Starting phenix.real_space_refine on Wed Sep 25 20:40:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zak_6904/09_2024/5zak_6904.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zak_6904/09_2024/5zak_6904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zak_6904/09_2024/5zak_6904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zak_6904/09_2024/5zak_6904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zak_6904/09_2024/5zak_6904.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zak_6904/09_2024/5zak_6904.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 7087 2.51 5 N 1906 2.21 5 O 2053 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11112 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1314, 10552 Classifications: {'peptide': 1314} Link IDs: {'CIS': 21, 'PCIS': 4, 'PTRANS': 64, 'TRANS': 1224} Chain breaks: 8 Chain: "B" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 560 Classifications: {'peptide': 75} Link IDs: {'PCIS': 2, 'TRANS': 72} Time building chain proxies: 6.07, per 1000 atoms: 0.55 Number of scatterers: 11112 At special positions: 0 Unit cell: (109.749, 104.523, 162.011, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2053 8.00 N 1906 7.00 C 7087 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 199 " distance=2.02 Simple disulfide: pdb=" SG CYS A 443 " - pdb=" SG CYS A 531 " distance=2.03 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: 2.38 Conformation dependent library (CDL) restraints added in 1.3 seconds 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2666 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 8 sheets defined 47.9% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 69 through 85 removed outlier: 3.850A pdb=" N ILE A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 115 removed outlier: 4.526A pdb=" N THR A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 159 removed outlier: 3.651A pdb=" N LEU A 156 " --> pdb=" O CYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 185 through 194 Processing helix chain 'A' and resid 218 through 231 Processing helix chain 'A' and resid 264 through 285 removed outlier: 4.486A pdb=" N ASN A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 314 removed outlier: 4.314A pdb=" N SER A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 336 removed outlier: 3.821A pdb=" N ALA A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 359 Processing helix chain 'A' and resid 377 through 386 Processing helix chain 'A' and resid 451 through 461 removed outlier: 3.642A pdb=" N VAL A 455 " --> pdb=" O ARG A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 510 removed outlier: 3.585A pdb=" N GLN A 501 " --> pdb=" O GLU A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 516 removed outlier: 3.548A pdb=" N ASN A 514 " --> pdb=" O ALA A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 551 Processing helix chain 'A' and resid 570 through 590 removed outlier: 4.327A pdb=" N ASN A 588 " --> pdb=" O LYS A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 639 removed outlier: 3.723A pdb=" N TYR A 637 " --> pdb=" O HIS A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 704 Processing helix chain 'A' and resid 713 through 726 removed outlier: 4.340A pdb=" N LYS A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 798 removed outlier: 3.967A pdb=" N ASP A 797 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR A 798 " --> pdb=" O PRO A 795 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 794 through 798' Processing helix chain 'A' and resid 839 through 855 Processing helix chain 'A' and resid 894 through 903 removed outlier: 3.766A pdb=" N GLU A 898 " --> pdb=" O PHE A 894 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 903 " --> pdb=" O ASP A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 907 removed outlier: 4.091A pdb=" N ILE A 907 " --> pdb=" O GLU A 904 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 904 through 907' Processing helix chain 'A' and resid 923 through 927 Processing helix chain 'A' and resid 967 through 975 removed outlier: 3.943A pdb=" N TYR A 971 " --> pdb=" O THR A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1010 Processing helix chain 'A' and resid 1015 through 1031 removed outlier: 3.987A pdb=" N GLN A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1052 Processing helix chain 'A' and resid 1053 through 1072 removed outlier: 3.776A pdb=" N CYS A1063 " --> pdb=" O TYR A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1302 Processing helix chain 'A' and resid 1312 through 1333 removed outlier: 4.522A pdb=" N SER A1321 " --> pdb=" O MET A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1352 Processing helix chain 'A' and resid 1352 through 1362 removed outlier: 3.702A pdb=" N LYS A1362 " --> pdb=" O ARG A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1368 Proline residue: A1366 - end of helix No H-bonds generated for 'chain 'A' and resid 1363 through 1368' Processing helix chain 'A' and resid 1558 through 1574 Processing helix chain 'A' and resid 1575 through 1587 removed outlier: 4.730A pdb=" N ALA A1579 " --> pdb=" O GLY A1575 " (cutoff:3.500A) Processing helix chain 'A' and resid 1594 through 1599 Processing helix chain 'A' and resid 1656 through 1674 removed outlier: 3.873A pdb=" N GLY A1665 " --> pdb=" O HIS A1661 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A1667 " --> pdb=" O ILE A1663 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASN A1668 " --> pdb=" O SER A1664 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE A1669 " --> pdb=" O GLY A1665 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS A1672 " --> pdb=" O ASN A1668 " (cutoff:3.500A) Processing helix chain 'A' and resid 1679 through 1687 removed outlier: 4.092A pdb=" N LEU A1683 " --> pdb=" O ASN A1679 " (cutoff:3.500A) Processing helix chain 'A' and resid 1701 through 1722 removed outlier: 4.173A pdb=" N ALA A1710 " --> pdb=" O PHE A1706 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A1711 " --> pdb=" O LEU A1707 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP A1713 " --> pdb=" O ASP A1709 " (cutoff:3.500A) Processing helix chain 'A' and resid 1728 through 1739 Processing helix chain 'A' and resid 1741 through 1752 removed outlier: 3.825A pdb=" N PHE A1745 " --> pdb=" O ASN A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1762 through 1774 removed outlier: 3.566A pdb=" N PHE A1766 " --> pdb=" O SER A1762 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1823 removed outlier: 4.164A pdb=" N GLY A1809 " --> pdb=" O PRO A1805 " (cutoff:3.500A) Processing helix chain 'A' and resid 1826 through 1845 Proline residue: A1836 - end of helix Proline residue: A1840 - end of helix Processing helix chain 'A' and resid 1853 through 1858 Processing helix chain 'A' and resid 1896 through 1911 Processing helix chain 'B' and resid 293 through 305 removed outlier: 3.876A pdb=" N VAL B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 362 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 63 removed outlier: 8.656A pdb=" N LEU A 172 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 9.417A pdb=" N LEU A 205 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 97 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N PHE A 98 " --> pdb=" O MET A 150 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 250 through 251 removed outlier: 5.807A pdb=" N VAL A 534 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 474 through 475 removed outlier: 3.705A pdb=" N HIS A 482 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 829 through 836 removed outlier: 6.595A pdb=" N LEU A 770 " --> pdb=" O LYS A 832 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N SER A 834 " --> pdb=" O CYS A 768 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N CYS A 768 " --> pdb=" O SER A 834 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE A 802 " --> pdb=" O ILE A 773 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 776 through 780 removed outlier: 6.632A pdb=" N GLU A 824 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 990 through 992 removed outlier: 4.581A pdb=" N ALA A 930 " --> pdb=" O VAL A 947 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL A 931 " --> pdb=" O HIS A1041 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1882 through 1884 Processing sheet with id=AA8, first strand: chain 'B' and resid 324 through 328 465 hydrogen bonds defined for protein. 1368 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3053 1.33 - 1.46: 2476 1.46 - 1.58: 5712 1.58 - 1.70: 1 1.70 - 1.83: 90 Bond restraints: 11332 Sorted by residual: bond pdb=" N LYS A 862 " pdb=" CA LYS A 862 " ideal model delta sigma weight residual 1.455 1.486 -0.031 9.60e-03 1.09e+04 1.04e+01 bond pdb=" CA VAL A1804 " pdb=" C VAL A1804 " ideal model delta sigma weight residual 1.522 1.543 -0.021 7.10e-03 1.98e+04 8.97e+00 bond pdb=" N LYS A1589 " pdb=" CA LYS A1589 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.20e-02 6.94e+03 7.66e+00 bond pdb=" N LYS A 135 " pdb=" CA LYS A 135 " ideal model delta sigma weight residual 1.458 1.507 -0.049 1.90e-02 2.77e+03 6.67e+00 bond pdb=" C MET A 713 " pdb=" N PRO A 714 " ideal model delta sigma weight residual 1.336 1.368 -0.032 1.25e-02 6.40e+03 6.54e+00 ... (remaining 11327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 14621 3.40 - 6.80: 578 6.80 - 10.19: 92 10.19 - 13.59: 24 13.59 - 16.99: 8 Bond angle restraints: 15323 Sorted by residual: angle pdb=" C THR A 134 " pdb=" N LYS A 135 " pdb=" CA LYS A 135 " ideal model delta sigma weight residual 121.70 137.95 -16.25 1.80e+00 3.09e-01 8.15e+01 angle pdb=" C HIS A 116 " pdb=" N SER A 117 " pdb=" CA SER A 117 " ideal model delta sigma weight residual 121.70 136.76 -15.06 1.80e+00 3.09e-01 7.00e+01 angle pdb=" C LEU A 649 " pdb=" N ALA A 650 " pdb=" CA ALA A 650 " ideal model delta sigma weight residual 121.70 135.01 -13.31 1.80e+00 3.09e-01 5.47e+01 angle pdb=" C ARG A 137 " pdb=" N TRP A 138 " pdb=" CA TRP A 138 " ideal model delta sigma weight residual 121.70 134.41 -12.71 1.80e+00 3.09e-01 4.99e+01 angle pdb=" C GLU A1551 " pdb=" N GLN A1552 " pdb=" CA GLN A1552 " ideal model delta sigma weight residual 121.70 134.32 -12.62 1.80e+00 3.09e-01 4.92e+01 ... (remaining 15318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 6453 17.24 - 34.47: 460 34.47 - 51.71: 60 51.71 - 68.94: 2 68.94 - 86.18: 4 Dihedral angle restraints: 6979 sinusoidal: 2876 harmonic: 4103 Sorted by residual: dihedral pdb=" CA PRO A1376 " pdb=" C PRO A1376 " pdb=" N PRO A1377 " pdb=" CA PRO A1377 " ideal model delta harmonic sigma weight residual -180.00 -135.70 -44.30 0 5.00e+00 4.00e-02 7.85e+01 dihedral pdb=" CA ALA A 207 " pdb=" C ALA A 207 " pdb=" N SER A 208 " pdb=" CA SER A 208 " ideal model delta harmonic sigma weight residual -180.00 -139.53 -40.47 0 5.00e+00 4.00e-02 6.55e+01 dihedral pdb=" CA SER A 165 " pdb=" C SER A 165 " pdb=" N LEU A 166 " pdb=" CA LEU A 166 " ideal model delta harmonic sigma weight residual -180.00 -141.53 -38.47 0 5.00e+00 4.00e-02 5.92e+01 ... (remaining 6976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1201 0.068 - 0.136: 443 0.136 - 0.204: 80 0.204 - 0.272: 17 0.272 - 0.340: 6 Chirality restraints: 1747 Sorted by residual: chirality pdb=" CB ILE A 479 " pdb=" CA ILE A 479 " pdb=" CG1 ILE A 479 " pdb=" CG2 ILE A 479 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CG LEU A 865 " pdb=" CB LEU A 865 " pdb=" CD1 LEU A 865 " pdb=" CD2 LEU A 865 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CB ILE A 813 " pdb=" CA ILE A 813 " pdb=" CG1 ILE A 813 " pdb=" CG2 ILE A 813 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 1744 not shown) Planarity restraints: 1954 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 682 " -0.063 5.00e-02 4.00e+02 9.57e-02 1.47e+01 pdb=" N PRO A 683 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 683 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 683 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 637 " 0.036 2.00e-02 2.50e+03 2.57e-02 1.32e+01 pdb=" CG TYR A 637 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR A 637 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 637 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 637 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 637 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A 637 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 637 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A1664 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C SER A1664 " 0.056 2.00e-02 2.50e+03 pdb=" O SER A1664 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY A1665 " -0.019 2.00e-02 2.50e+03 ... (remaining 1951 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 933 2.73 - 3.27: 11569 3.27 - 3.81: 19692 3.81 - 4.36: 24072 4.36 - 4.90: 37002 Nonbonded interactions: 93268 Sorted by model distance: nonbonded pdb=" O LEU A1684 " pdb=" OG1 THR A1688 " model vdw 2.185 3.040 nonbonded pdb=" O VAL A 75 " pdb=" OG1 THR A 78 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR B 331 " pdb=" O PRO B 333 " model vdw 2.211 3.040 nonbonded pdb=" OD2 ASP A 283 " pdb=" OG SER B 318 " model vdw 2.226 3.040 nonbonded pdb=" O SER A1868 " pdb=" OH TYR A1897 " model vdw 2.238 3.040 ... (remaining 93263 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.210 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.870 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 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 : 0.009 0.095 11332 Z= 0.571 Angle : 1.607 16.991 15323 Z= 0.871 Chirality : 0.073 0.340 1747 Planarity : 0.010 0.096 1954 Dihedral : 11.718 86.176 4307 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.29 % Allowed : 17.31 % Favored : 82.40 % Rotamer: Outliers : 0.72 % Allowed : 3.22 % Favored : 96.05 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.60 % Twisted Proline : 2.86 % Twisted General : 0.84 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.20 (0.18), residues: 1369 helix: -3.01 (0.15), residues: 576 sheet: -3.81 (0.40), residues: 97 loop : -3.86 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.005 TRP A 133 HIS 0.021 0.004 HIS A 703 PHE 0.042 0.005 PHE A 537 TYR 0.061 0.005 TYR A 637 ARG 0.012 0.001 ARG A 640 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 266 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.7747 (tp) cc_final: 0.7479 (tp) REVERT: A 80 GLU cc_start: 0.8731 (tt0) cc_final: 0.8280 (tp30) REVERT: A 190 MET cc_start: 0.8634 (ttp) cc_final: 0.8380 (tmm) REVERT: A 218 GLU cc_start: 0.9131 (pt0) cc_final: 0.8917 (pt0) REVERT: A 224 GLN cc_start: 0.8815 (tt0) cc_final: 0.8379 (tm-30) REVERT: A 239 ASP cc_start: 0.5620 (m-30) cc_final: 0.5401 (m-30) REVERT: A 458 ASN cc_start: 0.6512 (t0) cc_final: 0.6217 (t0) REVERT: A 479 ILE cc_start: 0.3082 (OUTLIER) cc_final: 0.2733 (mp) REVERT: A 560 TYR cc_start: 0.7210 (t80) cc_final: 0.6672 (t80) REVERT: A 580 LYS cc_start: 0.9197 (ttpt) cc_final: 0.8941 (tppt) REVERT: A 697 ILE cc_start: 0.7652 (mt) cc_final: 0.6961 (mt) REVERT: A 1068 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7675 (tp30) REVERT: A 1313 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7694 (mm-30) REVERT: A 1327 ILE cc_start: 0.8175 (mm) cc_final: 0.7849 (pt) REVERT: A 1346 MET cc_start: 0.7857 (mmm) cc_final: 0.7622 (mmm) REVERT: A 1358 ARG cc_start: 0.7458 (mtt180) cc_final: 0.7180 (mtt-85) REVERT: A 1363 LYS cc_start: 0.8667 (mmtt) cc_final: 0.8433 (mmmt) REVERT: A 1564 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8658 (mt-10) REVERT: A 1576 GLU cc_start: 0.8692 (tt0) cc_final: 0.8414 (mm-30) REVERT: A 1687 PHE cc_start: 0.8364 (m-80) cc_final: 0.7820 (m-80) REVERT: A 1692 TYR cc_start: 0.7894 (t80) cc_final: 0.7443 (t80) REVERT: A 1705 GLU cc_start: 0.7121 (tt0) cc_final: 0.6528 (tt0) REVERT: A 1768 VAL cc_start: 0.7740 (t) cc_final: 0.7374 (p) REVERT: A 1772 PHE cc_start: 0.6296 (t80) cc_final: 0.5960 (t80) REVERT: A 1782 MET cc_start: 0.4860 (mmt) cc_final: 0.4396 (mpp) REVERT: A 1810 ASP cc_start: 0.6632 (m-30) cc_final: 0.6152 (t0) REVERT: A 1813 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6638 (mm-30) REVERT: A 1825 MET cc_start: 0.7483 (mtt) cc_final: 0.7110 (mtm) REVERT: B 353 ARG cc_start: 0.8378 (ttp80) cc_final: 0.8112 (ttp80) outliers start: 9 outliers final: 1 residues processed: 273 average time/residue: 0.3119 time to fit residues: 111.5289 Evaluate side-chains 156 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 58 optimal weight: 0.1980 chunk 35 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 0.0980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 GLN A1029 ASN ** A1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1041 HIS A1305 ASN ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1661 HIS A1774 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11332 Z= 0.223 Angle : 0.945 12.192 15323 Z= 0.490 Chirality : 0.051 0.320 1747 Planarity : 0.007 0.082 1954 Dihedral : 8.096 33.621 1519 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 22.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.61 % Favored : 85.39 % Rotamer: Outliers : 0.16 % Allowed : 3.14 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.60 % Twisted Proline : 1.43 % Twisted General : 0.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.20), residues: 1369 helix: -1.89 (0.18), residues: 612 sheet: -3.24 (0.40), residues: 126 loop : -3.69 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 316 HIS 0.006 0.001 HIS A1661 PHE 0.020 0.002 PHE A1322 TYR 0.019 0.002 TYR A 972 ARG 0.006 0.001 ARG A 821 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 227 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.8628 (tt0) cc_final: 0.8050 (tp30) REVERT: A 133 TRP cc_start: 0.7177 (p90) cc_final: 0.6847 (p-90) REVERT: A 190 MET cc_start: 0.8486 (ttp) cc_final: 0.8217 (tmm) REVERT: A 224 GLN cc_start: 0.8798 (tt0) cc_final: 0.8338 (tm-30) REVERT: A 239 ASP cc_start: 0.4894 (m-30) cc_final: 0.4501 (m-30) REVERT: A 245 ARG cc_start: 0.6847 (mtp-110) cc_final: 0.6016 (tmt170) REVERT: A 351 PHE cc_start: 0.9126 (t80) cc_final: 0.8897 (t80) REVERT: A 378 ILE cc_start: 0.8508 (mm) cc_final: 0.8263 (mm) REVERT: A 462 LYS cc_start: 0.7725 (mttt) cc_final: 0.7495 (mtmt) REVERT: A 544 ARG cc_start: 0.7065 (ttp-110) cc_final: 0.5528 (tpp-160) REVERT: A 560 TYR cc_start: 0.6965 (t80) cc_final: 0.5836 (t80) REVERT: A 793 TYR cc_start: 0.8033 (m-80) cc_final: 0.7756 (m-80) REVERT: A 854 PHE cc_start: 0.9104 (m-10) cc_final: 0.8899 (m-10) REVERT: A 1068 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7859 (tp30) REVERT: A 1314 ARG cc_start: 0.6298 (mmm-85) cc_final: 0.6089 (mmm160) REVERT: A 1317 MET cc_start: 0.8172 (tpp) cc_final: 0.7944 (mtm) REVERT: A 1346 MET cc_start: 0.7688 (mmm) cc_final: 0.7403 (mmm) REVERT: A 1564 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8445 (mt-10) REVERT: A 1668 ASN cc_start: 0.8078 (t0) cc_final: 0.7320 (t0) REVERT: A 1682 TYR cc_start: 0.8333 (m-10) cc_final: 0.8130 (m-10) REVERT: A 1685 GLN cc_start: 0.8878 (tt0) cc_final: 0.8506 (tm-30) REVERT: A 1692 TYR cc_start: 0.7833 (t80) cc_final: 0.7473 (t80) REVERT: A 1748 LEU cc_start: 0.8839 (mm) cc_final: 0.8466 (tp) REVERT: A 1768 VAL cc_start: 0.7718 (t) cc_final: 0.7217 (p) REVERT: A 1772 PHE cc_start: 0.6237 (t80) cc_final: 0.5947 (t80) REVERT: A 1813 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6537 (mm-30) REVERT: A 1837 MET cc_start: 0.6462 (mtt) cc_final: 0.4757 (mtt) REVERT: B 311 TYR cc_start: 0.7752 (m-80) cc_final: 0.7343 (m-80) outliers start: 2 outliers final: 0 residues processed: 227 average time/residue: 0.3068 time to fit residues: 92.2093 Evaluate side-chains 156 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 0.0980 chunk 104 optimal weight: 0.0470 chunk 85 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 125 optimal weight: 0.0980 chunk 135 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.4480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 HIS ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN A1614 GLN ** A1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1702 GLN A1726 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11332 Z= 0.211 Angle : 0.890 12.396 15323 Z= 0.460 Chirality : 0.049 0.241 1747 Planarity : 0.006 0.085 1954 Dihedral : 7.259 32.547 1519 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.61 % Favored : 85.39 % Rotamer: Outliers : 0.08 % Allowed : 5.48 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.60 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.21), residues: 1369 helix: -1.14 (0.19), residues: 623 sheet: -2.96 (0.46), residues: 113 loop : -3.50 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 138 HIS 0.004 0.001 HIS A 703 PHE 0.018 0.002 PHE B 307 TYR 0.015 0.002 TYR A 267 ARG 0.006 0.001 ARG A 656 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 224 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9259 (mm) cc_final: 0.8901 (mm) REVERT: A 80 GLU cc_start: 0.8694 (tt0) cc_final: 0.7901 (pt0) REVERT: A 218 GLU cc_start: 0.9163 (pt0) cc_final: 0.8794 (pm20) REVERT: A 224 GLN cc_start: 0.8763 (tt0) cc_final: 0.8316 (tm-30) REVERT: A 239 ASP cc_start: 0.5479 (m-30) cc_final: 0.4981 (m-30) REVERT: A 245 ARG cc_start: 0.6950 (mtp-110) cc_final: 0.6070 (tmt170) REVERT: A 263 ARG cc_start: 0.4983 (tpt90) cc_final: 0.4644 (mtp180) REVERT: A 333 ILE cc_start: 0.6983 (mm) cc_final: 0.6690 (mm) REVERT: A 335 HIS cc_start: 0.8368 (t-90) cc_final: 0.7700 (m170) REVERT: A 506 ARG cc_start: 0.8294 (ttt180) cc_final: 0.7902 (mmt180) REVERT: A 544 ARG cc_start: 0.7041 (ttp-110) cc_final: 0.5674 (tpp-160) REVERT: A 560 TYR cc_start: 0.6352 (t80) cc_final: 0.5762 (t80) REVERT: A 562 MET cc_start: 0.7402 (tpt) cc_final: 0.7196 (tpt) REVERT: A 697 ILE cc_start: 0.7122 (mt) cc_final: 0.6597 (mt) REVERT: A 701 LYS cc_start: 0.7709 (mmtm) cc_final: 0.7382 (mmtm) REVERT: A 793 TYR cc_start: 0.8093 (m-80) cc_final: 0.7820 (m-80) REVERT: A 965 TYR cc_start: 0.8986 (m-80) cc_final: 0.8612 (m-80) REVERT: A 996 ARG cc_start: 0.6169 (ptt180) cc_final: 0.5633 (ptt180) REVERT: A 998 ASN cc_start: 0.8814 (t0) cc_final: 0.8388 (p0) REVERT: A 1313 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7449 (mm-30) REVERT: A 1358 ARG cc_start: 0.7216 (mtt180) cc_final: 0.6654 (mtt-85) REVERT: A 1564 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8376 (mt-10) REVERT: A 1664 SER cc_start: 0.7566 (t) cc_final: 0.7343 (p) REVERT: A 1668 ASN cc_start: 0.8183 (t0) cc_final: 0.7364 (t0) REVERT: A 1685 GLN cc_start: 0.8890 (tt0) cc_final: 0.8637 (tm-30) REVERT: A 1748 LEU cc_start: 0.8895 (mm) cc_final: 0.8556 (tp) REVERT: A 1765 LEU cc_start: 0.4895 (pp) cc_final: 0.4647 (pp) REVERT: A 1768 VAL cc_start: 0.7611 (t) cc_final: 0.7304 (p) REVERT: A 1808 MET cc_start: 0.6013 (mmt) cc_final: 0.5662 (mmm) REVERT: A 1837 MET cc_start: 0.6663 (mtt) cc_final: 0.5376 (mtt) REVERT: A 1890 PHE cc_start: 0.7495 (m-80) cc_final: 0.7173 (m-80) REVERT: B 311 TYR cc_start: 0.7876 (m-80) cc_final: 0.7317 (m-80) REVERT: B 348 ARG cc_start: 0.8875 (mtt180) cc_final: 0.8540 (tpt90) outliers start: 1 outliers final: 1 residues processed: 225 average time/residue: 0.3007 time to fit residues: 89.8474 Evaluate side-chains 153 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 133 optimal weight: 0.1980 chunk 119 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 ASN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN A 633 HIS A 943 HIS A1325 HIS ** A1339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1660 ASN ** A1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1767 HIS A1774 GLN B 338 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11332 Z= 0.228 Angle : 0.907 12.180 15323 Z= 0.466 Chirality : 0.050 0.296 1747 Planarity : 0.006 0.083 1954 Dihedral : 7.215 30.922 1519 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.68 % Favored : 85.32 % Rotamer: Outliers : 0.16 % Allowed : 3.22 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.60 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.22), residues: 1369 helix: -0.88 (0.20), residues: 627 sheet: -2.92 (0.47), residues: 109 loop : -3.36 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 138 HIS 0.005 0.001 HIS A 703 PHE 0.019 0.002 PHE A1812 TYR 0.019 0.002 TYR A1692 ARG 0.005 0.000 ARG A 536 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 199 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9316 (tt) cc_final: 0.9114 (tt) REVERT: A 64 LEU cc_start: 0.7452 (tp) cc_final: 0.7076 (tp) REVERT: A 79 LYS cc_start: 0.9350 (mtmm) cc_final: 0.9077 (mtmm) REVERT: A 80 GLU cc_start: 0.8637 (tt0) cc_final: 0.8114 (tp30) REVERT: A 218 GLU cc_start: 0.9086 (pt0) cc_final: 0.8766 (pm20) REVERT: A 224 GLN cc_start: 0.8752 (tt0) cc_final: 0.8305 (tm-30) REVERT: A 335 HIS cc_start: 0.8276 (t-90) cc_final: 0.7695 (m170) REVERT: A 458 ASN cc_start: 0.6387 (t0) cc_final: 0.6042 (t0) REVERT: A 506 ARG cc_start: 0.8248 (ttt180) cc_final: 0.7829 (mmt180) REVERT: A 560 TYR cc_start: 0.6862 (t80) cc_final: 0.5770 (t80) REVERT: A 697 ILE cc_start: 0.7419 (mt) cc_final: 0.6897 (mt) REVERT: A 793 TYR cc_start: 0.8157 (m-80) cc_final: 0.7878 (m-80) REVERT: A 965 TYR cc_start: 0.9012 (m-80) cc_final: 0.8590 (m-80) REVERT: A 1311 ASN cc_start: 0.7759 (p0) cc_final: 0.7510 (p0) REVERT: A 1313 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7530 (mm-30) REVERT: A 1564 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8467 (mt-10) REVERT: A 1668 ASN cc_start: 0.8023 (t0) cc_final: 0.7436 (t0) REVERT: A 1682 TYR cc_start: 0.8421 (m-10) cc_final: 0.8158 (m-10) REVERT: A 1692 TYR cc_start: 0.7956 (t80) cc_final: 0.7462 (t80) REVERT: A 1837 MET cc_start: 0.7011 (mtt) cc_final: 0.5976 (mtt) REVERT: B 338 HIS cc_start: 0.5048 (OUTLIER) cc_final: 0.4440 (p90) outliers start: 2 outliers final: 1 residues processed: 201 average time/residue: 0.2868 time to fit residues: 77.5451 Evaluate side-chains 147 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 145 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 7.9990 chunk 1 optimal weight: 0.0570 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 overall best weight: 2.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 HIS ** A1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1726 GLN A1767 HIS B 338 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11332 Z= 0.265 Angle : 0.945 13.939 15323 Z= 0.483 Chirality : 0.051 0.218 1747 Planarity : 0.007 0.091 1954 Dihedral : 7.286 30.688 1519 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 25.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.92 % Favored : 84.08 % Rotamer: Outliers : 0.08 % Allowed : 3.86 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.60 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.21), residues: 1369 helix: -0.85 (0.19), residues: 625 sheet: -2.78 (0.44), residues: 117 loop : -3.55 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 133 HIS 0.008 0.001 HIS A1727 PHE 0.037 0.002 PHE A1669 TYR 0.018 0.002 TYR A1059 ARG 0.005 0.001 ARG A 640 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 191 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.9320 (mtmm) cc_final: 0.9104 (mtmm) REVERT: A 80 GLU cc_start: 0.8661 (tt0) cc_final: 0.8240 (tp30) REVERT: A 224 GLN cc_start: 0.8756 (tt0) cc_final: 0.8335 (tm-30) REVERT: A 239 ASP cc_start: 0.5963 (m-30) cc_final: 0.5670 (m-30) REVERT: A 335 HIS cc_start: 0.8299 (t-90) cc_final: 0.7683 (m170) REVERT: A 349 ASP cc_start: 0.5113 (t70) cc_final: 0.4889 (t0) REVERT: A 458 ASN cc_start: 0.6571 (t0) cc_final: 0.6224 (t0) REVERT: A 506 ARG cc_start: 0.8268 (ttt180) cc_final: 0.7899 (mmt180) REVERT: A 544 ARG cc_start: 0.7075 (ttp-110) cc_final: 0.5701 (tpt90) REVERT: A 793 TYR cc_start: 0.8317 (m-80) cc_final: 0.8087 (m-80) REVERT: A 965 TYR cc_start: 0.8998 (m-80) cc_final: 0.8567 (m-80) REVERT: A 1062 HIS cc_start: 0.8847 (p-80) cc_final: 0.8569 (t70) REVERT: A 1315 LEU cc_start: 0.7985 (mm) cc_final: 0.7776 (mm) REVERT: A 1346 MET cc_start: 0.7671 (mmm) cc_final: 0.7374 (mmm) REVERT: A 1358 ARG cc_start: 0.7269 (mtt180) cc_final: 0.6293 (mtt-85) REVERT: A 1564 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8561 (mt-10) REVERT: A 1668 ASN cc_start: 0.8023 (t0) cc_final: 0.7432 (t0) REVERT: A 1682 TYR cc_start: 0.8406 (m-10) cc_final: 0.8164 (m-10) REVERT: A 1685 GLN cc_start: 0.8847 (tt0) cc_final: 0.8444 (tm-30) REVERT: A 1692 TYR cc_start: 0.7858 (t80) cc_final: 0.7384 (t80) REVERT: A 1837 MET cc_start: 0.7129 (mtt) cc_final: 0.5960 (mtt) outliers start: 1 outliers final: 1 residues processed: 192 average time/residue: 0.2714 time to fit residues: 70.8297 Evaluate side-chains 138 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 chunk 110 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 11 optimal weight: 0.0770 chunk 44 optimal weight: 0.0870 chunk 70 optimal weight: 0.4980 chunk 128 optimal weight: 0.0010 overall best weight: 0.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1767 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11332 Z= 0.201 Angle : 0.884 12.918 15323 Z= 0.451 Chirality : 0.049 0.277 1747 Planarity : 0.006 0.082 1954 Dihedral : 6.809 31.552 1519 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.32 % Favored : 85.68 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.60 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.22), residues: 1369 helix: -0.44 (0.20), residues: 625 sheet: -3.23 (0.49), residues: 98 loop : -3.21 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 138 HIS 0.006 0.001 HIS A 633 PHE 0.020 0.002 PHE A 347 TYR 0.020 0.002 TYR A 637 ARG 0.007 0.000 ARG A1358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.7528 (tp) cc_final: 0.7293 (tp) REVERT: A 218 GLU cc_start: 0.9041 (pt0) cc_final: 0.8712 (pm20) REVERT: A 224 GLN cc_start: 0.8806 (tt0) cc_final: 0.8361 (tm-30) REVERT: A 239 ASP cc_start: 0.5373 (m-30) cc_final: 0.4887 (m-30) REVERT: A 245 ARG cc_start: 0.6695 (mtp-110) cc_final: 0.5954 (tmt170) REVERT: A 281 ILE cc_start: 0.6856 (tt) cc_final: 0.6642 (tp) REVERT: A 335 HIS cc_start: 0.8255 (t-90) cc_final: 0.7627 (m170) REVERT: A 349 ASP cc_start: 0.5169 (t70) cc_final: 0.4935 (t0) REVERT: A 506 ARG cc_start: 0.8193 (ttt180) cc_final: 0.7803 (mmt180) REVERT: A 544 ARG cc_start: 0.7057 (ttp-110) cc_final: 0.5707 (tpp-160) REVERT: A 965 TYR cc_start: 0.8916 (m-80) cc_final: 0.8438 (m-80) REVERT: A 996 ARG cc_start: 0.5554 (ptt180) cc_final: 0.5070 (ptt180) REVERT: A 998 ASN cc_start: 0.8723 (t0) cc_final: 0.8507 (t0) REVERT: A 1062 HIS cc_start: 0.8797 (p-80) cc_final: 0.8564 (t70) REVERT: A 1303 LEU cc_start: 0.8499 (tp) cc_final: 0.8156 (tp) REVERT: A 1311 ASN cc_start: 0.7549 (p0) cc_final: 0.7197 (m-40) REVERT: A 1313 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7290 (mp0) REVERT: A 1337 ASP cc_start: 0.8940 (p0) cc_final: 0.8714 (p0) REVERT: A 1340 GLU cc_start: 0.7205 (tp30) cc_final: 0.6971 (tp30) REVERT: A 1358 ARG cc_start: 0.7492 (mtt180) cc_final: 0.7017 (mtt-85) REVERT: A 1664 SER cc_start: 0.7511 (t) cc_final: 0.7291 (p) REVERT: A 1668 ASN cc_start: 0.8008 (t0) cc_final: 0.7489 (t0) REVERT: A 1682 TYR cc_start: 0.8465 (m-10) cc_final: 0.8180 (m-10) REVERT: A 1687 PHE cc_start: 0.8499 (m-80) cc_final: 0.8183 (m-80) REVERT: A 1692 TYR cc_start: 0.7980 (t80) cc_final: 0.7778 (t80) REVERT: A 1748 LEU cc_start: 0.8468 (tp) cc_final: 0.8135 (tp) REVERT: A 1768 VAL cc_start: 0.7661 (t) cc_final: 0.7289 (p) REVERT: A 1837 MET cc_start: 0.6617 (mtt) cc_final: 0.5819 (mtt) REVERT: A 1897 TYR cc_start: 0.4472 (t80) cc_final: 0.3363 (p90) REVERT: B 348 ARG cc_start: 0.8855 (mtt180) cc_final: 0.8416 (tpt90) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2861 time to fit residues: 78.5048 Evaluate side-chains 153 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 133 optimal weight: 20.0000 chunk 83 optimal weight: 0.5980 chunk 81 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1767 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11332 Z= 0.223 Angle : 0.891 12.692 15323 Z= 0.456 Chirality : 0.049 0.239 1747 Planarity : 0.006 0.083 1954 Dihedral : 6.719 30.766 1519 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.97 % Favored : 85.03 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.60 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.22), residues: 1369 helix: -0.49 (0.20), residues: 630 sheet: -2.76 (0.52), residues: 98 loop : -3.34 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 138 HIS 0.005 0.001 HIS A 633 PHE 0.018 0.002 PHE A 347 TYR 0.030 0.002 TYR A 637 ARG 0.006 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.7439 (tp) cc_final: 0.7199 (tp) REVERT: A 218 GLU cc_start: 0.9018 (pt0) cc_final: 0.8707 (pm20) REVERT: A 224 GLN cc_start: 0.8689 (tt0) cc_final: 0.8324 (tm-30) REVERT: A 239 ASP cc_start: 0.5224 (m-30) cc_final: 0.4748 (m-30) REVERT: A 245 ARG cc_start: 0.6707 (mtp-110) cc_final: 0.5981 (tmt170) REVERT: A 335 HIS cc_start: 0.8335 (t-90) cc_final: 0.7605 (m90) REVERT: A 349 ASP cc_start: 0.5157 (t70) cc_final: 0.4956 (t0) REVERT: A 351 PHE cc_start: 0.9092 (t80) cc_final: 0.8864 (t80) REVERT: A 458 ASN cc_start: 0.6385 (t0) cc_final: 0.6012 (t0) REVERT: A 506 ARG cc_start: 0.8160 (ttt180) cc_final: 0.7730 (mmt180) REVERT: A 544 ARG cc_start: 0.7011 (ttp-110) cc_final: 0.5725 (tpp-160) REVERT: A 573 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8847 (mm-30) REVERT: A 688 ARG cc_start: 0.7512 (mtt180) cc_final: 0.6815 (mmm160) REVERT: A 697 ILE cc_start: 0.6680 (mt) cc_final: 0.6091 (mt) REVERT: A 701 LYS cc_start: 0.8144 (mmtm) cc_final: 0.7900 (mmtm) REVERT: A 965 TYR cc_start: 0.8977 (m-80) cc_final: 0.8544 (m-80) REVERT: A 1062 HIS cc_start: 0.8859 (p-80) cc_final: 0.8550 (t70) REVERT: A 1337 ASP cc_start: 0.8885 (p0) cc_final: 0.8675 (p0) REVERT: A 1340 GLU cc_start: 0.7120 (tp30) cc_final: 0.6908 (tp30) REVERT: A 1358 ARG cc_start: 0.7483 (mtt180) cc_final: 0.7002 (mtt-85) REVERT: A 1668 ASN cc_start: 0.8052 (t0) cc_final: 0.7487 (t0) REVERT: A 1682 TYR cc_start: 0.8519 (m-10) cc_final: 0.8309 (m-10) REVERT: A 1692 TYR cc_start: 0.8054 (t80) cc_final: 0.7829 (t80) REVERT: A 1768 VAL cc_start: 0.7691 (t) cc_final: 0.7312 (p) REVERT: A 1837 MET cc_start: 0.6882 (mtt) cc_final: 0.6268 (mtt) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2846 time to fit residues: 75.6498 Evaluate side-chains 151 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 84 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 104 optimal weight: 0.3980 chunk 120 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 ASN A1031 GLN ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1767 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11332 Z= 0.202 Angle : 0.869 12.709 15323 Z= 0.444 Chirality : 0.048 0.187 1747 Planarity : 0.006 0.066 1954 Dihedral : 6.555 30.642 1519 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.39 % Favored : 85.61 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.60 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.22), residues: 1369 helix: -0.38 (0.20), residues: 633 sheet: -2.61 (0.53), residues: 96 loop : -3.22 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 138 HIS 0.006 0.001 HIS A 633 PHE 0.028 0.002 PHE A1669 TYR 0.019 0.002 TYR A 637 ARG 0.004 0.000 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9318 (tt) cc_final: 0.8949 (tt) REVERT: A 56 LEU cc_start: 0.8565 (mp) cc_final: 0.7626 (tp) REVERT: A 64 LEU cc_start: 0.7404 (tp) cc_final: 0.7172 (tp) REVERT: A 80 GLU cc_start: 0.8622 (tt0) cc_final: 0.7933 (tp30) REVERT: A 133 TRP cc_start: 0.7281 (p90) cc_final: 0.6972 (p-90) REVERT: A 218 GLU cc_start: 0.8980 (pt0) cc_final: 0.8649 (pm20) REVERT: A 224 GLN cc_start: 0.8683 (tt0) cc_final: 0.8238 (tm-30) REVERT: A 239 ASP cc_start: 0.5178 (m-30) cc_final: 0.4691 (m-30) REVERT: A 245 ARG cc_start: 0.6751 (mtp-110) cc_final: 0.6052 (tmt170) REVERT: A 335 HIS cc_start: 0.8306 (t-90) cc_final: 0.7603 (m90) REVERT: A 349 ASP cc_start: 0.5205 (t70) cc_final: 0.4994 (t0) REVERT: A 351 PHE cc_start: 0.9085 (t80) cc_final: 0.8849 (t80) REVERT: A 458 ASN cc_start: 0.6404 (t0) cc_final: 0.6027 (t0) REVERT: A 506 ARG cc_start: 0.8163 (ttt180) cc_final: 0.7763 (mmt180) REVERT: A 544 ARG cc_start: 0.7190 (ttp-110) cc_final: 0.5885 (tpp-160) REVERT: A 573 GLU cc_start: 0.9084 (tm-30) cc_final: 0.8875 (mm-30) REVERT: A 575 ASP cc_start: 0.8995 (m-30) cc_final: 0.8660 (t0) REVERT: A 688 ARG cc_start: 0.7683 (mtt180) cc_final: 0.6936 (mmm160) REVERT: A 697 ILE cc_start: 0.6828 (mt) cc_final: 0.6306 (mt) REVERT: A 856 HIS cc_start: 0.7873 (t-90) cc_final: 0.7345 (m170) REVERT: A 891 ASP cc_start: 0.8659 (t70) cc_final: 0.8301 (m-30) REVERT: A 965 TYR cc_start: 0.8907 (m-80) cc_final: 0.8513 (m-80) REVERT: A 998 ASN cc_start: 0.8674 (t0) cc_final: 0.8472 (t0) REVERT: A 1303 LEU cc_start: 0.8496 (tp) cc_final: 0.8279 (tp) REVERT: A 1311 ASN cc_start: 0.7509 (p0) cc_final: 0.7071 (m-40) REVERT: A 1337 ASP cc_start: 0.8935 (p0) cc_final: 0.8675 (p0) REVERT: A 1340 GLU cc_start: 0.7032 (tp30) cc_final: 0.6724 (tp30) REVERT: A 1358 ARG cc_start: 0.7456 (mtt180) cc_final: 0.6950 (mtt-85) REVERT: A 1664 SER cc_start: 0.7527 (t) cc_final: 0.7305 (p) REVERT: A 1668 ASN cc_start: 0.7809 (t0) cc_final: 0.7326 (t0) REVERT: A 1682 TYR cc_start: 0.8528 (m-10) cc_final: 0.8307 (m-10) REVERT: B 348 ARG cc_start: 0.8735 (mtt180) cc_final: 0.8325 (tpt90) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2747 time to fit residues: 75.5525 Evaluate side-chains 150 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 74 optimal weight: 0.0370 chunk 53 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 131 optimal weight: 20.0000 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 HIS A1668 ASN ** A1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1693 HIS A1767 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.5983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11332 Z= 0.211 Angle : 0.886 12.569 15323 Z= 0.455 Chirality : 0.049 0.187 1747 Planarity : 0.006 0.064 1954 Dihedral : 6.572 30.449 1519 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.24 % Favored : 85.76 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.60 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.22), residues: 1369 helix: -0.25 (0.20), residues: 632 sheet: -2.66 (0.51), residues: 96 loop : -3.16 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 138 HIS 0.008 0.001 HIS A 703 PHE 0.016 0.002 PHE A 89 TYR 0.028 0.002 TYR A1692 ARG 0.004 0.000 ARG A 996 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9350 (tt) cc_final: 0.9059 (tt) REVERT: A 64 LEU cc_start: 0.7332 (tp) cc_final: 0.7065 (tp) REVERT: A 80 GLU cc_start: 0.8612 (tt0) cc_final: 0.7989 (tp30) REVERT: A 218 GLU cc_start: 0.8993 (pt0) cc_final: 0.8639 (pm20) REVERT: A 239 ASP cc_start: 0.5265 (m-30) cc_final: 0.4763 (m-30) REVERT: A 245 ARG cc_start: 0.6761 (mtp-110) cc_final: 0.6068 (tmt170) REVERT: A 335 HIS cc_start: 0.8285 (t-90) cc_final: 0.7588 (m90) REVERT: A 349 ASP cc_start: 0.5230 (t70) cc_final: 0.5012 (t0) REVERT: A 351 PHE cc_start: 0.9106 (t80) cc_final: 0.8869 (t80) REVERT: A 458 ASN cc_start: 0.6463 (t0) cc_final: 0.6256 (p0) REVERT: A 506 ARG cc_start: 0.8156 (ttt180) cc_final: 0.7746 (mmt180) REVERT: A 509 ARG cc_start: 0.7610 (mtp180) cc_final: 0.7261 (mtm110) REVERT: A 544 ARG cc_start: 0.7128 (ttp-110) cc_final: 0.5760 (tpp-160) REVERT: A 575 ASP cc_start: 0.9000 (m-30) cc_final: 0.8671 (t0) REVERT: A 688 ARG cc_start: 0.7766 (mtt180) cc_final: 0.7106 (mmm160) REVERT: A 856 HIS cc_start: 0.8148 (t-90) cc_final: 0.7465 (m170) REVERT: A 965 TYR cc_start: 0.8935 (m-80) cc_final: 0.8593 (m-80) REVERT: A 1337 ASP cc_start: 0.8932 (p0) cc_final: 0.8684 (p0) REVERT: A 1340 GLU cc_start: 0.6966 (tp30) cc_final: 0.6725 (tp30) REVERT: A 1346 MET cc_start: 0.7710 (mmm) cc_final: 0.7397 (mmm) REVERT: A 1358 ARG cc_start: 0.7466 (mtt180) cc_final: 0.6951 (mtt-85) REVERT: A 1580 GLN cc_start: 0.8276 (mt0) cc_final: 0.7455 (tm-30) REVERT: A 1664 SER cc_start: 0.7615 (t) cc_final: 0.7355 (p) REVERT: A 1668 ASN cc_start: 0.7948 (t160) cc_final: 0.7484 (t0) REVERT: B 348 ARG cc_start: 0.8731 (mtt180) cc_final: 0.8315 (tpt90) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.3234 time to fit residues: 82.6086 Evaluate side-chains 141 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1668 ASN ** A1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1693 HIS A1767 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.6107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11332 Z= 0.223 Angle : 0.895 12.574 15323 Z= 0.458 Chirality : 0.049 0.186 1747 Planarity : 0.006 0.065 1954 Dihedral : 6.622 30.331 1519 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.83 % Favored : 85.17 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.60 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.22), residues: 1369 helix: -0.34 (0.20), residues: 637 sheet: -2.63 (0.51), residues: 96 loop : -3.19 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP A 138 HIS 0.006 0.001 HIS A 633 PHE 0.020 0.002 PHE A1766 TYR 0.030 0.002 TYR A1692 ARG 0.003 0.000 ARG A 996 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9415 (mt-10) cc_final: 0.9201 (mt-10) REVERT: A 52 LEU cc_start: 0.9350 (tt) cc_final: 0.8971 (tt) REVERT: A 56 LEU cc_start: 0.8627 (mp) cc_final: 0.7638 (tp) REVERT: A 64 LEU cc_start: 0.7373 (tp) cc_final: 0.7040 (tp) REVERT: A 80 GLU cc_start: 0.8608 (tt0) cc_final: 0.7917 (tp30) REVERT: A 150 MET cc_start: 0.2910 (ptp) cc_final: 0.2446 (ptp) REVERT: A 218 GLU cc_start: 0.8969 (pt0) cc_final: 0.8609 (pm20) REVERT: A 239 ASP cc_start: 0.5775 (m-30) cc_final: 0.5119 (m-30) REVERT: A 245 ARG cc_start: 0.6676 (mtp-110) cc_final: 0.5971 (tmt170) REVERT: A 335 HIS cc_start: 0.8281 (t-90) cc_final: 0.7579 (m170) REVERT: A 349 ASP cc_start: 0.5220 (t70) cc_final: 0.4936 (t0) REVERT: A 458 ASN cc_start: 0.6244 (t0) cc_final: 0.5916 (t0) REVERT: A 506 ARG cc_start: 0.8028 (ttt180) cc_final: 0.7713 (mmt180) REVERT: A 544 ARG cc_start: 0.7019 (ttp-110) cc_final: 0.5745 (tpp-160) REVERT: A 575 ASP cc_start: 0.9043 (m-30) cc_final: 0.8697 (t0) REVERT: A 688 ARG cc_start: 0.7765 (mtt180) cc_final: 0.7100 (mmm160) REVERT: A 965 TYR cc_start: 0.8952 (m-80) cc_final: 0.8586 (m-80) REVERT: A 1315 LEU cc_start: 0.7753 (mm) cc_final: 0.7520 (mm) REVERT: A 1337 ASP cc_start: 0.8895 (p0) cc_final: 0.8664 (p0) REVERT: A 1340 GLU cc_start: 0.6978 (tp30) cc_final: 0.6734 (tp30) REVERT: A 1346 MET cc_start: 0.7625 (mmm) cc_final: 0.7316 (mmm) REVERT: A 1664 SER cc_start: 0.7587 (t) cc_final: 0.7364 (p) REVERT: A 1668 ASN cc_start: 0.7908 (t160) cc_final: 0.7606 (t0) REVERT: A 1685 GLN cc_start: 0.8770 (tt0) cc_final: 0.8500 (tm-30) REVERT: B 348 ARG cc_start: 0.8729 (mtt180) cc_final: 0.8331 (tpt90) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2942 time to fit residues: 74.0673 Evaluate side-chains 142 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 6 optimal weight: 0.0870 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1668 ASN ** A1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1693 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.091259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.071251 restraints weight = 76496.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.073394 restraints weight = 54479.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.075003 restraints weight = 42056.525| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.6167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11332 Z= 0.220 Angle : 0.904 12.534 15323 Z= 0.462 Chirality : 0.049 0.176 1747 Planarity : 0.006 0.064 1954 Dihedral : 6.597 30.303 1519 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 23.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.46 % Favored : 85.54 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.60 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.22), residues: 1369 helix: -0.32 (0.20), residues: 628 sheet: -2.46 (0.47), residues: 108 loop : -3.24 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP A 138 HIS 0.006 0.001 HIS A 633 PHE 0.017 0.002 PHE A 347 TYR 0.028 0.002 TYR A1692 ARG 0.004 0.000 ARG A 536 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2503.19 seconds wall clock time: 45 minutes 50.95 seconds (2750.95 seconds total)