=" CA GLY B 666 " pdb=" C GLY B 666 " pdb=" N ARG B 667 " pdb=" CA ARG B 667 " ideal model delta harmonic sigma weight residual 180.00 -154.88 -25.12 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA ARG B 667 " pdb=" C ARG B 667 " pdb=" N ALA B 668 " pdb=" CA ALA B 668 " ideal model delta harmonic sigma weight residual -180.00 -159.48 -20.52 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LEU B 739 " pdb=" C LEU B 739 " pdb=" N ARG B 740 " pdb=" CA ARG B 740 " ideal model delta harmonic sigma weight residual -180.00 -161.17 -18.83 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 3901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 836 0.045 - 0.090: 197 0.090 - 0.134: 54 0.134 - 0.179: 0 0.179 - 0.224: 1 Chirality restraints: 1088 Sorted by residual: chirality pdb=" CB ILE B 662 " pdb=" CA ILE B 662 " pdb=" CG1 ILE B 662 " pdb=" CG2 ILE B 662 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU B 804 " pdb=" CB LEU B 804 " pdb=" CD1 LEU B 804 " pdb=" CD2 LEU B 804 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE B 542 " pdb=" N ILE B 542 " pdb=" C ILE B 542 " pdb=" CB ILE B 542 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1085 not shown) Planarity restraints: 1123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 572 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO B 573 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 573 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 573 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 440 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.43e+00 pdb=" N PRO B 441 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 441 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 441 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 513 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO B 514 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 514 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 514 " -0.018 5.00e-02 4.00e+02 ... (remaining 1120 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 799 2.75 - 3.29: 6708 3.29 - 3.82: 10517 3.82 - 4.36: 11236 4.36 - 4.90: 19392 Nonbonded interactions: 48652 Sorted by model distance: nonbonded pdb=" O PRO B 167 " pdb=" OG SER B 170 " model vdw 2.211 3.040 nonbonded pdb=" OG SER B 829 " pdb=" OG1 THR B 834 " model vdw 2.256 3.040 nonbonded pdb=" O PHE B 392 " pdb=" OG1 THR B 395 " model vdw 2.261 3.040 nonbonded pdb=" O ARG B 98 " pdb=" NH1 ARG B 98 " model vdw 2.291 3.120 nonbonded pdb=" O PRO B 151 " pdb=" OG SER B 629 " model vdw 2.298 3.040 ... (remaining 48647 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.020 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.250 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 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 : 0.003 0.023 6466 Z= 0.130 Angle : 0.647 8.562 8830 Z= 0.342 Chirality : 0.040 0.224 1088 Planarity : 0.004 0.040 1123 Dihedral : 13.427 80.447 2308 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % 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: -1.89 (0.27), residues: 850 helix: -0.45 (0.20), residues: 562 sheet: -1.69 (0.88), residues: 38 loop : -2.89 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 525 TYR 0.011 0.001 TYR B 353 PHE 0.011 0.001 PHE B 270 TRP 0.003 0.001 TRP B 12 HIS 0.002 0.001 HIS B 810 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6466) covalent geometry : angle 0.64663 ( 8830) hydrogen bonds : bond 0.11874 ( 436) hydrogen bonds : angle 4.94987 ( 1272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 ARG cc_start: 0.7747 (mtt90) cc_final: 0.6873 (mtt90) REVERT: B 216 ARG cc_start: 0.7344 (mtm-85) cc_final: 0.6618 (mtm-85) REVERT: B 492 MET cc_start: 0.6525 (ptm) cc_final: 0.6195 (ptm) REVERT: B 632 LEU cc_start: 0.8448 (tp) cc_final: 0.8047 (tp) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.0835 time to fit residues: 16.8322 Evaluate side-chains 124 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 0.0010 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 70 ASN B 222 GLN B 474 HIS B 483 HIS B 548 GLN B 656 GLN B 722 GLN B 831 HIS B 856 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.235687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.213554 restraints weight = 9185.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.218218 restraints weight = 5386.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.221398 restraints weight = 3526.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.223681 restraints weight = 2505.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.225232 restraints weight = 1902.892| |-----------------------------------------------------------------------------| r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6466 Z= 0.123 Angle : 0.637 7.399 8830 Z= 0.312 Chirality : 0.041 0.193 1088 Planarity : 0.005 0.065 1123 Dihedral : 4.117 21.381 906 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.13 % Allowed : 14.33 % Favored : 83.54 % 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: -0.59 (0.29), residues: 850 helix: 0.53 (0.21), residues: 594 sheet: -0.75 (0.93), residues: 38 loop : -2.85 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 839 TYR 0.007 0.001 TYR B 353 PHE 0.021 0.001 PHE B 389 TRP 0.021 0.001 TRP B 827 HIS 0.003 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6466) covalent geometry : angle 0.63697 ( 8830) hydrogen bonds : bond 0.03589 ( 436) hydrogen bonds : angle 4.00846 ( 1272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 HIS cc_start: 0.5870 (OUTLIER) cc_final: 0.5066 (t-90) REVERT: B 38 HIS cc_start: 0.6843 (m-70) cc_final: 0.5817 (m-70) REVERT: B 324 VAL cc_start: 0.8469 (p) cc_final: 0.7912 (m) REVERT: B 492 MET cc_start: 0.7197 (ptm) cc_final: 0.6789 (ptm) REVERT: B 766 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7108 (tt) REVERT: B 794 MET cc_start: 0.4739 (mtp) cc_final: 0.4492 (mtm) REVERT: B 808 LEU cc_start: 0.5751 (mp) cc_final: 0.4590 (mt) REVERT: B 827 TRP cc_start: 0.7164 (t60) cc_final: 0.6778 (t60) REVERT: B 839 ARG cc_start: 0.7697 (ttp-110) cc_final: 0.7436 (ttp-110) outliers start: 14 outliers final: 5 residues processed: 135 average time/residue: 0.0722 time to fit residues: 13.2880 Evaluate side-chains 130 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 19 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 70 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.235110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.213302 restraints weight = 9118.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.217643 restraints weight = 5492.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.220748 restraints weight = 3678.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.222884 restraints weight = 2672.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.224437 restraints weight = 2073.234| |-----------------------------------------------------------------------------| r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6466 Z= 0.136 Angle : 0.656 7.809 8830 Z= 0.323 Chirality : 0.041 0.159 1088 Planarity : 0.005 0.052 1123 Dihedral : 4.170 24.358 906 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.90 % Allowed : 16.62 % Favored : 80.49 % 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: -0.20 (0.30), residues: 850 helix: 0.86 (0.22), residues: 584 sheet: -0.53 (0.94), residues: 38 loop : -2.69 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 621 TYR 0.006 0.001 TYR B 397 PHE 0.014 0.001 PHE B 720 TRP 0.013 0.001 TRP B 827 HIS 0.012 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6466) covalent geometry : angle 0.65625 ( 8830) hydrogen bonds : bond 0.03611 ( 436) hydrogen bonds : angle 3.94064 ( 1272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 HIS cc_start: 0.5904 (OUTLIER) cc_final: 0.5442 (t-90) REVERT: B 38 HIS cc_start: 0.6995 (m-70) cc_final: 0.6479 (m-70) REVERT: B 62 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7168 (tt) REVERT: B 104 ARG cc_start: 0.7764 (mtt90) cc_final: 0.6635 (mtt90) REVERT: B 216 ARG cc_start: 0.7717 (ptp90) cc_final: 0.7479 (ptp90) REVERT: B 380 LEU cc_start: 0.6278 (OUTLIER) cc_final: 0.5996 (tt) REVERT: B 492 MET cc_start: 0.7233 (ptm) cc_final: 0.6809 (ptm) REVERT: B 656 GLN cc_start: 0.7194 (tp-100) cc_final: 0.6218 (tp-100) REVERT: B 660 ASP cc_start: 0.7335 (m-30) cc_final: 0.6967 (m-30) REVERT: B 671 GLN cc_start: 0.7950 (tt0) cc_final: 0.7585 (tt0) REVERT: B 766 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7312 (tt) REVERT: B 794 MET cc_start: 0.4772 (mtp) cc_final: 0.4502 (mtm) REVERT: B 808 LEU cc_start: 0.5884 (mp) cc_final: 0.4726 (mt) REVERT: B 827 TRP cc_start: 0.7280 (t60) cc_final: 0.6978 (t60) REVERT: B 839 ARG cc_start: 0.7769 (ttp-110) cc_final: 0.7506 (ttp-110) outliers start: 19 outliers final: 10 residues processed: 134 average time/residue: 0.0737 time to fit residues: 13.2995 Evaluate side-chains 132 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 13 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.232809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.210617 restraints weight = 9181.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.214962 restraints weight = 5557.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.217953 restraints weight = 3745.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.220113 restraints weight = 2750.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.221411 restraints weight = 2150.447| |-----------------------------------------------------------------------------| r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6466 Z= 0.148 Angle : 0.666 7.835 8830 Z= 0.329 Chirality : 0.042 0.153 1088 Planarity : 0.005 0.047 1123 Dihedral : 4.254 24.803 906 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.96 % Allowed : 18.60 % Favored : 77.44 % 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: -0.05 (0.30), residues: 850 helix: 0.99 (0.22), residues: 580 sheet: -0.68 (0.91), residues: 38 loop : -2.59 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 98 TYR 0.007 0.001 TYR B 353 PHE 0.016 0.001 PHE B 392 TRP 0.010 0.001 TRP B 827 HIS 0.010 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 6466) covalent geometry : angle 0.66607 ( 8830) hydrogen bonds : bond 0.03624 ( 436) hydrogen bonds : angle 3.97765 ( 1272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 HIS cc_start: 0.5912 (OUTLIER) cc_final: 0.5338 (t-90) REVERT: B 38 HIS cc_start: 0.7021 (m-70) cc_final: 0.6326 (m-70) REVERT: B 62 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7288 (tt) REVERT: B 104 ARG cc_start: 0.7752 (mtt90) cc_final: 0.7279 (mtt180) REVERT: B 216 ARG cc_start: 0.7714 (ptp90) cc_final: 0.7500 (ptp90) REVERT: B 222 GLN cc_start: 0.7642 (pp30) cc_final: 0.7406 (pp30) REVERT: B 380 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.6035 (tt) REVERT: B 492 MET cc_start: 0.7243 (ptm) cc_final: 0.6823 (ptm) REVERT: B 499 LYS cc_start: 0.8295 (tptp) cc_final: 0.8077 (tptt) REVERT: B 656 GLN cc_start: 0.7237 (tp-100) cc_final: 0.6332 (tp-100) REVERT: B 660 ASP cc_start: 0.7415 (m-30) cc_final: 0.6985 (m-30) REVERT: B 671 GLN cc_start: 0.8034 (tt0) cc_final: 0.7688 (tt0) REVERT: B 766 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7227 (tt) REVERT: B 794 MET cc_start: 0.4922 (mtp) cc_final: 0.4595 (mtm) REVERT: B 808 LEU cc_start: 0.5863 (mp) cc_final: 0.5321 (mp) REVERT: B 827 TRP cc_start: 0.7320 (t60) cc_final: 0.7058 (t60) REVERT: B 839 ARG cc_start: 0.7799 (ttp-110) cc_final: 0.7578 (ttp-110) outliers start: 26 outliers final: 15 residues processed: 137 average time/residue: 0.0739 time to fit residues: 13.7810 Evaluate side-chains 138 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 854 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 40 optimal weight: 20.0000 chunk 7 optimal weight: 0.4980 chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 49 optimal weight: 40.0000 chunk 33 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 67 optimal weight: 30.0000 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 474 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.231014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.210928 restraints weight = 9299.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.215607 restraints weight = 5371.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.217388 restraints weight = 3453.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.219656 restraints weight = 2436.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.220600 restraints weight = 1923.821| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6466 Z= 0.161 Angle : 0.690 8.091 8830 Z= 0.338 Chirality : 0.043 0.154 1088 Planarity : 0.005 0.047 1123 Dihedral : 4.376 25.651 906 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 5.03 % Allowed : 20.43 % Favored : 74.54 % 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: -0.01 (0.30), residues: 850 helix: 1.03 (0.22), residues: 579 sheet: -0.75 (0.90), residues: 38 loop : -2.55 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 98 TYR 0.010 0.001 TYR B 353 PHE 0.017 0.001 PHE B 720 TRP 0.007 0.001 TRP B 827 HIS 0.009 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 6466) covalent geometry : angle 0.69030 ( 8830) hydrogen bonds : bond 0.03738 ( 436) hydrogen bonds : angle 4.03085 ( 1272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 HIS cc_start: 0.5839 (OUTLIER) cc_final: 0.5190 (t-90) REVERT: B 38 HIS cc_start: 0.7125 (m-70) cc_final: 0.6339 (m-70) REVERT: B 62 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7378 (tt) REVERT: B 216 ARG cc_start: 0.7699 (ptp90) cc_final: 0.7483 (ptp90) REVERT: B 222 GLN cc_start: 0.7600 (pp30) cc_final: 0.7379 (pp30) REVERT: B 380 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.6075 (tt) REVERT: B 486 ASP cc_start: 0.7392 (t0) cc_final: 0.7140 (t0) REVERT: B 492 MET cc_start: 0.7191 (ptm) cc_final: 0.6769 (ptm) REVERT: B 499 LYS cc_start: 0.8282 (tptp) cc_final: 0.8008 (tptt) REVERT: B 656 GLN cc_start: 0.7160 (tp-100) cc_final: 0.6209 (tp-100) REVERT: B 660 ASP cc_start: 0.7400 (m-30) cc_final: 0.6849 (m-30) REVERT: B 671 GLN cc_start: 0.8053 (tt0) cc_final: 0.7712 (tt0) REVERT: B 766 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7304 (tt) REVERT: B 794 MET cc_start: 0.4964 (mtp) cc_final: 0.4555 (mtm) REVERT: B 827 TRP cc_start: 0.7345 (t60) cc_final: 0.7051 (t60) REVERT: B 839 ARG cc_start: 0.7824 (ttp-110) cc_final: 0.7605 (ttp-110) outliers start: 33 outliers final: 21 residues processed: 142 average time/residue: 0.0616 time to fit residues: 12.1306 Evaluate side-chains 144 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 854 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 50 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 59 optimal weight: 0.0170 chunk 23 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 overall best weight: 2.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 722 GLN B 805 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.235116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.214685 restraints weight = 8817.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.218812 restraints weight = 5235.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.221775 restraints weight = 3468.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.223801 restraints weight = 2483.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.225190 restraints weight = 1905.088| |-----------------------------------------------------------------------------| r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6466 Z= 0.126 Angle : 0.665 8.779 8830 Z= 0.320 Chirality : 0.042 0.171 1088 Planarity : 0.005 0.047 1123 Dihedral : 4.275 24.292 906 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.27 % Allowed : 22.87 % Favored : 72.87 % 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: 0.25 (0.30), residues: 850 helix: 1.30 (0.22), residues: 566 sheet: -0.62 (0.87), residues: 38 loop : -2.47 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 98 TYR 0.008 0.001 TYR B 353 PHE 0.017 0.001 PHE B 392 TRP 0.007 0.001 TRP B 827 HIS 0.007 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6466) covalent geometry : angle 0.66549 ( 8830) hydrogen bonds : bond 0.03487 ( 436) hydrogen bonds : angle 3.91088 ( 1272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 HIS cc_start: 0.5832 (OUTLIER) cc_final: 0.5363 (t-90) REVERT: B 38 HIS cc_start: 0.7057 (m-70) cc_final: 0.6467 (m-70) REVERT: B 62 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7299 (tt) REVERT: B 71 GLN cc_start: 0.7527 (pm20) cc_final: 0.7306 (pm20) REVERT: B 222 GLN cc_start: 0.7645 (pp30) cc_final: 0.7370 (pp30) REVERT: B 270 PHE cc_start: 0.7653 (t80) cc_final: 0.7262 (t80) REVERT: B 380 LEU cc_start: 0.6372 (OUTLIER) cc_final: 0.6076 (tt) REVERT: B 492 MET cc_start: 0.7153 (ptm) cc_final: 0.6745 (ptm) REVERT: B 499 LYS cc_start: 0.8292 (tptp) cc_final: 0.8006 (tptt) REVERT: B 656 GLN cc_start: 0.7118 (tp-100) cc_final: 0.6047 (tp-100) REVERT: B 660 ASP cc_start: 0.7368 (m-30) cc_final: 0.6757 (m-30) REVERT: B 671 GLN cc_start: 0.8037 (tt0) cc_final: 0.7515 (tt0) REVERT: B 766 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7286 (tt) REVERT: B 794 MET cc_start: 0.4863 (mtp) cc_final: 0.4482 (mtm) REVERT: B 827 TRP cc_start: 0.7397 (t60) cc_final: 0.7161 (t60) outliers start: 28 outliers final: 18 residues processed: 142 average time/residue: 0.0662 time to fit residues: 12.9445 Evaluate side-chains 146 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 854 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 79 optimal weight: 0.0050 chunk 38 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.234388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.213774 restraints weight = 8758.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.217928 restraints weight = 5207.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.220854 restraints weight = 3445.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.222643 restraints weight = 2475.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.224263 restraints weight = 1930.916| |-----------------------------------------------------------------------------| r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6466 Z= 0.134 Angle : 0.682 9.746 8830 Z= 0.328 Chirality : 0.042 0.189 1088 Planarity : 0.005 0.047 1123 Dihedral : 4.300 24.841 906 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.96 % Allowed : 24.09 % Favored : 71.95 % 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: 0.25 (0.30), residues: 850 helix: 1.27 (0.22), residues: 574 sheet: -0.49 (0.87), residues: 38 loop : -2.55 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 98 TYR 0.010 0.001 TYR B 353 PHE 0.019 0.001 PHE B 720 TRP 0.008 0.001 TRP B 827 HIS 0.003 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6466) covalent geometry : angle 0.68214 ( 8830) hydrogen bonds : bond 0.03520 ( 436) hydrogen bonds : angle 3.90048 ( 1272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 HIS cc_start: 0.5872 (OUTLIER) cc_final: 0.5365 (t-90) REVERT: B 38 HIS cc_start: 0.7028 (m-70) cc_final: 0.6413 (m-70) REVERT: B 374 MET cc_start: 0.5038 (mmm) cc_final: 0.4733 (mmt) REVERT: B 380 LEU cc_start: 0.6410 (OUTLIER) cc_final: 0.6091 (tt) REVERT: B 492 MET cc_start: 0.7166 (ptm) cc_final: 0.6757 (ptm) REVERT: B 499 LYS cc_start: 0.8299 (tptp) cc_final: 0.7974 (tptt) REVERT: B 671 GLN cc_start: 0.7958 (tt0) cc_final: 0.7423 (tt0) REVERT: B 766 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7347 (tt) REVERT: B 794 MET cc_start: 0.4846 (mtp) cc_final: 0.4481 (mtm) REVERT: B 827 TRP cc_start: 0.7452 (t60) cc_final: 0.7092 (t60) outliers start: 26 outliers final: 19 residues processed: 142 average time/residue: 0.0698 time to fit residues: 13.5625 Evaluate side-chains 139 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 854 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 51 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 805 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.230914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.209277 restraints weight = 9100.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.213428 restraints weight = 5498.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.216466 restraints weight = 3734.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.218605 restraints weight = 2718.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.220084 restraints weight = 2114.591| |-----------------------------------------------------------------------------| r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6466 Z= 0.150 Angle : 0.724 10.336 8830 Z= 0.349 Chirality : 0.043 0.182 1088 Planarity : 0.005 0.046 1123 Dihedral : 4.406 24.167 906 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.57 % Allowed : 25.46 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.17 (0.30), residues: 850 helix: 1.20 (0.22), residues: 573 sheet: -0.54 (0.84), residues: 38 loop : -2.50 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 667 TYR 0.011 0.001 TYR B 353 PHE 0.021 0.001 PHE B 720 TRP 0.011 0.001 TRP B 827 HIS 0.008 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6466) covalent geometry : angle 0.72350 ( 8830) hydrogen bonds : bond 0.03615 ( 436) hydrogen bonds : angle 3.96199 ( 1272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: B 37 HIS cc_start: 0.5843 (OUTLIER) cc_final: 0.5356 (t-90) REVERT: B 38 HIS cc_start: 0.7038 (m-70) cc_final: 0.6436 (m-70) REVERT: B 216 ARG cc_start: 0.7699 (ptp90) cc_final: 0.7497 (ptp90) REVERT: B 380 LEU cc_start: 0.6354 (OUTLIER) cc_final: 0.6051 (tt) REVERT: B 492 MET cc_start: 0.7236 (ptm) cc_final: 0.6804 (ptm) REVERT: B 499 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7985 (tptt) REVERT: B 660 ASP cc_start: 0.7375 (m-30) cc_final: 0.6994 (m-30) REVERT: B 671 GLN cc_start: 0.7874 (tt0) cc_final: 0.7327 (tt0) REVERT: B 766 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7270 (tt) REVERT: B 827 TRP cc_start: 0.7261 (t60) cc_final: 0.6972 (t60) outliers start: 30 outliers final: 23 residues processed: 138 average time/residue: 0.0659 time to fit residues: 12.5420 Evaluate side-chains 145 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 854 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 43 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 4 optimal weight: 0.0270 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 overall best weight: 2.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.234105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.211968 restraints weight = 9184.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.216458 restraints weight = 5565.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.219451 restraints weight = 3748.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.221761 restraints weight = 2754.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.223248 restraints weight = 2126.415| |-----------------------------------------------------------------------------| r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6466 Z= 0.138 Angle : 0.716 8.350 8830 Z= 0.344 Chirality : 0.043 0.227 1088 Planarity : 0.005 0.046 1123 Dihedral : 4.338 24.660 906 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.12 % Allowed : 25.91 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.18 (0.30), residues: 850 helix: 1.22 (0.22), residues: 572 sheet: -0.37 (0.87), residues: 38 loop : -2.57 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 98 TYR 0.009 0.001 TYR B 353 PHE 0.022 0.001 PHE B 720 TRP 0.011 0.001 TRP B 827 HIS 0.008 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6466) covalent geometry : angle 0.71593 ( 8830) hydrogen bonds : bond 0.03532 ( 436) hydrogen bonds : angle 3.93343 ( 1272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: B 37 HIS cc_start: 0.5747 (OUTLIER) cc_final: 0.5218 (t-90) REVERT: B 38 HIS cc_start: 0.7030 (m-70) cc_final: 0.6550 (m-70) REVERT: B 216 ARG cc_start: 0.7658 (ptp90) cc_final: 0.7458 (ptp90) REVERT: B 380 LEU cc_start: 0.6334 (OUTLIER) cc_final: 0.6035 (tt) REVERT: B 492 MET cc_start: 0.7137 (ptm) cc_final: 0.6816 (ptm) REVERT: B 499 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7940 (tptt) REVERT: B 660 ASP cc_start: 0.7356 (m-30) cc_final: 0.6997 (m-30) REVERT: B 746 LEU cc_start: 0.7139 (tt) cc_final: 0.6896 (pp) REVERT: B 766 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7281 (tt) REVERT: B 794 MET cc_start: 0.4604 (mtp) cc_final: 0.4167 (mtm) REVERT: B 827 TRP cc_start: 0.7195 (t60) cc_final: 0.6948 (t60) outliers start: 27 outliers final: 22 residues processed: 134 average time/residue: 0.0687 time to fit residues: 12.6026 Evaluate side-chains 144 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 854 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 3 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 36 optimal weight: 0.0770 chunk 61 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 overall best weight: 2.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.235040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.214748 restraints weight = 8684.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.218922 restraints weight = 5163.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.221717 restraints weight = 3388.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.223875 restraints weight = 2427.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.225293 restraints weight = 1845.010| |-----------------------------------------------------------------------------| r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6253 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6466 Z= 0.138 Angle : 0.726 9.243 8830 Z= 0.348 Chirality : 0.042 0.183 1088 Planarity : 0.005 0.046 1123 Dihedral : 4.323 24.262 906 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.96 % Allowed : 26.68 % Favored : 69.36 % 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: 0.26 (0.30), residues: 850 helix: 1.27 (0.22), residues: 573 sheet: -0.38 (0.88), residues: 38 loop : -2.51 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 98 TYR 0.009 0.001 TYR B 353 PHE 0.023 0.001 PHE B 720 TRP 0.010 0.001 TRP B 827 HIS 0.005 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6466) covalent geometry : angle 0.72621 ( 8830) hydrogen bonds : bond 0.03490 ( 436) hydrogen bonds : angle 3.92304 ( 1272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: B 37 HIS cc_start: 0.5635 (OUTLIER) cc_final: 0.5056 (t-90) REVERT: B 38 HIS cc_start: 0.7059 (m-70) cc_final: 0.6541 (m-70) REVERT: B 50 GLU cc_start: 0.8274 (tp30) cc_final: 0.8074 (tp30) REVERT: B 380 LEU cc_start: 0.6312 (OUTLIER) cc_final: 0.6013 (tt) REVERT: B 492 MET cc_start: 0.7144 (ptm) cc_final: 0.6829 (ptm) REVERT: B 499 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7937 (tptt) REVERT: B 660 ASP cc_start: 0.7480 (m-30) cc_final: 0.7048 (m-30) REVERT: B 746 LEU cc_start: 0.7142 (tt) cc_final: 0.6891 (pp) REVERT: B 766 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7273 (tt) REVERT: B 794 MET cc_start: 0.4602 (mtp) cc_final: 0.4156 (mtm) REVERT: B 827 TRP cc_start: 0.7209 (t60) cc_final: 0.6964 (t60) outliers start: 26 outliers final: 22 residues processed: 137 average time/residue: 0.0635 time to fit residues: 12.0811 Evaluate side-chains 144 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 854 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 69 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 263 GLN ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.231941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.210865 restraints weight = 9150.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.215042 restraints weight = 5599.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.218008 restraints weight = 3787.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.220100 restraints weight = 2768.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.221600 restraints weight = 2151.599| |-----------------------------------------------------------------------------| r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6466 Z= 0.146 Angle : 0.729 9.556 8830 Z= 0.350 Chirality : 0.043 0.168 1088 Planarity : 0.005 0.043 1123 Dihedral : 4.357 25.167 906 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.27 % Allowed : 26.68 % Favored : 69.05 % 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: 0.29 (0.30), residues: 850 helix: 1.23 (0.22), residues: 580 sheet: -0.47 (0.87), residues: 38 loop : -2.39 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 621 TYR 0.010 0.002 TYR B 353 PHE 0.023 0.001 PHE B 720 TRP 0.009 0.001 TRP B 827 HIS 0.004 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6466) covalent geometry : angle 0.72940 ( 8830) hydrogen bonds : bond 0.03545 ( 436) hydrogen bonds : angle 3.94816 ( 1272) =============================================================================== Job complete usr+sys time: 1113.56 seconds wall clock time: 19 minutes 52.61 seconds (1192.61 seconds total)