Starting phenix.real_space_refine on Wed Sep 17 06:14:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eo1_19844/09_2025/9eo1_19844.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eo1_19844/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9eo1_19844/09_2025/9eo1_19844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eo1_19844/09_2025/9eo1_19844.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eo1_19844/09_2025/9eo1_19844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eo1_19844/09_2025/9eo1_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.70, per 1000 atoms: 0.29 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: 0.59 Conformation dependent library (CDL) restraints added in 320.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.87 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: 0.78 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.680 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:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.300 ------------------------------------------------------------------------------- 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= 0.335 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (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 covalent geometry : bond 0.00560 ( 6211) covalent geometry : angle 0.85947 ( 8667) hydrogen bonds : bond 0.15535 ( 321) hydrogen bonds : angle 5.70329 ( 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 : 0.183 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: 0.0961 time to fit residues: 16.3475 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 : 0.197 ------------------------------------------------------------------------------- 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: 1.9990 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... 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 = 0.4067 r_free = 0.4067 target = 0.154484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.129604 restraints weight = 8866.945| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.23 r_work: 0.3611 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6211 Z= 0.192 Angle : 0.607 6.882 8667 Z= 0.343 Chirality : 0.040 0.141 971 Planarity : 0.004 0.033 883 Dihedral : 25.912 132.398 1310 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.94 % Allowed : 16.96 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.34), residues: 568 helix: 1.51 (0.27), residues: 366 sheet: 1.05 (0.90), residues: 29 loop : -0.26 (0.46), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 823 TYR 0.013 0.002 TYR A 842 PHE 0.031 0.002 PHE A 500 TRP 0.011 0.002 TRP A 906 HIS 0.006 0.001 HIS A 718 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 6211) covalent geometry : angle 0.60715 ( 8667) hydrogen bonds : bond 0.04995 ( 321) hydrogen bonds : angle 4.51320 ( 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 153 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.257 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: 0.7894 (OUTLIER) cc_final: 0.7149 (pm20) REVERT: A 438 GLU cc_start: 0.7774 (tp30) cc_final: 0.7487 (tp30) REVERT: A 482 LYS cc_start: 0.8062 (mttt) cc_final: 0.7648 (mptt) REVERT: A 485 HIS cc_start: 0.7172 (p-80) cc_final: 0.6912 (p-80) REVERT: A 589 ILE cc_start: 0.8810 (mp) cc_final: 0.8534 (mt) REVERT: A 593 THR cc_start: 0.8141 (t) cc_final: 0.7940 (p) REVERT: A 604 ARG cc_start: 0.7426 (mtm180) cc_final: 0.7126 (mtm180) REVERT: A 625 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7026 (tp30) REVERT: A 626 GLU cc_start: 0.7537 (tt0) cc_final: 0.7143 (tt0) REVERT: A 648 ARG cc_start: 0.7357 (ttt-90) cc_final: 0.7153 (ttt-90) REVERT: A 652 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7722 (t0) REVERT: A 684 GLU cc_start: 0.7024 (tm-30) cc_final: 0.6660 (tm-30) REVERT: A 702 ASP cc_start: 0.7020 (p0) cc_final: 0.6770 (p0) REVERT: A 718 HIS cc_start: 0.7966 (m-70) cc_final: 0.7739 (m-70) REVERT: A 752 ARG cc_start: 0.6787 (ttp80) cc_final: 0.6564 (ttp-170) REVERT: A 896 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7220 (mm-30) REVERT: A 910 GLU cc_start: 0.7506 (tp30) cc_final: 0.7248 (tp30) REVERT: A 918 SER cc_start: 0.8294 (m) cc_final: 0.7431 (p) REVERT: A 963 VAL cc_start: 0.7775 (m) cc_final: 0.7420 (p) REVERT: A 972 LYS cc_start: 0.7001 (mttt) cc_final: 0.6730 (mtpt) REVERT: A 977 LYS cc_start: 0.8153 (mmmt) cc_final: 0.7732 (mmmm) REVERT: A 993 GLU cc_start: 0.7860 (tp30) cc_final: 0.7581 (tp30) outliers start: 20 outliers final: 10 residues processed: 142 average time/residue: 0.0899 time to fit residues: 16.4271 Evaluate side-chains 146 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 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 32 optimal weight: 0.5980 chunk 39 optimal weight: 0.0030 chunk 28 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.155090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.130359 restraints weight = 8775.974| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.25 r_work: 0.3630 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6211 Z= 0.164 Angle : 0.572 5.953 8667 Z= 0.321 Chirality : 0.039 0.173 971 Planarity : 0.003 0.037 883 Dihedral : 25.907 131.688 1295 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.73 % Allowed : 16.96 % 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 aren not related in a simple way. whole: 1.49 (0.35), residues: 568 helix: 1.60 (0.27), residues: 368 sheet: 0.98 (0.94), residues: 29 loop : -0.26 (0.47), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 824 TYR 0.012 0.002 TYR A 842 PHE 0.015 0.002 PHE A 500 TRP 0.009 0.001 TRP A 847 HIS 0.005 0.001 HIS A 644 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 6211) covalent geometry : angle 0.57167 ( 8667) hydrogen bonds : bond 0.04421 ( 321) hydrogen bonds : angle 4.31555 ( 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 150 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7696 (tp30) cc_final: 0.7355 (tp30) REVERT: A 482 LYS cc_start: 0.8002 (mttt) cc_final: 0.7755 (mptt) REVERT: A 589 ILE cc_start: 0.8786 (mp) cc_final: 0.8545 (mt) REVERT: A 604 ARG cc_start: 0.7451 (mtm180) cc_final: 0.6909 (mtm180) REVERT: A 625 GLU cc_start: 0.7420 (mm-30) cc_final: 0.6996 (tp30) REVERT: A 626 GLU cc_start: 0.7399 (tt0) cc_final: 0.7087 (tt0) REVERT: A 644 HIS cc_start: 0.7711 (t-90) cc_final: 0.7443 (t-90) REVERT: A 684 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6710 (tm-30) REVERT: A 702 ASP cc_start: 0.6904 (p0) cc_final: 0.6633 (p0) REVERT: A 718 HIS cc_start: 0.8000 (m-70) cc_final: 0.7780 (m-70) REVERT: A 752 ARG cc_start: 0.6812 (ttp80) cc_final: 0.6565 (ttp-170) REVERT: A 889 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8286 (tt) REVERT: A 909 GLN cc_start: 0.5883 (OUTLIER) cc_final: 0.5682 (pm20) REVERT: A 918 SER cc_start: 0.8310 (m) cc_final: 0.7449 (p) REVERT: A 922 PHE cc_start: 0.8362 (m-80) cc_final: 0.8054 (m-80) REVERT: A 932 VAL cc_start: 0.8045 (OUTLIER) cc_final: 0.7833 (t) REVERT: A 963 VAL cc_start: 0.7822 (m) cc_final: 0.7492 (p) REVERT: A 972 LYS cc_start: 0.6993 (mttt) cc_final: 0.6735 (mtpt) REVERT: A 993 GLU cc_start: 0.7852 (tp30) cc_final: 0.7577 (tp30) outliers start: 24 outliers final: 13 residues processed: 138 average time/residue: 0.0864 time to fit residues: 15.5661 Evaluate side-chains 140 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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 576 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 774 VAL 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 12 optimal weight: 0.0060 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.0770 chunk 8 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 0.0980 chunk 3 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 0.0020 overall best weight: 0.1762 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.157099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.132484 restraints weight = 8839.796| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.25 r_work: 0.3649 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.1888 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= 0.132 Angle : 0.543 6.556 8667 Z= 0.305 Chirality : 0.037 0.131 971 Planarity : 0.003 0.038 883 Dihedral : 25.801 131.317 1295 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.96 % Allowed : 20.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.35), residues: 568 helix: 1.74 (0.27), residues: 368 sheet: 0.83 (0.94), residues: 29 loop : -0.27 (0.48), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 823 TYR 0.011 0.001 TYR A 418 PHE 0.015 0.001 PHE A 500 TRP 0.009 0.001 TRP A 847 HIS 0.003 0.001 HIS A 644 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 6211) covalent geometry : angle 0.54297 ( 8667) hydrogen bonds : bond 0.03941 ( 321) hydrogen bonds : angle 4.17702 ( 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 143 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7814 (tp30) cc_final: 0.7453 (tp30) REVERT: A 482 LYS cc_start: 0.7965 (mttt) cc_final: 0.7671 (mptt) REVERT: A 554 LEU cc_start: 0.7056 (mt) cc_final: 0.6845 (mp) REVERT: A 589 ILE cc_start: 0.8782 (mp) cc_final: 0.8554 (mt) REVERT: A 604 ARG cc_start: 0.7448 (mtm180) cc_final: 0.6976 (mtm180) REVERT: A 625 GLU cc_start: 0.7410 (mm-30) cc_final: 0.6942 (tp30) REVERT: A 626 GLU cc_start: 0.7367 (tt0) cc_final: 0.7065 (tt0) REVERT: A 644 HIS cc_start: 0.7719 (t-90) cc_final: 0.7436 (t-90) REVERT: A 684 GLU cc_start: 0.7103 (tm-30) cc_final: 0.6851 (tm-30) REVERT: A 698 ILE cc_start: 0.7617 (mp) cc_final: 0.7407 (mm) REVERT: A 702 ASP cc_start: 0.6859 (p0) cc_final: 0.6522 (p0) REVERT: A 718 HIS cc_start: 0.7981 (m-70) cc_final: 0.7761 (m-70) REVERT: A 823 ARG cc_start: 0.8523 (ttm110) cc_final: 0.8308 (mtm-85) REVERT: A 889 LEU cc_start: 0.8566 (tp) cc_final: 0.8227 (tt) REVERT: A 918 SER cc_start: 0.8267 (m) cc_final: 0.7569 (t) REVERT: A 922 PHE cc_start: 0.8313 (m-80) cc_final: 0.8059 (m-80) REVERT: A 963 VAL cc_start: 0.7834 (m) cc_final: 0.7499 (p) REVERT: A 972 LYS cc_start: 0.6955 (mttt) cc_final: 0.6650 (mtpt) REVERT: A 977 LYS cc_start: 0.8202 (mmmt) cc_final: 0.7778 (mmmm) REVERT: A 989 ILE cc_start: 0.8132 (mm) cc_final: 0.7886 (mm) REVERT: A 993 GLU cc_start: 0.7804 (tp30) cc_final: 0.7535 (tp30) outliers start: 15 outliers final: 11 residues processed: 134 average time/residue: 0.0912 time to fit residues: 15.8265 Evaluate side-chains 133 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 464 GLU Chi-restraints excluded: chain A residue 576 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 772 MET Chi-restraints excluded: chain A residue 883 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 26 optimal weight: 0.0980 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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** A 717 GLN ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.156622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.131081 restraints weight = 9036.620| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.09 r_work: 0.3623 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2058 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= 0.166 Angle : 0.555 6.091 8667 Z= 0.311 Chirality : 0.038 0.136 971 Planarity : 0.004 0.038 883 Dihedral : 25.749 130.446 1294 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.34 % Allowed : 20.12 % 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 aren not related in a simple way. whole: 1.57 (0.35), residues: 568 helix: 1.70 (0.27), residues: 370 sheet: 0.51 (0.92), residues: 29 loop : -0.25 (0.48), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 823 TYR 0.011 0.002 TYR A 842 PHE 0.013 0.001 PHE A 875 TRP 0.009 0.001 TRP A 906 HIS 0.003 0.001 HIS A 644 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 6211) covalent geometry : angle 0.55505 ( 8667) hydrogen bonds : bond 0.04205 ( 321) hydrogen bonds : angle 4.19757 ( 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 144 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7708 (tp30) cc_final: 0.7344 (tp30) REVERT: A 482 LYS cc_start: 0.7941 (mttt) cc_final: 0.7671 (mptt) REVERT: A 554 LEU cc_start: 0.7285 (mt) cc_final: 0.7036 (mp) REVERT: A 589 ILE cc_start: 0.8808 (mp) cc_final: 0.8597 (mt) REVERT: A 604 ARG cc_start: 0.7503 (mtm180) cc_final: 0.7084 (mtm180) REVERT: A 626 GLU cc_start: 0.7221 (tt0) cc_final: 0.6987 (tt0) REVERT: A 644 HIS cc_start: 0.7589 (t-90) cc_final: 0.7388 (t-90) REVERT: A 684 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6846 (tm-30) REVERT: A 702 ASP cc_start: 0.6863 (p0) cc_final: 0.6560 (p0) REVERT: A 889 LEU cc_start: 0.8549 (tp) cc_final: 0.8234 (tt) REVERT: A 896 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7333 (mm-30) REVERT: A 908 GLU cc_start: 0.6599 (tm-30) cc_final: 0.6170 (tm-30) REVERT: A 909 GLN cc_start: 0.5851 (OUTLIER) cc_final: 0.5151 (pm20) REVERT: A 918 SER cc_start: 0.8336 (m) cc_final: 0.7509 (p) REVERT: A 922 PHE cc_start: 0.8275 (m-80) cc_final: 0.8071 (m-80) REVERT: A 963 VAL cc_start: 0.7920 (m) cc_final: 0.7611 (p) REVERT: A 977 LYS cc_start: 0.8249 (mmmt) cc_final: 0.7860 (mmmm) REVERT: A 993 GLU cc_start: 0.7822 (tp30) cc_final: 0.7542 (mm-30) outliers start: 22 outliers final: 16 residues processed: 134 average time/residue: 0.0908 time to fit residues: 15.7739 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 : 0.189 ------------------------------------------------------------------------------- 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 464 GLU 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 753 LEU Chi-restraints excluded: chain A residue 774 VAL 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 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: 0.5980 chunk 43 optimal weight: 0.0970 chunk 42 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 chunk 54 optimal weight: 0.0980 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 0.0470 overall best weight: 0.2676 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.158471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.132668 restraints weight = 8817.739| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.19 r_work: 0.3649 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2382 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= 0.139 Angle : 0.552 7.135 8667 Z= 0.306 Chirality : 0.037 0.134 971 Planarity : 0.003 0.037 883 Dihedral : 25.706 130.228 1294 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.75 % Allowed : 20.51 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.35), residues: 568 helix: 1.75 (0.27), residues: 371 sheet: 0.45 (0.91), residues: 29 loop : -0.19 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 823 TYR 0.010 0.001 TYR A 418 PHE 0.019 0.001 PHE A 827 TRP 0.010 0.001 TRP A 847 HIS 0.003 0.001 HIS A 718 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6211) covalent geometry : angle 0.55214 ( 8667) hydrogen bonds : bond 0.03942 ( 321) hydrogen bonds : angle 4.15809 ( 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: 19 poor density : 124 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7810 (tp30) cc_final: 0.7423 (tp30) REVERT: A 482 LYS cc_start: 0.7952 (mttt) cc_final: 0.7608 (mmtt) REVERT: A 604 ARG cc_start: 0.7461 (mtm180) cc_final: 0.7131 (mtp180) REVERT: A 626 GLU cc_start: 0.7323 (tt0) cc_final: 0.7018 (tt0) REVERT: A 644 HIS cc_start: 0.7710 (t-90) cc_final: 0.7505 (t-90) REVERT: A 684 GLU cc_start: 0.7068 (tm-30) cc_final: 0.6741 (tm-30) REVERT: A 702 ASP cc_start: 0.6838 (p0) cc_final: 0.6462 (p0) REVERT: A 823 ARG cc_start: 0.8556 (ttm110) cc_final: 0.8191 (mtm-85) REVERT: A 889 LEU cc_start: 0.8570 (tp) cc_final: 0.8224 (tt) REVERT: A 896 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7347 (mm-30) REVERT: A 908 GLU cc_start: 0.6725 (tm-30) cc_final: 0.6491 (tm-30) REVERT: A 909 GLN cc_start: 0.5951 (OUTLIER) cc_final: 0.5336 (pm20) REVERT: A 918 SER cc_start: 0.8213 (m) cc_final: 0.7496 (t) REVERT: A 963 VAL cc_start: 0.7867 (m) cc_final: 0.7543 (p) REVERT: A 977 LYS cc_start: 0.8183 (mmmt) cc_final: 0.7761 (mmmm) REVERT: A 989 ILE cc_start: 0.8136 (mm) cc_final: 0.7909 (mm) REVERT: A 993 GLU cc_start: 0.7815 (tp30) cc_final: 0.7485 (mm-30) outliers start: 19 outliers final: 12 residues processed: 131 average time/residue: 0.0910 time to fit residues: 15.3562 Evaluate side-chains 131 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 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 774 VAL Chi-restraints excluded: chain A residue 853 ASP Chi-restraints excluded: chain A residue 909 GLN Chi-restraints excluded: chain A residue 932 VAL 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 26 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 0.0270 chunk 3 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.156118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.130210 restraints weight = 8805.775| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.18 r_work: 0.3613 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.2409 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= 0.200 Angle : 0.578 7.809 8667 Z= 0.320 Chirality : 0.039 0.143 971 Planarity : 0.004 0.040 883 Dihedral : 25.747 129.516 1293 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.75 % Allowed : 20.51 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.35), residues: 568 helix: 1.66 (0.27), residues: 371 sheet: 0.52 (0.95), residues: 29 loop : -0.28 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 860 TYR 0.014 0.002 TYR A 842 PHE 0.018 0.002 PHE A 827 TRP 0.009 0.002 TRP A 847 HIS 0.003 0.001 HIS A1005 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 6211) covalent geometry : angle 0.57767 ( 8667) hydrogen bonds : bond 0.04405 ( 321) hydrogen bonds : angle 4.22547 ( 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 145 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7777 (tp30) cc_final: 0.7379 (tp30) REVERT: A 482 LYS cc_start: 0.8000 (mttt) cc_final: 0.7665 (mptt) REVERT: A 604 ARG cc_start: 0.7407 (mtm180) cc_final: 0.7106 (mtp180) REVERT: A 626 GLU cc_start: 0.7354 (tt0) cc_final: 0.7023 (tt0) REVERT: A 644 HIS cc_start: 0.7729 (t-90) cc_final: 0.7519 (t-90) REVERT: A 684 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6774 (tm-30) REVERT: A 702 ASP cc_start: 0.6919 (p0) cc_final: 0.6567 (p0) REVERT: A 858 VAL cc_start: 0.8127 (m) cc_final: 0.7864 (p) REVERT: A 889 LEU cc_start: 0.8638 (tp) cc_final: 0.8287 (tt) REVERT: A 896 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7352 (mm-30) REVERT: A 909 GLN cc_start: 0.5979 (OUTLIER) cc_final: 0.5339 (pm20) REVERT: A 918 SER cc_start: 0.8340 (m) cc_final: 0.7607 (t) REVERT: A 963 VAL cc_start: 0.7861 (m) cc_final: 0.7544 (p) REVERT: A 977 LYS cc_start: 0.8201 (mmmt) cc_final: 0.7773 (mmmm) REVERT: A 993 GLU cc_start: 0.7860 (tp30) cc_final: 0.7534 (mm-30) outliers start: 19 outliers final: 12 residues processed: 134 average time/residue: 0.0905 time to fit residues: 15.7703 Evaluate side-chains 134 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 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 883 LEU Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 909 GLN Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 972 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 4 optimal weight: 0.9980 chunk 50 optimal weight: 0.0000 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 0.0770 chunk 41 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5142 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.156494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.130727 restraints weight = 8749.938| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.19 r_work: 0.3622 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6211 Z= 0.178 Angle : 0.596 10.899 8667 Z= 0.325 Chirality : 0.039 0.136 971 Planarity : 0.004 0.042 883 Dihedral : 25.681 129.363 1293 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.75 % Allowed : 21.30 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.35), residues: 568 helix: 1.66 (0.27), residues: 371 sheet: 0.44 (0.94), residues: 29 loop : -0.29 (0.48), residues: 168 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 827 TRP 0.009 0.001 TRP A 847 HIS 0.003 0.001 HIS A 718 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 6211) covalent geometry : angle 0.59617 ( 8667) hydrogen bonds : bond 0.04264 ( 321) hydrogen bonds : angle 4.20270 ( 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 133 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6854 (tp30) REVERT: A 438 GLU cc_start: 0.7800 (tp30) cc_final: 0.7418 (tp30) REVERT: A 482 LYS cc_start: 0.7987 (mttt) cc_final: 0.7644 (mptt) REVERT: A 604 ARG cc_start: 0.7402 (mtm180) cc_final: 0.7075 (mtp180) REVERT: A 626 GLU cc_start: 0.7379 (tt0) cc_final: 0.7042 (tt0) REVERT: A 644 HIS cc_start: 0.7751 (t-90) cc_final: 0.7525 (t-90) REVERT: A 702 ASP cc_start: 0.6874 (p0) cc_final: 0.6541 (p0) REVERT: A 889 LEU cc_start: 0.8637 (tp) cc_final: 0.8277 (tt) REVERT: A 896 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7338 (mm-30) REVERT: A 909 GLN cc_start: 0.5709 (OUTLIER) cc_final: 0.5388 (pm20) REVERT: A 918 SER cc_start: 0.8343 (m) cc_final: 0.7612 (t) REVERT: A 932 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.7833 (p) REVERT: A 963 VAL cc_start: 0.7870 (m) cc_final: 0.7561 (p) REVERT: A 977 LYS cc_start: 0.8207 (mmmt) cc_final: 0.7778 (mmmm) REVERT: A 993 GLU cc_start: 0.7851 (tp30) cc_final: 0.7511 (mm-30) outliers start: 19 outliers final: 13 residues processed: 125 average time/residue: 0.0936 time to fit residues: 15.0512 Evaluate side-chains 142 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 577 VAL 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 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 909 GLN Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 932 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 32 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 42 optimal weight: 0.0010 chunk 35 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.156697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.131077 restraints weight = 8773.481| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.19 r_work: 0.3625 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6211 Z= 0.173 Angle : 0.610 11.751 8667 Z= 0.328 Chirality : 0.039 0.137 971 Planarity : 0.004 0.057 883 Dihedral : 25.615 129.308 1290 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.76 % Allowed : 22.68 % 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 aren not related in a simple way. whole: 1.37 (0.35), residues: 568 helix: 1.55 (0.27), residues: 376 sheet: 0.44 (0.95), residues: 29 loop : -0.41 (0.48), residues: 163 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 0.013 0.002 PHE A 827 TRP 0.009 0.002 TRP A 428 HIS 0.003 0.001 HIS A 644 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 6211) covalent geometry : angle 0.60974 ( 8667) hydrogen bonds : bond 0.04270 ( 321) hydrogen bonds : angle 4.19567 ( 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 139 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7793 (tp30) cc_final: 0.7410 (tp30) REVERT: A 482 LYS cc_start: 0.7956 (mttt) cc_final: 0.7617 (mptt) REVERT: A 604 ARG cc_start: 0.7395 (mtm180) cc_final: 0.7066 (mtp180) REVERT: A 625 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6890 (tp30) REVERT: A 626 GLU cc_start: 0.7386 (tt0) cc_final: 0.7035 (tt0) REVERT: A 644 HIS cc_start: 0.7715 (t-90) cc_final: 0.7502 (t-90) REVERT: A 684 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6845 (tm-30) REVERT: A 702 ASP cc_start: 0.6880 (p0) cc_final: 0.6526 (p0) REVERT: A 737 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7440 (mm-30) REVERT: A 823 ARG cc_start: 0.8427 (ttm110) cc_final: 0.8190 (mtm-85) REVERT: A 868 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8291 (mp) REVERT: A 889 LEU cc_start: 0.8619 (tp) cc_final: 0.8252 (tt) REVERT: A 895 GLU cc_start: 0.7556 (pm20) cc_final: 0.7295 (pm20) REVERT: A 896 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7161 (mm-30) REVERT: A 910 GLU cc_start: 0.7688 (tp30) cc_final: 0.7348 (tp30) REVERT: A 918 SER cc_start: 0.8344 (m) cc_final: 0.7611 (t) REVERT: A 932 VAL cc_start: 0.8068 (OUTLIER) cc_final: 0.7856 (p) REVERT: A 963 VAL cc_start: 0.7881 (m) cc_final: 0.7572 (p) REVERT: A 977 LYS cc_start: 0.8202 (mmmt) cc_final: 0.7770 (mmmm) REVERT: A 993 GLU cc_start: 0.7852 (tp30) cc_final: 0.7590 (tp30) outliers start: 14 outliers final: 10 residues processed: 130 average time/residue: 0.0879 time to fit residues: 14.9082 Evaluate side-chains 126 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 THR 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 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 923 THR Chi-restraints excluded: chain A residue 932 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 32 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.154798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.130144 restraints weight = 8845.131| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.12 r_work: 0.3617 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6211 Z= 0.202 Angle : 0.624 10.960 8667 Z= 0.339 Chirality : 0.040 0.142 971 Planarity : 0.004 0.058 883 Dihedral : 25.489 128.951 1290 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.96 % Allowed : 22.68 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.35), residues: 568 helix: 1.56 (0.27), residues: 370 sheet: 0.48 (0.99), residues: 29 loop : -0.34 (0.47), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 823 TYR 0.015 0.002 TYR A 842 PHE 0.016 0.002 PHE A 875 TRP 0.014 0.002 TRP A 847 HIS 0.003 0.001 HIS A1005 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 6211) covalent geometry : angle 0.62446 ( 8667) hydrogen bonds : bond 0.04534 ( 321) hydrogen bonds : angle 4.27586 ( 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 141 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6719 (tp30) REVERT: A 438 GLU cc_start: 0.7775 (tp30) cc_final: 0.7386 (tp30) REVERT: A 482 LYS cc_start: 0.7958 (mttt) cc_final: 0.7658 (mptt) REVERT: A 626 GLU cc_start: 0.7366 (tt0) cc_final: 0.7061 (tt0) REVERT: A 644 HIS cc_start: 0.7678 (t-90) cc_final: 0.7427 (t-90) REVERT: A 702 ASP cc_start: 0.7023 (p0) cc_final: 0.6718 (p0) REVERT: A 823 ARG cc_start: 0.8496 (ttm110) cc_final: 0.8207 (mtm-85) REVERT: A 868 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8364 (mp) REVERT: A 899 ARG cc_start: 0.7831 (ttm170) cc_final: 0.7070 (mtt180) REVERT: A 908 GLU cc_start: 0.6729 (tm-30) cc_final: 0.6420 (tm-30) REVERT: A 918 SER cc_start: 0.8476 (m) cc_final: 0.7794 (t) REVERT: A 932 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7896 (p) REVERT: A 963 VAL cc_start: 0.7892 (m) cc_final: 0.7588 (p) REVERT: A 977 LYS cc_start: 0.8244 (mmmt) cc_final: 0.7833 (mmmm) REVERT: A 987 GLN cc_start: 0.8285 (mt0) cc_final: 0.7889 (tt0) REVERT: A 993 GLU cc_start: 0.7898 (tp30) cc_final: 0.7602 (mm-30) outliers start: 15 outliers final: 12 residues processed: 130 average time/residue: 0.0872 time to fit residues: 14.7924 Evaluate side-chains 134 residues out of total 507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 THR 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 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 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 6 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 55 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 0.0030 chunk 14 optimal weight: 0.6980 overall best weight: 0.4190 ------------------------------------------------------------------------------- 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 864 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.155873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.131356 restraints weight = 8900.055| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.15 r_work: 0.3638 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2881 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= 0.165 Angle : 0.615 10.934 8667 Z= 0.332 Chirality : 0.039 0.135 971 Planarity : 0.004 0.052 883 Dihedral : 25.386 129.118 1290 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.96 % Allowed : 23.27 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.35), residues: 568 helix: 1.54 (0.27), residues: 376 sheet: 0.34 (0.98), residues: 29 loop : -0.54 (0.48), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 899 TYR 0.011 0.002 TYR A 842 PHE 0.013 0.002 PHE A 584 TRP 0.013 0.002 TRP A 847 HIS 0.004 0.001 HIS A 681 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 6211) covalent geometry : angle 0.61547 ( 8667) hydrogen bonds : bond 0.04296 ( 321) hydrogen bonds : angle 4.20332 ( 894) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1572.38 seconds wall clock time: 27 minutes 47.70 seconds (1667.70 seconds total)