Starting phenix.real_space_refine on Fri Oct 23 12:17:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y4j_72484/10_2026/9y4j_72484.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y4j_72484/10_2026/9y4j_72484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y4j_72484/10_2026/9y4j_72484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y4j_72484/10_2026/9y4j_72484.map" model { file = "/net/cci-nas-00/data/ceres_data/9y4j_72484/10_2026/9y4j_72484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y4j_72484/10_2026/9y4j_72484.cif" } resolution = 2.81 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= -0.000 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4705 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 29 5.49 5 Mg 2 5.21 5 S 38 5.16 5 C 3661 2.51 5 N 1033 2.21 5 O 1180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5943 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5354 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 22, 'TRANS': 641} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 282 Classifications: {'RNA': 13} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 5} Link IDs: {'rna3p': 12} Chain: "C" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'RNA': 13} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 8} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' MG': 2, 'ANP': 1} Classifications: {'undetermined': 3, 'water': 2} Link IDs: {None: 4} Time building chain proxies: 1.45, per 1000 atoms: 0.24 Number of scatterers: 5943 At special positions: 0 Unit cell: (85.696, 99.008, 70.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 38 16.00 P 29 15.00 Mg 2 11.99 O 1180 8.00 N 1033 7.00 C 3661 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 910 " - pdb=" SG CYS A 964 " distance=2.04 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: 0.57 Conformation dependent library (CDL) restraints added in 294.5 milliseconds 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1270 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 5 sheets defined 53.0% alpha, 13.0% beta 13 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 309 through 317 removed outlier: 3.772A pdb=" N GLU A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 316 " --> pdb=" O GLN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.603A pdb=" N VAL A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 375 removed outlier: 3.581A pdb=" N VAL A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 399 through 407 Processing helix chain 'A' and resid 414 through 422 removed outlier: 4.651A pdb=" N ASN A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'A' and resid 445 through 448 Processing helix chain 'A' and resid 452 through 473 removed outlier: 4.199A pdb=" N LYS A 473 " --> pdb=" O ASN A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 513 Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.510A pdb=" N GLN A 531 " --> pdb=" O GLN A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 565 removed outlier: 3.543A pdb=" N CYS A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 593 Processing helix chain 'A' and resid 594 through 617 removed outlier: 3.603A pdb=" N LYS A 606 " --> pdb=" O GLU A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 637 removed outlier: 3.515A pdb=" N ALA A 622 " --> pdb=" O ARG A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 682 Processing helix chain 'A' and resid 683 through 692 Processing helix chain 'A' and resid 693 through 697 removed outlier: 3.572A pdb=" N TYR A 696 " --> pdb=" O ASN A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 712 Processing helix chain 'A' and resid 727 through 740 Processing helix chain 'A' and resid 741 through 747 removed outlier: 4.027A pdb=" N ALA A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 779 Processing helix chain 'A' and resid 812 through 821 Processing helix chain 'A' and resid 839 through 863 removed outlier: 3.723A pdb=" N ASN A 847 " --> pdb=" O HIS A 843 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 886 Processing helix chain 'A' and resid 887 through 894 Processing helix chain 'A' and resid 899 through 901 No H-bonds generated for 'chain 'A' and resid 899 through 901' Processing helix chain 'A' and resid 932 through 937 removed outlier: 3.514A pdb=" N LYS A 936 " --> pdb=" O THR A 932 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 937 " --> pdb=" O PRO A 933 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 932 through 937' Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 390 removed outlier: 6.504A pdb=" N ILE A 326 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 536 through 542 removed outlier: 5.995A pdb=" N CYS A 536 " --> pdb=" O TYR A 830 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU A 832 " --> pdb=" O CYS A 536 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS A 538 " --> pdb=" O LEU A 832 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ALA A 834 " --> pdb=" O LYS A 538 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA A 540 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY A 721 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N THR A 790 " --> pdb=" O GLY A 721 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ILE A 723 " --> pdb=" O THR A 790 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N HIS A 752 " --> pdb=" O THR A 789 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 913 through 916 removed outlier: 6.907A pdb=" N PHE A 905 " --> pdb=" O ALA A 914 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N SER A 916 " --> pdb=" O ILE A 903 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE A 903 " --> pdb=" O SER A 916 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 920 through 923 Processing sheet with id=AA5, first strand: chain 'A' and resid 939 through 941 removed outlier: 6.837A pdb=" N ILE A 960 " --> pdb=" O TRP A 968 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 795 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.22: 31 1.22 - 1.37: 1900 1.37 - 1.52: 2562 1.52 - 1.67: 1540 1.67 - 1.82: 63 Bond restraints: 6096 Sorted by residual: bond pdb=" C LYS A 782 " pdb=" O LYS A 782 " ideal model delta sigma weight residual 1.236 1.069 0.167 1.47e-02 4.63e+03 1.29e+02 bond pdb=" C THR A 789 " pdb=" O THR A 789 " ideal model delta sigma weight residual 1.234 1.111 0.123 1.19e-02 7.06e+03 1.07e+02 bond pdb=" N VAL A 315 " pdb=" CA VAL A 315 " ideal model delta sigma weight residual 1.456 1.348 0.109 1.08e-02 8.57e+03 1.01e+02 bond pdb=" CA LYS A 782 " pdb=" C LYS A 782 " ideal model delta sigma weight residual 1.523 1.357 0.166 1.80e-02 3.09e+03 8.55e+01 bond pdb=" C GLN A 317 " pdb=" O GLN A 317 " ideal model delta sigma weight residual 1.243 1.159 0.084 9.50e-03 1.11e+04 7.83e+01 ... (remaining 6091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.40: 8212 4.40 - 8.80: 86 8.80 - 13.20: 18 13.20 - 17.60: 6 17.60 - 22.00: 8 Bond angle restraints: 8330 Sorted by residual: angle pdb=" C LYS A 476 " pdb=" N PRO A 477 " pdb=" CA PRO A 477 " ideal model delta sigma weight residual 120.03 100.86 19.17 9.90e-01 1.02e+00 3.75e+02 angle pdb=" N LYS A 782 " pdb=" CA LYS A 782 " pdb=" C LYS A 782 " ideal model delta sigma weight residual 113.15 133.53 -20.38 1.19e+00 7.06e-01 2.93e+02 angle pdb=" N ARG A 779 " pdb=" CA ARG A 779 " pdb=" C ARG A 779 " ideal model delta sigma weight residual 112.93 132.96 -20.03 1.33e+00 5.65e-01 2.27e+02 angle pdb=" N LYS A 884 " pdb=" CA LYS A 884 " pdb=" C LYS A 884 " ideal model delta sigma weight residual 113.97 94.96 19.01 1.28e+00 6.10e-01 2.20e+02 angle pdb=" O ASN A 475 " pdb=" C ASN A 475 " pdb=" N LYS A 476 " ideal model delta sigma weight residual 122.91 106.71 16.20 1.19e+00 7.06e-01 1.85e+02 ... (remaining 8325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.48: 3598 26.48 - 52.96: 155 52.96 - 79.43: 58 79.43 - 105.91: 5 105.91 - 132.39: 1 Dihedral angle restraints: 3817 sinusoidal: 1866 harmonic: 1951 Sorted by residual: dihedral pdb=" C MET A 882 " pdb=" N MET A 882 " pdb=" CA MET A 882 " pdb=" CB MET A 882 " ideal model delta harmonic sigma weight residual -122.60 -104.40 -18.20 0 2.50e+00 1.60e-01 5.30e+01 dihedral pdb=" CA ASN A 475 " pdb=" C ASN A 475 " pdb=" N LYS A 476 " pdb=" CA LYS A 476 " ideal model delta harmonic sigma weight residual 180.00 -150.81 -29.19 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" C THR A 780 " pdb=" N THR A 780 " pdb=" CA THR A 780 " pdb=" CB THR A 780 " ideal model delta harmonic sigma weight residual -122.00 -108.98 -13.02 0 2.50e+00 1.60e-01 2.71e+01 ... (remaining 3814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 935 0.163 - 0.325: 17 0.325 - 0.488: 2 0.488 - 0.651: 1 0.651 - 0.813: 1 Chirality restraints: 956 Sorted by residual: chirality pdb=" CA LYS A 782 " pdb=" N LYS A 782 " pdb=" C LYS A 782 " pdb=" CB LYS A 782 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.81 2.00e-01 2.50e+01 1.65e+01 chirality pdb=" CA LYS A 476 " pdb=" N LYS A 476 " pdb=" C LYS A 476 " pdb=" CB LYS A 476 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.39e+00 chirality pdb=" CA GLN A 317 " pdb=" N GLN A 317 " pdb=" C GLN A 317 " pdb=" CB GLN A 317 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 ... (remaining 953 not shown) Planarity restraints: 957 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 475 " -0.068 2.00e-02 2.50e+03 1.14e-01 1.30e+02 pdb=" C ASN A 475 " 0.197 2.00e-02 2.50e+03 pdb=" O ASN A 475 " -0.071 2.00e-02 2.50e+03 pdb=" N LYS A 476 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 476 " -0.045 2.00e-02 2.50e+03 9.90e-02 9.80e+01 pdb=" C LYS A 476 " 0.170 2.00e-02 2.50e+03 pdb=" O LYS A 476 " -0.074 2.00e-02 2.50e+03 pdb=" N PRO A 477 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 313 " 0.034 2.00e-02 2.50e+03 6.83e-02 4.66e+01 pdb=" C MET A 313 " -0.118 2.00e-02 2.50e+03 pdb=" O MET A 313 " 0.044 2.00e-02 2.50e+03 pdb=" N GLU A 314 " 0.040 2.00e-02 2.50e+03 ... (remaining 954 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 35 2.46 - 3.07: 3524 3.07 - 3.68: 9449 3.68 - 4.29: 14666 4.29 - 4.90: 22944 Nonbonded interactions: 50618 Sorted by model distance: nonbonded pdb=" O LEU A 471 " pdb=" CB LYS A 476 " model vdw 1.853 3.440 nonbonded pdb=" O3G ANP A1101 " pdb="MG MG A1102 " model vdw 2.091 2.170 nonbonded pdb=" O GLU A 474 " pdb=" CG LYS A 476 " model vdw 2.213 3.440 nonbonded pdb=" OE1 GLN A 562 " pdb=" OH TYR A 578 " model vdw 2.283 3.040 nonbonded pdb=" O2B ANP A1101 " pdb=" O3G ANP A1101 " model vdw 2.294 3.040 ... (remaining 50613 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: 8.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.900 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4446 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 : 0.010 0.167 6097 Z= 0.680 Angle : 1.304 22.002 8332 Z= 0.860 Chirality : 0.071 0.813 956 Planarity : 0.008 0.114 957 Dihedral : 16.680 132.389 2544 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.17 % Allowed : 1.18 % Favored : 98.65 % Cbeta Deviations : 1.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.30), residues: 656 helix: -0.66 (0.27), residues: 328 sheet: -0.62 (0.49), residues: 99 loop : -1.67 (0.35), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 595 TYR 0.013 0.002 TYR A 623 PHE 0.010 0.002 PHE A 680 TRP 0.006 0.001 TRP A1003 HIS 0.005 0.001 HIS A 625 Details of bonding type rmsd/Z covalent geometry : bond 0.01003 / 0.68 ( 6096) covalent geometry : angle 1.30435 / 0.86 ( 8330) SS BOND : bond 0.00458 / 0.22 ( 1) SS BOND : angle 1.16643 / 0.56 ( 2) hydrogen bonds : bond 0.18772 / 12.17 ( 306) hydrogen bonds : angle 6.65821 / 4.77 ( 863) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 321 GLU cc_start: 0.4504 (mt-10) cc_final: 0.4282 (mm-30) REVERT: A 383 LYS cc_start: 0.5402 (tttm) cc_final: 0.4653 (mptt) REVERT: A 523 GLU cc_start: 0.4136 (tt0) cc_final: 0.3651 (tm-30) REVERT: A 682 GLU cc_start: 0.4359 (mm-30) cc_final: 0.3996 (pt0) REVERT: A 709 MET cc_start: 0.4695 (mmm) cc_final: 0.4432 (mmm) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.6514 time to fit residues: 94.0328 Evaluate side-chains 102 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 27] chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN A 614 ASN A 769 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.170533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.149870 restraints weight = 5855.301| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.26 r_work: 0.3538 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6097 Z= 0.168 Angle : 0.602 7.689 8332 Z= 0.332 Chirality : 0.044 0.217 956 Planarity : 0.004 0.037 957 Dihedral : 16.295 149.080 1146 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.53 % Allowed : 11.32 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.31), residues: 656 helix: 0.19 (0.28), residues: 339 sheet: -0.73 (0.54), residues: 87 loop : -1.25 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 824 TYR 0.014 0.002 TYR A 623 PHE 0.017 0.002 PHE A 516 TRP 0.005 0.001 TRP A1003 HIS 0.005 0.001 HIS A 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 ( 6096) covalent geometry : angle 0.60177 / 0.33 ( 8330) SS BOND : bond 0.00470 / 0.22 ( 1) SS BOND : angle 1.42631 / 0.73 ( 2) hydrogen bonds : bond 0.05272 / 3.50 ( 306) hydrogen bonds : angle 4.66059 / 3.26 ( 863) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 352 LYS cc_start: 0.8213 (mttt) cc_final: 0.7703 (mppt) REVERT: A 383 LYS cc_start: 0.8150 (tttm) cc_final: 0.7693 (mptt) REVERT: A 508 LYS cc_start: 0.8306 (mtmt) cc_final: 0.8012 (mttm) REVERT: A 523 GLU cc_start: 0.6482 (tt0) cc_final: 0.6084 (tm-30) REVERT: A 709 MET cc_start: 0.8304 (mmm) cc_final: 0.8077 (tpp) REVERT: A 785 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7237 (tp) REVERT: A 881 ILE cc_start: 0.7183 (OUTLIER) cc_final: 0.6766 (mp) REVERT: A 925 LYS cc_start: 0.8700 (mtmm) cc_final: 0.8425 (mtpt) REVERT: A 931 MET cc_start: 0.7200 (mtm) cc_final: 0.6965 (mmm) outliers start: 15 outliers final: 3 residues processed: 110 average time/residue: 0.6609 time to fit residues: 75.5158 Evaluate side-chains 99 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 881 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: [54, 51, 7, 39, 22, 21, 41, 15, 64, 57, 20] chunk 54 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 0.0970 chunk 39 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 371 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 = 0.3854 r_free = 0.3854 target = 0.172352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.151640 restraints weight = 5822.511| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.26 r_work: 0.3513 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6097 Z= 0.163 Angle : 0.554 7.159 8332 Z= 0.302 Chirality : 0.043 0.184 956 Planarity : 0.004 0.037 957 Dihedral : 16.255 154.016 1146 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.04 % Allowed : 12.50 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.32), residues: 656 helix: 0.61 (0.29), residues: 332 sheet: -0.93 (0.51), residues: 89 loop : -1.15 (0.38), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 595 TYR 0.016 0.002 TYR A 623 PHE 0.017 0.001 PHE A 516 TRP 0.007 0.001 TRP A1003 HIS 0.005 0.001 HIS A 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 6096) covalent geometry : angle 0.55327 / 0.30 ( 8330) SS BOND : bond 0.00450 / 0.21 ( 1) SS BOND : angle 1.41258 / 0.72 ( 2) hydrogen bonds : bond 0.04679 / 3.07 ( 306) hydrogen bonds : angle 4.29122 / 3.03 ( 863) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 352 LYS cc_start: 0.8219 (mttt) cc_final: 0.7728 (mppt) REVERT: A 508 LYS cc_start: 0.8262 (mtmt) cc_final: 0.7959 (mttm) REVERT: A 523 GLU cc_start: 0.6459 (tt0) cc_final: 0.5912 (tm-30) REVERT: A 709 MET cc_start: 0.8263 (mmm) cc_final: 0.8058 (tpp) REVERT: A 785 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7077 (tp) REVERT: A 992 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6591 (mttp) REVERT: A 998 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7895 (mmmt) outliers start: 18 outliers final: 7 residues processed: 108 average time/residue: 0.6369 time to fit residues: 71.4641 Evaluate side-chains 101 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 992 LYS Chi-restraints excluded: chain A residue 998 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: [24, 29, 57, 53, 14, 0, 65, 16, 21, 12, 23] chunk 24 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 0.0040 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 GLN ** A 371 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 = 0.3847 r_free = 0.3847 target = 0.171447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.150805 restraints weight = 5918.524| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.27 r_work: 0.3512 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6097 Z= 0.146 Angle : 0.520 6.770 8332 Z= 0.285 Chirality : 0.042 0.178 956 Planarity : 0.004 0.036 957 Dihedral : 16.273 158.680 1146 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.87 % Allowed : 14.36 % Favored : 82.77 % 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 are not related in a simple way. whole: -0.23 (0.32), residues: 656 helix: 0.73 (0.29), residues: 340 sheet: -0.96 (0.51), residues: 89 loop : -1.03 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 720 TYR 0.014 0.001 TYR A 623 PHE 0.013 0.001 PHE A 516 TRP 0.006 0.001 TRP A1003 HIS 0.005 0.001 HIS A 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 6096) covalent geometry : angle 0.51990 / 0.28 ( 8330) SS BOND : bond 0.00423 / 0.20 ( 1) SS BOND : angle 1.19238 / 0.62 ( 2) hydrogen bonds : bond 0.04379 / 2.89 ( 306) hydrogen bonds : angle 4.16932 / 2.94 ( 863) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 352 LYS cc_start: 0.8183 (mttt) cc_final: 0.7746 (mppt) REVERT: A 508 LYS cc_start: 0.8267 (mtmt) cc_final: 0.8021 (ttmm) REVERT: A 523 GLU cc_start: 0.6477 (tt0) cc_final: 0.5872 (tm-30) REVERT: A 677 MET cc_start: 0.8175 (mmm) cc_final: 0.7971 (tpp) REVERT: A 705 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7747 (ttp80) REVERT: A 709 MET cc_start: 0.8298 (mmm) cc_final: 0.8097 (tpp) REVERT: A 785 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7036 (tp) REVERT: A 992 LYS cc_start: 0.7041 (OUTLIER) cc_final: 0.6546 (mttp) REVERT: A 998 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7894 (mmmt) outliers start: 17 outliers final: 8 residues processed: 104 average time/residue: 0.6321 time to fit residues: 68.4641 Evaluate side-chains 101 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 992 LYS Chi-restraints excluded: chain A residue 998 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: [28, 7, 15, 3, 44, 19, 46, 37, 49, 58, 57] chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 0.0270 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 GLN ** A 371 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 = 0.3820 r_free = 0.3820 target = 0.168871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.147648 restraints weight = 5967.764| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.32 r_work: 0.3511 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6097 Z= 0.143 Angle : 0.507 6.577 8332 Z= 0.278 Chirality : 0.042 0.176 956 Planarity : 0.004 0.037 957 Dihedral : 16.280 162.309 1146 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.55 % Allowed : 14.53 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.33), residues: 656 helix: 0.99 (0.29), residues: 332 sheet: -1.08 (0.51), residues: 89 loop : -1.01 (0.38), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 595 TYR 0.014 0.001 TYR A 623 PHE 0.021 0.001 PHE A 516 TRP 0.006 0.001 TRP A1003 HIS 0.005 0.001 HIS A 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 6096) covalent geometry : angle 0.50647 / 0.28 ( 8330) SS BOND : bond 0.00387 / 0.18 ( 1) SS BOND : angle 1.16001 / 0.60 ( 2) hydrogen bonds : bond 0.04248 / 2.79 ( 306) hydrogen bonds : angle 4.09085 / 2.89 ( 863) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 352 LYS cc_start: 0.8150 (mttt) cc_final: 0.7694 (mppt) REVERT: A 508 LYS cc_start: 0.8258 (mtmt) cc_final: 0.8000 (ttmm) REVERT: A 523 GLU cc_start: 0.6505 (tt0) cc_final: 0.5896 (tm-30) REVERT: A 705 ARG cc_start: 0.7949 (ttp80) cc_final: 0.7673 (ttp80) REVERT: A 785 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7018 (tp) REVERT: A 992 LYS cc_start: 0.6985 (OUTLIER) cc_final: 0.6480 (mttp) REVERT: A 998 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7887 (mmmt) outliers start: 21 outliers final: 11 residues processed: 109 average time/residue: 0.6611 time to fit residues: 74.8153 Evaluate side-chains 107 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 784 ASN Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 992 LYS Chi-restraints excluded: chain A residue 998 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: [8, 53, 11, 57, 14, 43, 62, 58, 41, 50, 22] chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 GLN ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.170366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.149230 restraints weight = 5956.135| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.32 r_work: 0.3500 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6097 Z= 0.158 Angle : 0.525 6.551 8332 Z= 0.286 Chirality : 0.042 0.179 956 Planarity : 0.004 0.036 957 Dihedral : 16.311 165.593 1146 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.55 % Allowed : 15.20 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.33), residues: 656 helix: 1.00 (0.29), residues: 332 sheet: -1.03 (0.51), residues: 88 loop : -1.04 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 546 TYR 0.015 0.002 TYR A 623 PHE 0.018 0.001 PHE A 516 TRP 0.007 0.001 TRP A1003 HIS 0.005 0.001 HIS A 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 6096) covalent geometry : angle 0.52506 / 0.29 ( 8330) SS BOND : bond 0.00448 / 0.21 ( 1) SS BOND : angle 1.29537 / 0.67 ( 2) hydrogen bonds : bond 0.04363 / 2.87 ( 306) hydrogen bonds : angle 4.10490 / 2.90 ( 863) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 352 LYS cc_start: 0.8169 (mttt) cc_final: 0.7699 (mppt) REVERT: A 433 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7902 (mp-120) REVERT: A 508 LYS cc_start: 0.8264 (mtmt) cc_final: 0.8007 (ttmm) REVERT: A 523 GLU cc_start: 0.6541 (tt0) cc_final: 0.5897 (tm-30) REVERT: A 710 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6508 (mm-30) REVERT: A 785 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7019 (tp) REVERT: A 992 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6490 (mttp) REVERT: A 998 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7899 (mmmt) outliers start: 21 outliers final: 10 residues processed: 107 average time/residue: 0.6537 time to fit residues: 72.6942 Evaluate side-chains 105 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 992 LYS Chi-restraints excluded: chain A residue 998 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: [15, 0, 32, 14, 42, 11, 19, 45, 24, 51, 53] chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 32 optimal weight: 0.0670 chunk 14 optimal weight: 0.9990 chunk 42 optimal weight: 0.0370 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 GLN A 711 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.172174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.152062 restraints weight = 5869.467| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.23 r_work: 0.3507 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6097 Z= 0.129 Angle : 0.498 6.320 8332 Z= 0.273 Chirality : 0.041 0.172 956 Planarity : 0.003 0.033 957 Dihedral : 16.258 167.738 1146 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.04 % Allowed : 16.05 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.33), residues: 656 helix: 1.12 (0.30), residues: 332 sheet: -1.02 (0.50), residues: 90 loop : -0.99 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 850 TYR 0.013 0.001 TYR A 623 PHE 0.018 0.001 PHE A 516 TRP 0.004 0.001 TRP A1003 HIS 0.004 0.001 HIS A 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 6096) covalent geometry : angle 0.49772 / 0.27 ( 8330) SS BOND : bond 0.00383 / 0.18 ( 1) SS BOND : angle 1.11228 / 0.58 ( 2) hydrogen bonds : bond 0.04058 / 2.69 ( 306) hydrogen bonds : angle 4.04630 / 2.86 ( 863) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 352 LYS cc_start: 0.8184 (mttt) cc_final: 0.7747 (mppt) REVERT: A 433 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7862 (mp-120) REVERT: A 508 LYS cc_start: 0.8247 (mtmt) cc_final: 0.7988 (ttmm) REVERT: A 523 GLU cc_start: 0.6557 (tt0) cc_final: 0.5891 (tm-30) REVERT: A 710 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6837 (tm-30) REVERT: A 769 ASN cc_start: 0.8261 (m110) cc_final: 0.7302 (t0) REVERT: A 785 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6942 (tp) REVERT: A 925 LYS cc_start: 0.8694 (mtmm) cc_final: 0.8425 (mtpt) REVERT: A 998 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7907 (mmmt) outliers start: 18 outliers final: 9 residues processed: 104 average time/residue: 0.6516 time to fit residues: 70.4882 Evaluate side-chains 103 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 784 ASN Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 998 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: [45, 67, 56, 22, 58, 61, 29, 1, 6, 54, 2] chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 GLN ** A 711 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 = 0.3846 r_free = 0.3846 target = 0.170475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.150199 restraints weight = 5953.105| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.25 r_work: 0.3489 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6097 Z= 0.161 Angle : 0.529 6.457 8332 Z= 0.287 Chirality : 0.042 0.177 956 Planarity : 0.004 0.036 957 Dihedral : 16.290 168.302 1146 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.53 % Allowed : 17.06 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.33), residues: 656 helix: 1.06 (0.29), residues: 331 sheet: -1.05 (0.51), residues: 88 loop : -1.01 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 595 TYR 0.015 0.002 TYR A 623 PHE 0.015 0.001 PHE A 516 TRP 0.007 0.001 TRP A1003 HIS 0.005 0.001 HIS A 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 6096) covalent geometry : angle 0.52842 / 0.29 ( 8330) SS BOND : bond 0.00403 / 0.19 ( 1) SS BOND : angle 1.25114 / 0.64 ( 2) hydrogen bonds : bond 0.04347 / 2.86 ( 306) hydrogen bonds : angle 4.08014 / 2.89 ( 863) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 352 LYS cc_start: 0.8200 (mttt) cc_final: 0.7746 (mppt) REVERT: A 433 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7909 (mp-120) REVERT: A 508 LYS cc_start: 0.8264 (mtmt) cc_final: 0.8002 (ttmm) REVERT: A 523 GLU cc_start: 0.6563 (tt0) cc_final: 0.5897 (tm-30) REVERT: A 710 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6871 (tm-30) REVERT: A 785 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7028 (tp) REVERT: A 925 LYS cc_start: 0.8708 (mtmm) cc_final: 0.8442 (mtpt) REVERT: A 998 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7931 (mmmt) outliers start: 15 outliers final: 9 residues processed: 95 average time/residue: 0.6696 time to fit residues: 66.1570 Evaluate side-chains 100 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 784 ASN Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 998 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: [6, 23, 25, 48, 38, 66, 30, 49, 57, 39, 32] chunk 6 optimal weight: 0.7980 chunk 23 optimal weight: 0.1980 chunk 25 optimal weight: 0.0670 chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.0980 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 GLN A 711 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.173279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.153175 restraints weight = 5929.463| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.24 r_work: 0.3520 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6097 Z= 0.114 Angle : 0.481 6.313 8332 Z= 0.264 Chirality : 0.040 0.166 956 Planarity : 0.003 0.032 957 Dihedral : 16.200 169.872 1146 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.20 % Allowed : 17.57 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.33), residues: 656 helix: 1.28 (0.30), residues: 330 sheet: -1.09 (0.50), residues: 92 loop : -0.87 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 850 TYR 0.012 0.001 TYR A 623 PHE 0.017 0.001 PHE A 516 TRP 0.004 0.001 TRP A 737 HIS 0.003 0.001 HIS A 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 6096) covalent geometry : angle 0.48110 / 0.26 ( 8330) SS BOND : bond 0.00291 / 0.14 ( 1) SS BOND : angle 0.89064 / 0.47 ( 2) hydrogen bonds : bond 0.03892 / 2.58 ( 306) hydrogen bonds : angle 3.98320 / 2.81 ( 863) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 352 LYS cc_start: 0.8203 (mttt) cc_final: 0.7775 (mppt) REVERT: A 433 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7909 (mp-120) REVERT: A 508 LYS cc_start: 0.8259 (mtmt) cc_final: 0.8009 (ttmm) REVERT: A 523 GLU cc_start: 0.6507 (tt0) cc_final: 0.5921 (tm-30) REVERT: A 769 ASN cc_start: 0.8243 (m110) cc_final: 0.7303 (t0) REVERT: A 785 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6849 (tp) REVERT: A 925 LYS cc_start: 0.8696 (mtmm) cc_final: 0.8457 (mtpt) REVERT: A 998 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7916 (mmmt) outliers start: 13 outliers final: 6 residues processed: 104 average time/residue: 0.6359 time to fit residues: 68.8383 Evaluate side-chains 97 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 998 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: [39, 21, 34, 57, 43, 25, 64, 49, 8, 55, 6] chunk 39 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 25 optimal weight: 0.0030 chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 0.0970 chunk 8 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 GLN ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 GLN A 784 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.173083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.153082 restraints weight = 5939.461| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.24 r_work: 0.3518 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6097 Z= 0.120 Angle : 0.493 6.263 8332 Z= 0.269 Chirality : 0.040 0.167 956 Planarity : 0.003 0.033 957 Dihedral : 16.173 169.709 1146 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.69 % Allowed : 18.58 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.33), residues: 656 helix: 1.31 (0.29), residues: 330 sheet: -1.06 (0.50), residues: 92 loop : -0.81 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 714 TYR 0.012 0.001 TYR A 623 PHE 0.030 0.001 PHE A 516 TRP 0.005 0.001 TRP A 737 HIS 0.004 0.001 HIS A 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 6096) covalent geometry : angle 0.49333 / 0.27 ( 8330) SS BOND : bond 0.00249 / 0.12 ( 1) SS BOND : angle 0.89514 / 0.47 ( 2) hydrogen bonds : bond 0.03918 / 2.58 ( 306) hydrogen bonds : angle 3.95292 / 2.79 ( 863) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 352 LYS cc_start: 0.8199 (mttt) cc_final: 0.7771 (mppt) REVERT: A 508 LYS cc_start: 0.8263 (mtmt) cc_final: 0.8005 (ttmm) REVERT: A 523 GLU cc_start: 0.6535 (tt0) cc_final: 0.5865 (tm-30) REVERT: A 710 GLU cc_start: 0.7395 (tm-30) cc_final: 0.6714 (tm-30) REVERT: A 769 ASN cc_start: 0.8250 (m110) cc_final: 0.7299 (t0) REVERT: A 785 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6857 (tp) REVERT: A 912 VAL cc_start: 0.7521 (p) cc_final: 0.6931 (m) REVERT: A 925 LYS cc_start: 0.8695 (mtmm) cc_final: 0.8464 (mtpt) outliers start: 10 outliers final: 7 residues processed: 96 average time/residue: 0.6453 time to fit residues: 64.3878 Evaluate side-chains 98 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain A residue 784 ASN Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 836 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: [19, 34, 45, 46, 59, 52, 42, 64, 18, 8, 6] chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 chunk 45 optimal weight: 0.2980 chunk 46 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 42 optimal weight: 0.0470 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 GLN ** A 711 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 = 0.3873 r_free = 0.3873 target = 0.173060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.153001 restraints weight = 5921.144| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.24 r_work: 0.3518 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.237 6097 Z= 0.259 Angle : 1.015 59.200 8332 Z= 0.611 Chirality : 0.056 1.196 956 Planarity : 0.004 0.033 957 Dihedral : 16.183 169.719 1146 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.96 % Favored : 95.88 % Rotamer: Outliers : 1.35 % Allowed : 18.92 % Favored : 79.73 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.33), residues: 656 helix: 1.31 (0.29), residues: 330 sheet: -1.06 (0.50), residues: 92 loop : -0.86 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 714 TYR 0.012 0.001 TYR A 623 PHE 0.028 0.001 PHE A 516 TRP 0.005 0.001 TRP A 737 HIS 0.004 0.001 HIS A 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.26 ( 6096) covalent geometry : angle 1.01521 / 0.61 ( 8330) SS BOND : bond 0.00262 / 0.12 ( 1) SS BOND : angle 0.88893 / 0.47 ( 2) hydrogen bonds : bond 0.03915 / 2.58 ( 306) hydrogen bonds : angle 3.95230 / 2.79 ( 863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2475.48 seconds wall clock time: 42 minutes 53.67 seconds (2573.67 seconds total)