Starting phenix.real_space_refine on Tue Aug 4 18:22:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eo1_19844/08_2026/9eo1_19844.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eo1_19844/08_2026/9eo1_19844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9eo1_19844/08_2026/9eo1_19844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eo1_19844/08_2026/9eo1_19844.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eo1_19844/08_2026/9eo1_19844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eo1_19844/08_2026/9eo1_19844.map" } resolution = 3.2 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= 0.001 sd= 0.021 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 P 63 5.49 5 S 22 5.16 5 C 3587 2.51 5 N 1072 2.21 5 O 1213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5957 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4665 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 20, 'TRANS': 555} Chain breaks: 3 Chain: "B" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 647 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "C" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 290 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "D" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 355 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Time building chain proxies: 1.05, per 1000 atoms: 0.18 Number of scatterers: 5957 At special positions: 0 Unit cell: (74.0502, 99.6478, 97.8194, 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 22 16.00 P 63 15.00 O 1213 8.00 N 1072 7.00 C 3587 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: 0.46 Conformation dependent library (CDL) restraints added in 194.7 milliseconds 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1096 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 2 sheets defined 67.0% alpha, 5.2% beta 17 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 373 through 389 removed outlier: 3.602A pdb=" N ASN A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 396 removed outlier: 3.729A pdb=" N LEU A 395 " --> pdb=" O ASP A 391 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 409 Processing helix chain 'A' and resid 411 through 424 Processing helix chain 'A' and resid 443 through 453 removed outlier: 3.544A pdb=" N GLU A 448 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 462 Processing helix chain 'A' and resid 464 through 472 Processing helix chain 'A' and resid 473 through 484 Processing helix chain 'A' and resid 492 through 506 Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 538 through 555 removed outlier: 3.999A pdb=" N THR A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 622 Processing helix chain 'A' and resid 624 through 640 Processing helix chain 'A' and resid 645 through 652 removed outlier: 3.655A pdb=" N CYS A 649 " --> pdb=" O PRO A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 661 through 680 Processing helix chain 'A' and resid 682 through 694 Processing helix chain 'A' and resid 703 through 718 Processing helix chain 'A' and resid 722 through 735 Processing helix chain 'A' and resid 740 through 755 Processing helix chain 'A' and resid 814 through 825 Processing helix chain 'A' and resid 835 through 851 removed outlier: 5.497A pdb=" N ASP A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 879 removed outlier: 3.729A pdb=" N THR A 877 " --> pdb=" O ASP A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 892 Processing helix chain 'A' and resid 894 through 910 Processing helix chain 'A' and resid 924 through 936 Processing helix chain 'A' and resid 936 through 950 Processing helix chain 'A' and resid 950 through 956 removed outlier: 4.329A pdb=" N GLY A 956 " --> pdb=" O ARG A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 997 Processing sheet with id=AA1, first strand: chain 'A' and resid 429 through 430 removed outlier: 3.776A pdb=" N ILE A 429 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 535 " --> pdb=" O ILE A 429 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 778 through 783 removed outlier: 3.977A pdb=" N LYS A 778 " --> pdb=" O VAL A1001 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE A 971 " --> pdb=" O GLU A1000 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N GLU A1002 " --> pdb=" O PHE A 971 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU A 973 " --> pdb=" O GLU A1002 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N CYS A1004 " --> pdb=" O LEU A 973 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU A 975 " --> pdb=" O CYS A1004 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL A1006 " --> pdb=" O GLU A 975 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS A 970 " --> pdb=" O ASN A 965 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 1.16 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 880 1.32 - 1.44: 1979 1.44 - 1.57: 3198 1.57 - 1.69: 123 1.69 - 1.81: 31 Bond restraints: 6211 Sorted by residual: bond pdb=" C3' DG D 8 " pdb=" C2' DG D 8 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DG B 4 " pdb=" C2' DG B 4 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DC D 16 " pdb=" C2' DC D 16 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.86e+00 bond pdb=" N VAL A 487 " pdb=" CA VAL A 487 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.11e-02 8.12e+03 9.75e+00 bond pdb=" C3' DT C 16 " pdb=" C2' DT C 16 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.45e+00 ... (remaining 6206 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 7809 1.47 - 2.95: 725 2.95 - 4.42: 100 4.42 - 5.90: 22 5.90 - 7.37: 11 Bond angle restraints: 8667 Sorted by residual: angle pdb=" N LEU A 486 " pdb=" CA LEU A 486 " pdb=" C LEU A 486 " ideal model delta sigma weight residual 113.16 106.57 6.59 1.24e+00 6.50e-01 2.82e+01 angle pdb=" N ILE A 595 " pdb=" CA ILE A 595 " pdb=" C ILE A 595 " ideal model delta sigma weight residual 110.62 105.37 5.25 1.02e+00 9.61e-01 2.64e+01 angle pdb=" C TYR A 436 " pdb=" CA TYR A 436 " pdb=" CB TYR A 436 " ideal model delta sigma weight residual 110.74 103.37 7.37 1.61e+00 3.86e-01 2.10e+01 angle pdb=" CA GLY A 936 " pdb=" C GLY A 936 " pdb=" O GLY A 936 " ideal model delta sigma weight residual 122.29 118.69 3.60 8.10e-01 1.52e+00 1.97e+01 angle pdb=" N PRO A 894 " pdb=" CA PRO A 894 " pdb=" C PRO A 894 " ideal model delta sigma weight residual 111.41 104.91 6.50 1.50e+00 4.44e-01 1.87e+01 ... (remaining 8662 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.59: 3023 26.59 - 53.19: 407 53.19 - 79.78: 89 79.78 - 106.37: 11 106.37 - 132.96: 2 Dihedral angle restraints: 3532 sinusoidal: 1851 harmonic: 1681 Sorted by residual: dihedral pdb=" C TYR A 436 " pdb=" N TYR A 436 " pdb=" CA TYR A 436 " pdb=" CB TYR A 436 " ideal model delta harmonic sigma weight residual -122.60 -111.85 -10.75 0 2.50e+00 1.60e-01 1.85e+01 dihedral pdb=" C4' DC B 1 " pdb=" C3' DC B 1 " pdb=" O3' DC B 1 " pdb=" P DC B 2 " ideal model delta sinusoidal sigma weight residual 220.00 87.04 132.96 1 3.50e+01 8.16e-04 1.32e+01 dihedral pdb=" CA GLU A 464 " pdb=" C GLU A 464 " pdb=" N LEU A 465 " pdb=" CA LEU A 465 " ideal model delta harmonic sigma weight residual -180.00 -162.19 -17.81 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 3529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 769 0.064 - 0.127: 172 0.127 - 0.191: 23 0.191 - 0.255: 6 0.255 - 0.319: 1 Chirality restraints: 971 Sorted by residual: chirality pdb=" CA TYR A 436 " pdb=" N TYR A 436 " pdb=" C TYR A 436 " pdb=" CB TYR A 436 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CA MET A 772 " pdb=" N MET A 772 " pdb=" C MET A 772 " pdb=" CB MET A 772 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ILE A 439 " pdb=" N ILE A 439 " pdb=" C ILE A 439 " pdb=" CB ILE A 439 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 968 not shown) Planarity restraints: 883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 500 " -0.016 2.00e-02 2.50e+03 1.88e-02 6.18e+00 pdb=" CG PHE A 500 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE A 500 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 500 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 500 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 500 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 500 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 905 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C THR A 905 " 0.035 2.00e-02 2.50e+03 pdb=" O THR A 905 " -0.013 2.00e-02 2.50e+03 pdb=" N TRP A 906 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 892 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.63e+00 pdb=" C ASP A 892 " -0.033 2.00e-02 2.50e+03 pdb=" O ASP A 892 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA A 893 " 0.011 2.00e-02 2.50e+03 ... (remaining 880 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1083 2.76 - 3.30: 6092 3.30 - 3.83: 11240 3.83 - 4.37: 13300 4.37 - 4.90: 19694 Nonbonded interactions: 51409 Sorted by model distance: nonbonded pdb=" N GLU A 464 " pdb=" OE1 GLU A 464 " model vdw 2.230 3.120 nonbonded pdb=" O6 DG B 23 " pdb=" N1 DA C 10 " model vdw 2.278 2.496 nonbonded pdb=" OG SER A 966 " pdb=" OE1 GLN A 967 " model vdw 2.330 3.040 nonbonded pdb=" N GLN A 533 " pdb=" OE1 GLN A 533 " model vdw 2.351 3.120 nonbonded pdb=" N GLU A 583 " pdb=" OE1 GLU A 583 " model vdw 2.352 3.120 ... (remaining 51404 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.590 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: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 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 : 0.006 0.037 6211 Z= 0.479 Angle : 0.915 7.374 8667 Z= 0.689 Chirality : 0.055 0.319 971 Planarity : 0.004 0.038 883 Dihedral : 22.932 132.964 2436 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.16 % Allowed : 18.15 % Favored : 78.70 % 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: 1.46 (0.35), residues: 568 helix: 1.56 (0.27), residues: 372 sheet: 1.12 (0.95), residues: 29 loop : -0.29 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 824 TYR 0.024 0.002 TYR A 587 PHE 0.044 0.003 PHE A 500 TRP 0.022 0.002 TRP A 906 HIS 0.005 0.001 HIS A 644 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.48 ( 6211) covalent geometry : angle 0.91539 / 0.69 ( 8667) hydrogen bonds : bond 0.15535 / 9.85 ( 321) hydrogen bonds : angle 5.70329 / 3.99 ( 894) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 GLU cc_start: 0.7259 (mt-10) cc_final: 0.7027 (mt-10) REVERT: A 399 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7166 (pm20) REVERT: A 438 GLU cc_start: 0.7654 (tp30) cc_final: 0.7325 (tp30) REVERT: A 482 LYS cc_start: 0.8244 (mttt) cc_final: 0.7887 (mptt) REVERT: A 485 HIS cc_start: 0.7103 (p-80) cc_final: 0.6896 (p-80) REVERT: A 587 TYR cc_start: 0.7998 (p90) cc_final: 0.7795 (p90) REVERT: A 593 THR cc_start: 0.8028 (t) cc_final: 0.7823 (p) REVERT: A 604 ARG cc_start: 0.7263 (mtm180) cc_final: 0.7007 (mtp180) REVERT: A 625 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7220 (mm-30) REVERT: A 626 GLU cc_start: 0.7569 (tt0) cc_final: 0.7118 (tt0) REVERT: A 652 ASP cc_start: 0.8056 (m-30) cc_final: 0.7831 (t0) REVERT: A 737 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7238 (mm-30) REVERT: A 752 ARG cc_start: 0.6666 (ttp80) cc_final: 0.6437 (ttp-170) REVERT: A 823 ARG cc_start: 0.8647 (ttm110) cc_final: 0.8371 (mtm-85) REVERT: A 824 ARG cc_start: 0.8526 (ttm110) cc_final: 0.8270 (mtm110) REVERT: A 896 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7107 (mm-30) REVERT: A 910 GLU cc_start: 0.7510 (tp30) cc_final: 0.7139 (tp30) REVERT: A 918 SER cc_start: 0.8341 (m) cc_final: 0.7462 (p) REVERT: A 922 PHE cc_start: 0.8482 (m-80) cc_final: 0.8077 (m-80) REVERT: A 950 ASP cc_start: 0.7560 (p0) cc_final: 0.7218 (p0) REVERT: A 963 VAL cc_start: 0.7826 (m) cc_final: 0.7433 (p) REVERT: A 972 LYS cc_start: 0.7140 (mttt) cc_final: 0.6828 (mtpt) REVERT: A 993 GLU cc_start: 0.7872 (tp30) cc_final: 0.7556 (tp30) outliers start: 16 outliers final: 10 residues processed: 135 average time/residue: 0.0752 time to fit residues: 12.9348 Evaluate side-chains 136 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 853 ASP Chi-restraints excluded: chain A residue 855 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 HIS ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.154394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.129508 restraints weight = 8881.775| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.23 r_work: 0.3611 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6211 Z= 0.195 Angle : 0.666 7.441 8667 Z= 0.381 Chirality : 0.045 0.250 971 Planarity : 0.004 0.030 883 Dihedral : 25.888 131.988 1310 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.94 % Allowed : 17.16 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.35), residues: 568 helix: 1.50 (0.27), residues: 366 sheet: 1.26 (0.91), residues: 29 loop : -0.24 (0.46), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 823 TYR 0.012 0.002 TYR A 842 PHE 0.030 0.002 PHE A 500 TRP 0.010 0.002 TRP A 906 HIS 0.006 0.001 HIS A 718 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.20 ( 6211) covalent geometry : angle 0.66640 / 0.38 ( 8667) hydrogen bonds : bond 0.05562 / 3.71 ( 321) hydrogen bonds : angle 4.59932 / 3.18 ( 894) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7169 (pm20) REVERT: A 438 GLU cc_start: 0.7730 (tp30) cc_final: 0.7377 (tp30) REVERT: A 482 LYS cc_start: 0.8069 (mttt) cc_final: 0.7690 (mptt) REVERT: A 485 HIS cc_start: 0.7123 (p-80) cc_final: 0.6865 (p-80) REVERT: A 589 ILE cc_start: 0.8768 (mp) cc_final: 0.8500 (mt) REVERT: A 604 ARG cc_start: 0.7436 (mtm180) cc_final: 0.7099 (mtm180) REVERT: A 625 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7040 (tp30) REVERT: A 626 GLU cc_start: 0.7526 (tt0) cc_final: 0.7166 (tt0) REVERT: A 652 ASP cc_start: 0.8059 (m-30) cc_final: 0.7744 (t0) REVERT: A 684 GLU cc_start: 0.7020 (tm-30) cc_final: 0.6779 (tm-30) REVERT: A 702 ASP cc_start: 0.7088 (p0) cc_final: 0.6817 (p0) REVERT: A 718 HIS cc_start: 0.7971 (m-70) cc_final: 0.7737 (m-70) REVERT: A 896 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7211 (mm-30) REVERT: A 910 GLU cc_start: 0.7443 (tp30) cc_final: 0.7163 (tp30) REVERT: A 918 SER cc_start: 0.8327 (m) cc_final: 0.7484 (p) REVERT: A 963 VAL cc_start: 0.7785 (m) cc_final: 0.7432 (p) REVERT: A 972 LYS cc_start: 0.7031 (mttt) cc_final: 0.6745 (mtpt) REVERT: A 977 LYS cc_start: 0.8186 (mmmt) cc_final: 0.7784 (mmmm) REVERT: A 993 GLU cc_start: 0.7865 (tp30) cc_final: 0.7582 (tp30) outliers start: 20 outliers final: 10 residues processed: 145 average time/residue: 0.0697 time to fit residues: 13.1833 Evaluate side-chains 144 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 1004 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 HIS ** A 716 HIS ** 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 = 0.4057 r_free = 0.4057 target = 0.153268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.128443 restraints weight = 8824.543| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.22 r_work: 0.3614 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6211 Z= 0.208 Angle : 0.644 7.516 8667 Z= 0.366 Chirality : 0.046 0.242 971 Planarity : 0.004 0.039 883 Dihedral : 25.894 132.021 1298 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.55 % Allowed : 18.15 % Favored : 78.30 % 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: 1.32 (0.34), residues: 568 helix: 1.45 (0.27), residues: 366 sheet: 0.93 (0.89), residues: 29 loop : -0.28 (0.46), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 860 TYR 0.015 0.002 TYR A 842 PHE 0.024 0.002 PHE A 500 TRP 0.010 0.002 TRP A 906 HIS 0.006 0.001 HIS A 644 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.21 ( 6211) covalent geometry : angle 0.64436 / 0.37 ( 8667) hydrogen bonds : bond 0.05124 / 3.46 ( 321) hydrogen bonds : angle 4.41950 / 3.05 ( 894) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7726 (tp30) cc_final: 0.7401 (tp30) REVERT: A 482 LYS cc_start: 0.8145 (mttt) cc_final: 0.7689 (mptt) REVERT: A 485 HIS cc_start: 0.7093 (p-80) cc_final: 0.6806 (p-80) REVERT: A 589 ILE cc_start: 0.8845 (mp) cc_final: 0.8596 (mt) REVERT: A 604 ARG cc_start: 0.7445 (mtm180) cc_final: 0.6913 (mtm180) REVERT: A 626 GLU cc_start: 0.7396 (tt0) cc_final: 0.7106 (tt0) REVERT: A 644 HIS cc_start: 0.7740 (t-90) cc_final: 0.7468 (t-90) REVERT: A 652 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7710 (t0) REVERT: A 682 MET cc_start: 0.7477 (mtp) cc_final: 0.7260 (mtp) REVERT: A 684 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6714 (tm-30) REVERT: A 702 ASP cc_start: 0.7057 (p0) cc_final: 0.6777 (p0) REVERT: A 718 HIS cc_start: 0.8004 (m-70) cc_final: 0.7721 (m-70) REVERT: A 752 ARG cc_start: 0.6852 (ttp80) cc_final: 0.6630 (ttp-170) REVERT: A 899 ARG cc_start: 0.7810 (ttm170) cc_final: 0.7572 (ttm170) REVERT: A 910 GLU cc_start: 0.7594 (tp30) cc_final: 0.7363 (tp30) REVERT: A 918 SER cc_start: 0.8355 (m) cc_final: 0.7490 (p) REVERT: A 963 VAL cc_start: 0.7827 (m) cc_final: 0.7486 (p) REVERT: A 972 LYS cc_start: 0.7048 (mttt) cc_final: 0.6784 (mtpt) REVERT: A 977 LYS cc_start: 0.8180 (mmmt) cc_final: 0.7741 (mmmm) REVERT: A 993 GLU cc_start: 0.7867 (tp30) cc_final: 0.7593 (tp30) outliers start: 18 outliers final: 12 residues processed: 137 average time/residue: 0.0775 time to fit residues: 13.5354 Evaluate side-chains 137 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 909 GLN Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 1004 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 0.1980 chunk 49 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 970 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.154235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.129386 restraints weight = 8876.218| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.24 r_work: 0.3626 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6211 Z= 0.172 Angle : 0.619 7.694 8667 Z= 0.349 Chirality : 0.044 0.221 971 Planarity : 0.004 0.039 883 Dihedral : 25.948 131.714 1295 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.14 % Allowed : 19.13 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.35), residues: 568 helix: 1.53 (0.27), residues: 367 sheet: 0.79 (0.92), residues: 29 loop : -0.24 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 860 TYR 0.013 0.002 TYR A 842 PHE 0.016 0.002 PHE A 500 TRP 0.010 0.001 TRP A 847 HIS 0.004 0.001 HIS A 644 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 ( 6211) covalent geometry : angle 0.61880 / 0.35 ( 8667) hydrogen bonds : bond 0.04699 / 3.18 ( 321) hydrogen bonds : angle 4.36881 / 3.00 ( 894) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7701 (tp30) cc_final: 0.7350 (tp30) REVERT: A 482 LYS cc_start: 0.7996 (mttt) cc_final: 0.7777 (mptt) REVERT: A 589 ILE cc_start: 0.8839 (mp) cc_final: 0.8608 (mt) REVERT: A 604 ARG cc_start: 0.7477 (mtm180) cc_final: 0.6930 (mtm180) REVERT: A 625 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7074 (tp30) REVERT: A 626 GLU cc_start: 0.7393 (tt0) cc_final: 0.7089 (tt0) REVERT: A 644 HIS cc_start: 0.7717 (t-90) cc_final: 0.7446 (t-90) REVERT: A 652 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7682 (t0) REVERT: A 684 GLU cc_start: 0.7083 (tm-30) cc_final: 0.6713 (tm-30) REVERT: A 702 ASP cc_start: 0.6999 (p0) cc_final: 0.6698 (p0) REVERT: A 752 ARG cc_start: 0.6898 (ttp80) cc_final: 0.6643 (ttp-170) REVERT: A 889 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8281 (tt) REVERT: A 918 SER cc_start: 0.8352 (m) cc_final: 0.7504 (p) REVERT: A 922 PHE cc_start: 0.8342 (m-80) cc_final: 0.8052 (m-80) REVERT: A 963 VAL cc_start: 0.7848 (m) cc_final: 0.7514 (p) REVERT: A 972 LYS cc_start: 0.7052 (mttt) cc_final: 0.6803 (mtpt) REVERT: A 993 GLU cc_start: 0.7863 (tp30) cc_final: 0.7595 (tp30) outliers start: 21 outliers final: 15 residues processed: 133 average time/residue: 0.0673 time to fit residues: 11.7144 Evaluate side-chains 135 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 909 GLN Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 939 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 0.0980 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.154633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.129781 restraints weight = 9044.053| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.26 r_work: 0.3615 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6211 Z= 0.162 Angle : 0.606 7.340 8667 Z= 0.341 Chirality : 0.043 0.204 971 Planarity : 0.004 0.038 883 Dihedral : 25.898 131.324 1295 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.73 % Allowed : 18.93 % Favored : 76.33 % 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: 1.47 (0.35), residues: 568 helix: 1.61 (0.27), residues: 368 sheet: 0.72 (0.96), residues: 29 loop : -0.29 (0.48), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 823 TYR 0.012 0.002 TYR A 842 PHE 0.014 0.002 PHE A 500 TRP 0.010 0.001 TRP A 847 HIS 0.004 0.001 HIS A 644 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 ( 6211) covalent geometry : angle 0.60562 / 0.34 ( 8667) hydrogen bonds : bond 0.04486 / 3.04 ( 321) hydrogen bonds : angle 4.30313 / 2.93 ( 894) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7724 (tp30) cc_final: 0.7349 (tp30) REVERT: A 482 LYS cc_start: 0.7975 (mttt) cc_final: 0.7741 (mptt) REVERT: A 589 ILE cc_start: 0.8827 (mp) cc_final: 0.8602 (mt) REVERT: A 604 ARG cc_start: 0.7471 (mtm180) cc_final: 0.7184 (mtm180) REVERT: A 625 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6989 (tp30) REVERT: A 626 GLU cc_start: 0.7411 (tt0) cc_final: 0.7075 (tt0) REVERT: A 652 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7643 (t0) REVERT: A 684 GLU cc_start: 0.7103 (tm-30) cc_final: 0.6714 (tm-30) REVERT: A 702 ASP cc_start: 0.6985 (p0) cc_final: 0.6658 (p0) REVERT: A 752 ARG cc_start: 0.6918 (ttp80) cc_final: 0.6683 (ttp-170) REVERT: A 823 ARG cc_start: 0.8678 (ttm110) cc_final: 0.8349 (mtm-85) REVERT: A 918 SER cc_start: 0.8363 (m) cc_final: 0.7506 (p) REVERT: A 922 PHE cc_start: 0.8368 (m-80) cc_final: 0.8108 (m-80) REVERT: A 963 VAL cc_start: 0.7818 (m) cc_final: 0.7495 (p) REVERT: A 972 LYS cc_start: 0.7012 (mttt) cc_final: 0.6790 (mtmt) REVERT: A 977 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7613 (mmmm) REVERT: A 993 GLU cc_start: 0.7865 (tp30) cc_final: 0.7588 (tp30) outliers start: 24 outliers final: 19 residues processed: 131 average time/residue: 0.0690 time to fit residues: 11.9391 Evaluate side-chains 137 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 909 GLN Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1004 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 30 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.0770 chunk 55 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 717 GLN ** A 864 GLN ** 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 = 0.4067 r_free = 0.4067 target = 0.154300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.129487 restraints weight = 8924.082| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.22 r_work: 0.3594 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6211 Z= 0.185 Angle : 0.610 6.647 8667 Z= 0.342 Chirality : 0.043 0.206 971 Planarity : 0.004 0.038 883 Dihedral : 25.829 130.797 1294 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 5.13 % Allowed : 18.74 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.35), residues: 568 helix: 1.58 (0.26), residues: 369 sheet: 0.55 (0.94), residues: 29 loop : -0.29 (0.48), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 823 TYR 0.013 0.002 TYR A 842 PHE 0.014 0.002 PHE A 875 TRP 0.010 0.002 TRP A 906 HIS 0.003 0.001 HIS A1005 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 ( 6211) covalent geometry : angle 0.61040 / 0.34 ( 8667) hydrogen bonds : bond 0.04562 / 3.06 ( 321) hydrogen bonds : angle 4.31962 / 2.94 ( 894) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7764 (tp30) cc_final: 0.7373 (tp30) REVERT: A 482 LYS cc_start: 0.8018 (mttt) cc_final: 0.7751 (mptt) REVERT: A 604 ARG cc_start: 0.7445 (mtm180) cc_final: 0.7188 (mtm180) REVERT: A 625 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6990 (tp30) REVERT: A 626 GLU cc_start: 0.7441 (tt0) cc_final: 0.7069 (tt0) REVERT: A 652 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7631 (t0) REVERT: A 684 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6843 (tm-30) REVERT: A 702 ASP cc_start: 0.7026 (p0) cc_final: 0.6692 (p0) REVERT: A 737 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7515 (mm-30) REVERT: A 889 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8304 (tt) REVERT: A 896 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7449 (mm-30) REVERT: A 918 SER cc_start: 0.8354 (m) cc_final: 0.7625 (t) REVERT: A 922 PHE cc_start: 0.8391 (m-80) cc_final: 0.8131 (m-80) REVERT: A 963 VAL cc_start: 0.7837 (m) cc_final: 0.7509 (p) REVERT: A 972 LYS cc_start: 0.7029 (mttt) cc_final: 0.6817 (mtmt) REVERT: A 977 LYS cc_start: 0.8146 (mmmt) cc_final: 0.7504 (mmmm) REVERT: A 993 GLU cc_start: 0.7867 (tp30) cc_final: 0.7607 (tp30) outliers start: 26 outliers final: 19 residues processed: 133 average time/residue: 0.0610 time to fit residues: 10.8640 Evaluate side-chains 136 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 853 ASP Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 1004 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 26 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 54 optimal weight: 0.1980 chunk 47 optimal weight: 0.0980 chunk 20 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 27 optimal weight: 0.5980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.155955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.131306 restraints weight = 9020.037| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.25 r_work: 0.3622 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6211 Z= 0.143 Angle : 0.607 7.310 8667 Z= 0.337 Chirality : 0.042 0.202 971 Planarity : 0.004 0.039 883 Dihedral : 25.704 130.689 1294 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.35 % Allowed : 20.51 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.35), residues: 568 helix: 1.68 (0.27), residues: 369 sheet: 0.49 (0.93), residues: 29 loop : -0.29 (0.48), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 823 TYR 0.011 0.002 TYR A 587 PHE 0.014 0.001 PHE A 584 TRP 0.012 0.001 TRP A 847 HIS 0.003 0.001 HIS A 644 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 ( 6211) covalent geometry : angle 0.60749 / 0.34 ( 8667) hydrogen bonds : bond 0.04258 / 2.88 ( 321) hydrogen bonds : angle 4.21923 / 2.88 ( 894) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7794 (tp30) cc_final: 0.7379 (tp30) REVERT: A 482 LYS cc_start: 0.7984 (mttt) cc_final: 0.7706 (mptt) REVERT: A 604 ARG cc_start: 0.7408 (mtm180) cc_final: 0.7156 (mtm180) REVERT: A 625 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6940 (tp30) REVERT: A 626 GLU cc_start: 0.7433 (tt0) cc_final: 0.7057 (tt0) REVERT: A 684 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6845 (tm-30) REVERT: A 702 ASP cc_start: 0.6957 (p0) cc_final: 0.6595 (p0) REVERT: A 737 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7534 (mm-30) REVERT: A 823 ARG cc_start: 0.8623 (ttm110) cc_final: 0.8254 (mtm-85) REVERT: A 896 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7446 (mm-30) REVERT: A 918 SER cc_start: 0.8331 (m) cc_final: 0.7614 (t) REVERT: A 922 PHE cc_start: 0.8355 (m-80) cc_final: 0.8117 (m-80) REVERT: A 963 VAL cc_start: 0.7833 (m) cc_final: 0.7504 (p) REVERT: A 972 LYS cc_start: 0.6991 (mttt) cc_final: 0.6755 (mtmt) REVERT: A 977 LYS cc_start: 0.8155 (mmmt) cc_final: 0.7495 (mmmm) REVERT: A 993 GLU cc_start: 0.7839 (tp30) cc_final: 0.7576 (tp30) outliers start: 17 outliers final: 13 residues processed: 128 average time/residue: 0.0643 time to fit residues: 10.7440 Evaluate side-chains 130 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 853 ASP Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 1004 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 4 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 chunk 19 optimal weight: 0.3980 chunk 55 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.155829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.130156 restraints weight = 8893.553| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.12 r_work: 0.3612 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6211 Z= 0.176 Angle : 0.640 11.734 8667 Z= 0.348 Chirality : 0.044 0.208 971 Planarity : 0.004 0.037 883 Dihedral : 25.616 130.279 1290 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.55 % Allowed : 20.51 % Favored : 75.94 % 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: 1.44 (0.35), residues: 568 helix: 1.57 (0.27), residues: 371 sheet: 0.54 (0.95), residues: 29 loop : -0.25 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 823 TYR 0.013 0.002 TYR A 842 PHE 0.013 0.001 PHE A 875 TRP 0.014 0.002 TRP A 847 HIS 0.003 0.001 HIS A1005 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.18 ( 6211) covalent geometry : angle 0.63956 / 0.35 ( 8667) hydrogen bonds : bond 0.04478 / 3.00 ( 321) hydrogen bonds : angle 4.29168 / 2.96 ( 894) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7693 (tp30) cc_final: 0.7288 (tp30) REVERT: A 482 LYS cc_start: 0.7993 (mttt) cc_final: 0.7721 (mptt) REVERT: A 604 ARG cc_start: 0.7458 (mtm180) cc_final: 0.6997 (mtm180) REVERT: A 626 GLU cc_start: 0.7397 (tt0) cc_final: 0.7042 (tt0) REVERT: A 644 HIS cc_start: 0.7718 (t-90) cc_final: 0.7401 (t-90) REVERT: A 684 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6900 (tm-30) REVERT: A 702 ASP cc_start: 0.6902 (p0) cc_final: 0.6550 (p0) REVERT: A 737 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7557 (mm-30) REVERT: A 823 ARG cc_start: 0.8652 (ttm110) cc_final: 0.8332 (mtm-85) REVERT: A 889 LEU cc_start: 0.8648 (tp) cc_final: 0.8286 (tt) REVERT: A 896 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7503 (mm-30) REVERT: A 918 SER cc_start: 0.8313 (m) cc_final: 0.7588 (t) REVERT: A 922 PHE cc_start: 0.8317 (m-80) cc_final: 0.8090 (m-80) REVERT: A 963 VAL cc_start: 0.7857 (m) cc_final: 0.7529 (p) REVERT: A 972 LYS cc_start: 0.7067 (mttt) cc_final: 0.6840 (mtmt) REVERT: A 977 LYS cc_start: 0.8160 (mmmt) cc_final: 0.7510 (mmmm) REVERT: A 993 GLU cc_start: 0.7865 (tp30) cc_final: 0.7597 (tp30) outliers start: 18 outliers final: 15 residues processed: 127 average time/residue: 0.0730 time to fit residues: 12.0565 Evaluate side-chains 132 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 815 GLU Chi-restraints excluded: chain A residue 853 ASP Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 1004 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 42 optimal weight: 0.2980 chunk 35 optimal weight: 0.0050 chunk 58 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 463 GLN ** A 864 GLN ** 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 = 0.4086 r_free = 0.4086 target = 0.156126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.130375 restraints weight = 8919.799| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.20 r_work: 0.3608 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6211 Z= 0.175 Angle : 0.635 11.725 8667 Z= 0.348 Chirality : 0.043 0.207 971 Planarity : 0.004 0.036 883 Dihedral : 25.530 129.962 1290 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.75 % Allowed : 20.91 % Favored : 75.35 % 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: 1.49 (0.36), residues: 568 helix: 1.63 (0.27), residues: 371 sheet: 0.52 (0.97), residues: 29 loop : -0.28 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 823 TYR 0.012 0.002 TYR A 842 PHE 0.012 0.001 PHE A 875 TRP 0.012 0.002 TRP A 847 HIS 0.003 0.001 HIS A1005 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 ( 6211) covalent geometry : angle 0.63457 / 0.35 ( 8667) hydrogen bonds : bond 0.04446 / 2.99 ( 321) hydrogen bonds : angle 4.24286 / 2.90 ( 894) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7713 (tp30) cc_final: 0.7306 (tp30) REVERT: A 482 LYS cc_start: 0.7996 (mttt) cc_final: 0.7704 (mptt) REVERT: A 604 ARG cc_start: 0.7441 (mtm180) cc_final: 0.6989 (mtm180) REVERT: A 626 GLU cc_start: 0.7449 (tt0) cc_final: 0.7055 (tt0) REVERT: A 644 HIS cc_start: 0.7770 (t-90) cc_final: 0.7417 (t-90) REVERT: A 684 GLU cc_start: 0.7122 (tm-30) cc_final: 0.6882 (tm-30) REVERT: A 702 ASP cc_start: 0.6908 (p0) cc_final: 0.6553 (p0) REVERT: A 737 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7560 (mm-30) REVERT: A 823 ARG cc_start: 0.8655 (ttm110) cc_final: 0.8319 (mtm-85) REVERT: A 918 SER cc_start: 0.8318 (m) cc_final: 0.7583 (t) REVERT: A 922 PHE cc_start: 0.8326 (m-80) cc_final: 0.8091 (m-80) REVERT: A 963 VAL cc_start: 0.7863 (m) cc_final: 0.7524 (p) REVERT: A 977 LYS cc_start: 0.8144 (mmmt) cc_final: 0.7740 (mmmm) REVERT: A 993 GLU cc_start: 0.7867 (tp30) cc_final: 0.7606 (tp30) outliers start: 19 outliers final: 15 residues processed: 125 average time/residue: 0.0627 time to fit residues: 10.2615 Evaluate side-chains 130 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 815 GLU Chi-restraints excluded: chain A residue 853 ASP Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 1004 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.154785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.129249 restraints weight = 8831.093| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.11 r_work: 0.3600 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6211 Z= 0.208 Angle : 0.657 11.368 8667 Z= 0.358 Chirality : 0.044 0.213 971 Planarity : 0.004 0.037 883 Dihedral : 25.489 129.410 1290 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.16 % Allowed : 21.30 % Favored : 75.54 % 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: 1.38 (0.35), residues: 568 helix: 1.54 (0.27), residues: 368 sheet: 0.41 (1.00), residues: 29 loop : -0.28 (0.48), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 823 TYR 0.015 0.002 TYR A 842 PHE 0.016 0.002 PHE A 875 TRP 0.011 0.002 TRP A 847 HIS 0.004 0.001 HIS A1005 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.21 ( 6211) covalent geometry : angle 0.65675 / 0.36 ( 8667) hydrogen bonds : bond 0.04724 / 3.13 ( 321) hydrogen bonds : angle 4.34153 / 2.97 ( 894) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7685 (tp30) cc_final: 0.7280 (tp30) REVERT: A 460 SER cc_start: 0.8412 (p) cc_final: 0.8091 (t) REVERT: A 482 LYS cc_start: 0.7987 (mttt) cc_final: 0.7723 (mptt) REVERT: A 604 ARG cc_start: 0.7449 (mtm180) cc_final: 0.6980 (mtm180) REVERT: A 626 GLU cc_start: 0.7352 (tt0) cc_final: 0.6995 (tt0) REVERT: A 644 HIS cc_start: 0.7690 (t-90) cc_final: 0.7368 (t-90) REVERT: A 684 GLU cc_start: 0.7112 (tm-30) cc_final: 0.6880 (tm-30) REVERT: A 702 ASP cc_start: 0.6973 (p0) cc_final: 0.6649 (p0) REVERT: A 918 SER cc_start: 0.8389 (m) cc_final: 0.7696 (t) REVERT: A 922 PHE cc_start: 0.8341 (m-80) cc_final: 0.8123 (m-80) REVERT: A 932 VAL cc_start: 0.8169 (t) cc_final: 0.7921 (p) REVERT: A 963 VAL cc_start: 0.7912 (m) cc_final: 0.7609 (p) REVERT: A 977 LYS cc_start: 0.8200 (mmmt) cc_final: 0.7795 (mmmm) REVERT: A 993 GLU cc_start: 0.7874 (tp30) cc_final: 0.7601 (tp30) outliers start: 16 outliers final: 14 residues processed: 128 average time/residue: 0.0716 time to fit residues: 12.0415 Evaluate side-chains 136 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 815 GLU Chi-restraints excluded: chain A residue 853 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 923 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 6 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 42 optimal weight: 0.0370 chunk 14 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.155798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.130249 restraints weight = 8822.443| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.14 r_work: 0.3615 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6211 Z= 0.173 Angle : 0.644 11.802 8667 Z= 0.351 Chirality : 0.043 0.209 971 Planarity : 0.004 0.041 883 Dihedral : 25.480 129.370 1290 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.55 % Allowed : 21.89 % Favored : 74.56 % 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: 1.44 (0.35), residues: 568 helix: 1.60 (0.27), residues: 369 sheet: 0.47 (1.00), residues: 29 loop : -0.30 (0.48), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 823 TYR 0.013 0.002 TYR A 842 PHE 0.014 0.002 PHE A 827 TRP 0.011 0.002 TRP A 847 HIS 0.003 0.001 HIS A 718 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 ( 6211) covalent geometry : angle 0.64430 / 0.35 ( 8667) hydrogen bonds : bond 0.04538 / 3.04 ( 321) hydrogen bonds : angle 4.28725 / 2.94 ( 894) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1244.02 seconds wall clock time: 22 minutes 7.50 seconds (1327.50 seconds total)