Starting phenix.real_space_refine on Tue Feb 11 14:23:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eo1_19844/02_2025/9eo1_19844.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eo1_19844/02_2025/9eo1_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9eo1_19844/02_2025/9eo1_19844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eo1_19844/02_2025/9eo1_19844.map" model { file = "/net/cci-nas-00/data/ceres_data/9eo1_19844/02_2025/9eo1_19844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eo1_19844/02_2025/9eo1_19844.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.37, per 1000 atoms: 0.73 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: 1.45 Conformation dependent library (CDL) restraints added in 672.2 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: 2.31 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: 2.18 Time building geometry restraints manager: 1.70 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=" 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=" N THR A 444 " pdb=" CA THR A 444 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.04e-02 9.25e+03 8.83e+00 bond pdb=" C PRO A 445 " pdb=" O PRO A 445 " ideal model delta sigma weight residual 1.235 1.198 0.037 1.30e-02 5.92e+03 8.31e+00 bond pdb=" N GLY A 937 " pdb=" CA GLY A 937 " ideal model delta sigma weight residual 1.444 1.469 -0.025 8.80e-03 1.29e+04 8.25e+00 bond pdb=" N VAL A 932 " pdb=" CA VAL A 932 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.21e-02 6.83e+03 8.14e+00 ... (remaining 6206 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 7966 1.47 - 2.95: 573 2.95 - 4.42: 98 4.42 - 5.90: 19 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: 810 0.064 - 0.127: 136 0.127 - 0.191: 18 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: 1.310 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.390 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 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 0.038 6211 Z= 0.351 Angle : 0.859 7.374 8667 Z= 0.571 Chirality : 0.050 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.35), 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 TRP 0.022 0.002 TRP A 906 HIS 0.005 0.001 HIS A 644 PHE 0.044 0.003 PHE A 500 TYR 0.024 0.002 TYR A 587 ARG 0.011 0.001 ARG A 824 *********************** 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 : 0.473 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: 0.7796 (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: 0.2212 time to fit residues: 37.9824 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 : 0.534 ------------------------------------------------------------------------------- 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 52 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 36 optimal weight: 0.1980 chunk 56 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN ** A 716 HIS ** 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 = 0.4068 r_free = 0.4068 target = 0.154584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.129728 restraints weight = 8690.321| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.20 r_work: 0.3615 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6211 Z= 0.254 Angle : 0.605 7.292 8667 Z= 0.341 Chirality : 0.040 0.137 971 Planarity : 0.004 0.034 883 Dihedral : 25.905 132.324 1310 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 4.54 % Allowed : 16.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.34), residues: 568 helix: 1.50 (0.27), residues: 366 sheet: 0.98 (0.90), residues: 29 loop : -0.27 (0.46), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 906 HIS 0.005 0.001 HIS A 644 PHE 0.031 0.002 PHE A 500 TYR 0.013 0.002 TYR A 842 ARG 0.004 0.001 ARG A 823 *********************** 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 157 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.526 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: 0.7892 (OUTLIER) cc_final: 0.7134 (pm20) REVERT: A 438 GLU cc_start: 0.7768 (tp30) cc_final: 0.7466 (tp30) REVERT: A 470 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7964 (mm-30) REVERT: A 482 LYS cc_start: 0.8094 (mttt) cc_final: 0.7672 (mptt) REVERT: A 485 HIS cc_start: 0.7112 (p-80) cc_final: 0.6840 (p-80) REVERT: A 589 ILE cc_start: 0.8800 (mp) cc_final: 0.8529 (mt) REVERT: A 593 THR cc_start: 0.8143 (t) cc_final: 0.7909 (p) REVERT: A 604 ARG cc_start: 0.7430 (mtm180) cc_final: 0.7134 (mtm180) REVERT: A 625 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7028 (tp30) REVERT: A 626 GLU cc_start: 0.7451 (tt0) cc_final: 0.7090 (tt0) REVERT: A 648 ARG cc_start: 0.7362 (ttt-90) cc_final: 0.7142 (ttt-90) REVERT: A 652 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7725 (t0) REVERT: A 684 GLU cc_start: 0.7045 (tm-30) cc_final: 0.6677 (tm-30) REVERT: A 702 ASP cc_start: 0.7003 (p0) cc_final: 0.6753 (p0) REVERT: A 718 HIS cc_start: 0.7963 (m-70) cc_final: 0.7759 (m-70) REVERT: A 753 LEU cc_start: 0.7318 (mt) cc_final: 0.7117 (mp) REVERT: A 823 ARG cc_start: 0.8692 (ttm110) cc_final: 0.8474 (mtm-85) REVERT: A 889 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8343 (tt) REVERT: A 896 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7233 (mm-30) REVERT: A 910 GLU cc_start: 0.7520 (tp30) cc_final: 0.7275 (tp30) REVERT: A 918 SER cc_start: 0.8303 (m) cc_final: 0.7432 (p) REVERT: A 963 VAL cc_start: 0.7775 (m) cc_final: 0.7419 (p) REVERT: A 972 LYS cc_start: 0.6980 (mttt) cc_final: 0.6703 (mtpt) REVERT: A 977 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7745 (mmmm) REVERT: A 993 GLU cc_start: 0.7861 (tp30) cc_final: 0.7581 (tp30) outliers start: 23 outliers final: 11 residues processed: 144 average time/residue: 0.1945 time to fit residues: 35.7793 Evaluate side-chains 146 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 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 831 ILE 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 1004 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 33 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.1980 chunk 25 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4070 r_free = 0.4070 target = 0.154413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.129892 restraints weight = 8752.669| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.22 r_work: 0.3616 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.1511 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= 0.240 Angle : 0.577 5.779 8667 Z= 0.324 Chirality : 0.040 0.167 971 Planarity : 0.004 0.038 883 Dihedral : 25.921 131.402 1295 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.54 % Allowed : 17.36 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.35), residues: 568 helix: 1.55 (0.27), residues: 368 sheet: 0.89 (0.93), residues: 29 loop : -0.26 (0.46), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 664 HIS 0.006 0.001 HIS A 644 PHE 0.020 0.002 PHE A 500 TYR 0.014 0.002 TYR A 842 ARG 0.004 0.000 ARG A 824 *********************** 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 149 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7747 (tp30) cc_final: 0.7383 (tp30) REVERT: A 482 LYS cc_start: 0.8015 (mttt) cc_final: 0.7787 (mptt) REVERT: A 589 ILE cc_start: 0.8814 (mp) cc_final: 0.8575 (mt) REVERT: A 604 ARG cc_start: 0.7454 (mtm180) cc_final: 0.6917 (mtm180) REVERT: A 625 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7005 (tp30) REVERT: A 626 GLU cc_start: 0.7415 (tt0) cc_final: 0.7096 (tt0) REVERT: A 644 HIS cc_start: 0.7716 (t-90) cc_final: 0.7434 (t-90) REVERT: A 684 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6744 (tm-30) REVERT: A 702 ASP cc_start: 0.6961 (p0) cc_final: 0.6687 (p0) REVERT: A 718 HIS cc_start: 0.8007 (m-70) cc_final: 0.7767 (m-70) REVERT: A 889 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8290 (tt) REVERT: A 909 GLN cc_start: 0.5900 (OUTLIER) cc_final: 0.5694 (pm20) REVERT: A 918 SER cc_start: 0.8343 (m) cc_final: 0.7484 (p) REVERT: A 922 PHE cc_start: 0.8384 (m-80) cc_final: 0.8085 (m-80) REVERT: A 932 VAL cc_start: 0.8067 (OUTLIER) cc_final: 0.7857 (t) REVERT: A 963 VAL cc_start: 0.7818 (m) cc_final: 0.7484 (p) REVERT: A 972 LYS cc_start: 0.7023 (mttt) cc_final: 0.6758 (mtpt) REVERT: A 993 GLU cc_start: 0.7866 (tp30) cc_final: 0.7589 (tp30) outliers start: 23 outliers final: 14 residues processed: 138 average time/residue: 0.1948 time to fit residues: 34.4873 Evaluate side-chains 140 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 546 SER Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 740 THR 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 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 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 716 HIS ** 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 = 0.4078 r_free = 0.4078 target = 0.155194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.129828 restraints weight = 8861.629| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.28 r_work: 0.3621 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6211 Z= 0.209 Angle : 0.554 6.496 8667 Z= 0.311 Chirality : 0.038 0.129 971 Planarity : 0.003 0.039 883 Dihedral : 25.835 130.911 1294 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 4.14 % Allowed : 18.93 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.35), residues: 568 helix: 1.63 (0.27), residues: 368 sheet: 0.61 (0.94), residues: 29 loop : -0.29 (0.47), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 906 HIS 0.003 0.001 HIS A 644 PHE 0.013 0.001 PHE A 500 TYR 0.011 0.002 TYR A 842 ARG 0.003 0.000 ARG A 823 *********************** 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 141 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7814 (tp30) cc_final: 0.7449 (tp30) REVERT: A 482 LYS cc_start: 0.7988 (mttt) cc_final: 0.7703 (mptt) REVERT: A 554 LEU cc_start: 0.7107 (mt) cc_final: 0.6877 (mp) REVERT: A 589 ILE cc_start: 0.8823 (mp) cc_final: 0.8599 (mt) REVERT: A 604 ARG cc_start: 0.7467 (mtm180) cc_final: 0.6992 (mtm180) REVERT: A 625 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6918 (tp30) REVERT: A 626 GLU cc_start: 0.7307 (tt0) cc_final: 0.7010 (tt0) REVERT: A 644 HIS cc_start: 0.7725 (t-90) cc_final: 0.7436 (t-90) REVERT: A 684 GLU cc_start: 0.7104 (tm-30) cc_final: 0.6717 (tm-30) REVERT: A 702 ASP cc_start: 0.6944 (p0) cc_final: 0.6645 (p0) REVERT: A 718 HIS cc_start: 0.7984 (m-70) cc_final: 0.7780 (m-70) REVERT: A 823 ARG cc_start: 0.8582 (ttm110) cc_final: 0.8183 (mtm-85) REVERT: A 896 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7443 (mm-30) REVERT: A 918 SER cc_start: 0.8334 (m) cc_final: 0.7469 (p) REVERT: A 922 PHE cc_start: 0.8405 (m-80) cc_final: 0.8135 (m-80) REVERT: A 963 VAL cc_start: 0.7840 (m) cc_final: 0.7498 (p) REVERT: A 972 LYS cc_start: 0.6974 (mttt) cc_final: 0.6684 (mtpt) REVERT: A 977 LYS cc_start: 0.8212 (mmmt) cc_final: 0.7632 (mmmm) REVERT: A 993 GLU cc_start: 0.7885 (tp30) cc_final: 0.7609 (tp30) outliers start: 21 outliers final: 13 residues processed: 132 average time/residue: 0.2023 time to fit residues: 34.4733 Evaluate side-chains 127 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 662 VAL Chi-restraints excluded: chain A residue 740 THR 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 939 VAL Chi-restraints excluded: chain A residue 1004 CYS 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 58 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 chunk 19 optimal weight: 0.0770 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4103 r_free = 0.4103 target = 0.157480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.131817 restraints weight = 8843.715| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.14 r_work: 0.3630 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6211 Z= 0.193 Angle : 0.552 6.146 8667 Z= 0.310 Chirality : 0.038 0.134 971 Planarity : 0.003 0.037 883 Dihedral : 25.757 130.611 1294 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.75 % Allowed : 20.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.36), residues: 568 helix: 1.70 (0.27), residues: 370 sheet: 0.47 (0.92), residues: 29 loop : -0.25 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 847 HIS 0.003 0.001 HIS A 644 PHE 0.011 0.001 PHE A 584 TYR 0.010 0.002 TYR A 842 ARG 0.003 0.000 ARG A 823 *********************** 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 143 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7794 (tp30) cc_final: 0.7428 (tp30) REVERT: A 470 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7853 (tp30) REVERT: A 482 LYS cc_start: 0.7953 (mttt) cc_final: 0.7645 (mptt) REVERT: A 589 ILE cc_start: 0.8820 (mp) cc_final: 0.8611 (mt) REVERT: A 604 ARG cc_start: 0.7450 (mtm180) cc_final: 0.7234 (mtm180) REVERT: A 626 GLU cc_start: 0.7320 (tt0) cc_final: 0.7020 (tt0) REVERT: A 702 ASP cc_start: 0.6831 (p0) cc_final: 0.6475 (p0) REVERT: A 889 LEU cc_start: 0.8588 (tp) cc_final: 0.8253 (tt) REVERT: A 896 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7349 (mm-30) REVERT: A 908 GLU cc_start: 0.6670 (tm-30) cc_final: 0.6238 (tm-30) REVERT: A 909 GLN cc_start: 0.5890 (OUTLIER) cc_final: 0.5155 (pm20) REVERT: A 918 SER cc_start: 0.8274 (m) cc_final: 0.7397 (p) REVERT: A 922 PHE cc_start: 0.8279 (m-80) cc_final: 0.8041 (m-80) REVERT: A 963 VAL cc_start: 0.7873 (m) cc_final: 0.7536 (p) REVERT: A 977 LYS cc_start: 0.8192 (mmmt) cc_final: 0.7527 (mmmm) REVERT: A 993 GLU cc_start: 0.7806 (tp30) cc_final: 0.7491 (mm-30) outliers start: 19 outliers final: 10 residues processed: 133 average time/residue: 0.2002 time to fit residues: 34.2155 Evaluate side-chains 129 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 579 LEU 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4073 r_free = 0.4073 target = 0.154675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.129294 restraints weight = 8767.827| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.03 r_work: 0.3606 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6211 Z= 0.303 Angle : 0.599 6.474 8667 Z= 0.334 Chirality : 0.040 0.133 971 Planarity : 0.004 0.038 883 Dihedral : 25.803 129.693 1291 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.14 % Allowed : 19.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.35), residues: 568 helix: 1.58 (0.27), residues: 370 sheet: 0.52 (0.95), residues: 29 loop : -0.35 (0.47), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 847 HIS 0.005 0.001 HIS A1005 PHE 0.020 0.002 PHE A 827 TYR 0.017 0.002 TYR A 842 ARG 0.006 0.000 ARG A 823 *********************** 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 140 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 482 LYS cc_start: 0.7917 (mttt) cc_final: 0.7680 (mptt) REVERT: A 589 ILE cc_start: 0.8847 (mp) cc_final: 0.8645 (mt) REVERT: A 626 GLU cc_start: 0.7184 (tt0) cc_final: 0.6949 (tt0) REVERT: A 684 GLU cc_start: 0.7144 (tm-30) cc_final: 0.6878 (tm-30) REVERT: A 702 ASP cc_start: 0.6921 (p0) cc_final: 0.6606 (p0) REVERT: A 823 ARG cc_start: 0.8621 (ttm110) cc_final: 0.8229 (mtm-85) REVERT: A 896 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7321 (mm-30) REVERT: A 908 GLU cc_start: 0.6774 (tm-30) cc_final: 0.6457 (tm-30) REVERT: A 909 GLN cc_start: 0.6012 (OUTLIER) cc_final: 0.5323 (pm20) REVERT: A 918 SER cc_start: 0.8391 (m) cc_final: 0.7727 (t) REVERT: A 922 PHE cc_start: 0.8318 (m-80) cc_final: 0.8108 (m-80) REVERT: A 963 VAL cc_start: 0.7884 (m) cc_final: 0.7594 (p) REVERT: A 977 LYS cc_start: 0.8277 (mmmt) cc_final: 0.7622 (mmmm) REVERT: A 993 GLU cc_start: 0.7862 (tp30) cc_final: 0.7566 (mm-30) outliers start: 21 outliers final: 16 residues processed: 128 average time/residue: 0.2057 time to fit residues: 33.3770 Evaluate side-chains 134 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 577 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 619 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 853 ASP 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 909 GLN Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 939 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 42 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4093 r_free = 0.4093 target = 0.156238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.130881 restraints weight = 8734.374| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.06 r_work: 0.3628 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2461 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= 0.242 Angle : 0.578 6.094 8667 Z= 0.323 Chirality : 0.039 0.135 971 Planarity : 0.004 0.036 883 Dihedral : 25.801 129.644 1290 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.34 % Allowed : 20.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.35), residues: 568 helix: 1.69 (0.27), residues: 369 sheet: 0.58 (0.97), residues: 29 loop : -0.40 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 847 HIS 0.005 0.001 HIS A 644 PHE 0.015 0.001 PHE A 827 TYR 0.013 0.002 TYR A 842 ARG 0.004 0.000 ARG A 604 *********************** 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 135 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 482 LYS cc_start: 0.7923 (mttt) cc_final: 0.7673 (mptt) REVERT: A 589 ILE cc_start: 0.8834 (mp) cc_final: 0.8626 (mt) REVERT: A 626 GLU cc_start: 0.7205 (tt0) cc_final: 0.6956 (tt0) REVERT: A 684 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6802 (tm-30) REVERT: A 702 ASP cc_start: 0.6888 (p0) cc_final: 0.6549 (p0) REVERT: A 858 VAL cc_start: 0.8097 (m) cc_final: 0.7840 (p) REVERT: A 889 LEU cc_start: 0.8582 (tp) cc_final: 0.8250 (tt) REVERT: A 896 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7364 (mm-30) REVERT: A 909 GLN cc_start: 0.5897 (OUTLIER) cc_final: 0.5272 (pm20) REVERT: A 918 SER cc_start: 0.8369 (m) cc_final: 0.7704 (t) REVERT: A 922 PHE cc_start: 0.8316 (m-80) cc_final: 0.8108 (m-80) REVERT: A 963 VAL cc_start: 0.7896 (m) cc_final: 0.7623 (p) REVERT: A 977 LYS cc_start: 0.8256 (mmmt) cc_final: 0.7847 (mmmm) REVERT: A 993 GLU cc_start: 0.7842 (tp30) cc_final: 0.7543 (mm-30) outliers start: 22 outliers final: 15 residues processed: 121 average time/residue: 0.2075 time to fit residues: 32.2563 Evaluate side-chains 125 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 472 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 582 MET 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 700 CYS Chi-restraints excluded: chain A residue 853 ASP Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 909 GLN Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 939 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 50 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4081 r_free = 0.4081 target = 0.155218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.129905 restraints weight = 8748.088| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.06 r_work: 0.3615 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2589 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= 0.272 Angle : 0.584 7.429 8667 Z= 0.326 Chirality : 0.039 0.139 971 Planarity : 0.004 0.036 883 Dihedral : 25.718 129.310 1290 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.93 % Allowed : 19.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.35), residues: 568 helix: 1.65 (0.27), residues: 370 sheet: 0.59 (1.00), residues: 29 loop : -0.39 (0.47), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 428 HIS 0.003 0.001 HIS A1005 PHE 0.017 0.002 PHE A 827 TYR 0.014 0.002 TYR A 842 ARG 0.007 0.000 ARG A 823 *********************** 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 134 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 482 LYS cc_start: 0.7923 (mttt) cc_final: 0.7664 (mptt) REVERT: A 577 VAL cc_start: 0.8041 (OUTLIER) cc_final: 0.7838 (t) REVERT: A 589 ILE cc_start: 0.8843 (mp) cc_final: 0.8640 (mt) REVERT: A 626 GLU cc_start: 0.7232 (tt0) cc_final: 0.6966 (tt0) REVERT: A 702 ASP cc_start: 0.6928 (p0) cc_final: 0.6587 (p0) REVERT: A 889 LEU cc_start: 0.8601 (tp) cc_final: 0.8268 (tt) REVERT: A 896 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7375 (mm-30) REVERT: A 918 SER cc_start: 0.8408 (m) cc_final: 0.7756 (t) REVERT: A 932 VAL cc_start: 0.8081 (t) cc_final: 0.7838 (p) REVERT: A 963 VAL cc_start: 0.7888 (m) cc_final: 0.7608 (p) REVERT: A 977 LYS cc_start: 0.8267 (mmmt) cc_final: 0.7863 (mmmm) REVERT: A 993 GLU cc_start: 0.7867 (tp30) cc_final: 0.7568 (mm-30) outliers start: 25 outliers final: 18 residues processed: 121 average time/residue: 0.1858 time to fit residues: 29.2397 Evaluate side-chains 126 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 472 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 619 MET 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 883 LEU Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 972 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 10 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 44 optimal weight: 0.1980 chunk 48 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4095 r_free = 0.4095 target = 0.156466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.131285 restraints weight = 8706.375| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.05 r_work: 0.3633 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2729 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= 0.224 Angle : 0.596 12.568 8667 Z= 0.327 Chirality : 0.039 0.140 971 Planarity : 0.004 0.036 883 Dihedral : 25.642 129.392 1290 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.94 % Allowed : 21.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.35), residues: 568 helix: 1.70 (0.27), residues: 369 sheet: 0.62 (0.99), residues: 29 loop : -0.40 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 847 HIS 0.002 0.001 HIS A 644 PHE 0.012 0.002 PHE A 827 TYR 0.012 0.002 TYR A 842 ARG 0.006 0.000 ARG A 823 *********************** 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 129 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 482 LYS cc_start: 0.7923 (mttt) cc_final: 0.7646 (mptt) REVERT: A 589 ILE cc_start: 0.8835 (mp) cc_final: 0.8631 (mt) REVERT: A 626 GLU cc_start: 0.7194 (tt0) cc_final: 0.6968 (tt0) REVERT: A 702 ASP cc_start: 0.6888 (p0) cc_final: 0.6551 (p0) REVERT: A 823 ARG cc_start: 0.8451 (ttm110) cc_final: 0.8236 (mtm-85) REVERT: A 868 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8371 (mp) REVERT: A 889 LEU cc_start: 0.8562 (tp) cc_final: 0.8239 (tt) REVERT: A 896 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7355 (mm-30) REVERT: A 908 GLU cc_start: 0.6842 (tm-30) cc_final: 0.5443 (tt0) REVERT: A 918 SER cc_start: 0.8399 (m) cc_final: 0.7736 (t) REVERT: A 963 VAL cc_start: 0.7908 (m) cc_final: 0.7618 (p) REVERT: A 977 LYS cc_start: 0.8258 (mmmt) cc_final: 0.7855 (mmmm) REVERT: A 993 GLU cc_start: 0.7861 (tp30) cc_final: 0.7589 (tp30) outliers start: 20 outliers final: 18 residues processed: 117 average time/residue: 0.2016 time to fit residues: 30.7579 Evaluate side-chains 133 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 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 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 857 ASP 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 923 THR Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 972 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 18 optimal weight: 0.0060 chunk 0 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 19 optimal weight: 0.0020 chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4089 r_free = 0.4089 target = 0.156406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.131391 restraints weight = 8886.720| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.05 r_work: 0.3635 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2879 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= 0.235 Angle : 0.589 10.811 8667 Z= 0.325 Chirality : 0.039 0.140 971 Planarity : 0.004 0.036 883 Dihedral : 25.455 129.262 1290 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.35 % Allowed : 22.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.36), residues: 568 helix: 1.70 (0.27), residues: 369 sheet: 0.63 (0.99), residues: 29 loop : -0.38 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 847 HIS 0.003 0.001 HIS A1005 PHE 0.012 0.002 PHE A 827 TYR 0.013 0.001 TYR A 842 ARG 0.006 0.000 ARG A 823 ********************** 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 126 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 482 LYS cc_start: 0.7897 (mttt) cc_final: 0.7618 (mptt) REVERT: A 583 GLU cc_start: 0.6995 (pm20) cc_final: 0.6692 (pm20) REVERT: A 589 ILE cc_start: 0.8782 (mp) cc_final: 0.8564 (mt) REVERT: A 626 GLU cc_start: 0.7307 (tt0) cc_final: 0.7019 (tt0) REVERT: A 702 ASP cc_start: 0.6938 (p0) cc_final: 0.6586 (p0) REVERT: A 823 ARG cc_start: 0.8444 (ttm110) cc_final: 0.8212 (mtm-85) REVERT: A 858 VAL cc_start: 0.8153 (m) cc_final: 0.7725 (p) REVERT: A 868 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8201 (mp) REVERT: A 889 LEU cc_start: 0.8577 (tp) cc_final: 0.8260 (tt) REVERT: A 896 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7371 (mm-30) REVERT: A 918 SER cc_start: 0.8430 (m) cc_final: 0.7744 (t) REVERT: A 963 VAL cc_start: 0.7877 (m) cc_final: 0.7574 (p) REVERT: A 977 LYS cc_start: 0.8239 (mmmt) cc_final: 0.7830 (mmmm) REVERT: A 993 GLU cc_start: 0.7857 (tp30) cc_final: 0.7586 (tp30) outliers start: 17 outliers final: 16 residues processed: 117 average time/residue: 0.2043 time to fit residues: 30.6780 Evaluate side-chains 132 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 THR 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 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 868 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 888 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 Chi-restraints excluded: chain A residue 972 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 45 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 50 optimal weight: 0.6980 chunk 49 optimal weight: 0.4980 chunk 29 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.156142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.131191 restraints weight = 8960.489| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.06 r_work: 0.3630 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2996 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= 0.241 Angle : 0.593 10.896 8667 Z= 0.327 Chirality : 0.039 0.140 971 Planarity : 0.004 0.036 883 Dihedral : 25.351 129.018 1290 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.34 % Allowed : 22.29 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.35), residues: 568 helix: 1.69 (0.27), residues: 369 sheet: 0.62 (0.99), residues: 29 loop : -0.48 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 428 HIS 0.003 0.001 HIS A 764 PHE 0.013 0.002 PHE A 827 TYR 0.013 0.002 TYR A 842 ARG 0.005 0.000 ARG A 823 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2872.48 seconds wall clock time: 51 minutes 53.08 seconds (3113.08 seconds total)