Starting phenix.real_space_refine on Sat Dec 9 12:56:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zak_6904/12_2023/5zak_6904.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zak_6904/12_2023/5zak_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_6904/12_2023/5zak_6904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zak_6904/12_2023/5zak_6904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zak_6904/12_2023/5zak_6904.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zak_6904/12_2023/5zak_6904.pdb" } 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 Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 944": "NH1" <-> "NH2" Residue "A ARG 996": "NH1" <-> "NH2" Residue "A TYR 1694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1736": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 6.18, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 4.23 Conformation dependent library (CDL) restraints added in 1.9 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: 1.16 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: 3.41 Time building geometry restraints manager: 4.58 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: 98.73 - 106.61: 430 106.61 - 114.50: 6497 114.50 - 122.38: 6573 122.38 - 130.27: 1750 130.27 - 138.15: 73 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 2.440 nonbonded pdb=" O VAL A 75 " pdb=" OG1 THR A 78 " model vdw 2.197 2.440 nonbonded pdb=" OG1 THR B 331 " pdb=" O PRO B 333 " model vdw 2.211 2.440 nonbonded pdb=" OD2 ASP A 283 " pdb=" OG SER B 318 " model vdw 2.226 2.440 nonbonded pdb=" O SER A1868 " pdb=" OH TYR A1897 " model vdw 2.238 2.440 ... (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 ========== 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: 0.260 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: 1.720 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 31.540 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.950 ------------------------------------------------------------------------------- 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 : 1.439 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 outliers start: 9 outliers final: 1 residues processed: 273 average time/residue: 0.3221 time to fit residues: 115.7128 Evaluate side-chains 149 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 1.404 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1089 time to fit residues: 2.0494 ------------------------------------------------------------------------------- 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: 7.9990 chunk 104 optimal weight: 0.0870 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 125 optimal weight: 0.0070 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 GLN A1029 ASN ** A1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1041 HIS A1305 ASN A1661 HIS ** A1774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11332 Z= 0.230 Angle : 0.943 11.889 15323 Z= 0.488 Chirality : 0.050 0.209 1747 Planarity : 0.007 0.080 1954 Dihedral : 8.002 33.670 1519 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 24.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.88 % Favored : 86.05 % 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 : 0.00 % Twisted General : 0.38 % 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: -4.18 (0.20), residues: 1369 helix: -1.79 (0.18), residues: 614 sheet: -3.21 (0.40), residues: 131 loop : -3.74 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 316 HIS 0.006 0.001 HIS A 703 PHE 0.020 0.002 PHE A1322 TYR 0.024 0.002 TYR A1692 ARG 0.005 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 226 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 224 time to evaluate : 1.299 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 outliers start: 2 outliers final: 0 residues processed: 224 average time/residue: 0.2893 time to fit residues: 87.2655 Evaluate side-chains 149 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.778 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7734 ------------------------------------------------------------------------------- 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: 0.0870 chunk 38 optimal weight: 10.0000 chunk 104 optimal weight: 0.0370 chunk 85 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 GLN ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 943 HIS ** A1339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11332 Z= 0.206 Angle : 0.875 12.585 15323 Z= 0.453 Chirality : 0.048 0.203 1747 Planarity : 0.006 0.086 1954 Dihedral : 7.320 34.973 1519 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.32 % Favored : 85.68 % Rotamer: Outliers : 0.08 % Allowed : 4.83 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.60 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -3.39 (0.21), residues: 1369 helix: -1.00 (0.20), residues: 612 sheet: -2.92 (0.46), residues: 113 loop : -3.47 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 138 HIS 0.004 0.001 HIS A 335 PHE 0.024 0.002 PHE A1322 TYR 0.023 0.002 TYR A 637 ARG 0.008 0.000 ARG A1342 *********************** 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 222 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 1.226 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 outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 0.2798 time to fit residues: 83.7708 Evaluate side-chains 150 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.299 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8186 ------------------------------------------------------------------------------- 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: 6.9990 chunk 94 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 84 optimal weight: 6.9990 chunk 125 optimal weight: 0.0670 chunk 133 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 overall best weight: 2.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN A 335 HIS ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1726 GLN ** A1774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11332 Z= 0.242 Angle : 0.909 12.499 15323 Z= 0.466 Chirality : 0.049 0.241 1747 Planarity : 0.006 0.081 1954 Dihedral : 7.261 33.865 1519 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 28.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.19 % Favored : 84.81 % Rotamer: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % 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: -3.22 (0.21), residues: 1369 helix: -0.84 (0.19), residues: 628 sheet: -3.08 (0.44), residues: 110 loop : -3.39 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 133 HIS 0.007 0.001 HIS B 338 PHE 0.033 0.002 PHE A 347 TYR 0.018 0.002 TYR A 267 ARG 0.004 0.001 ARG A 640 *********************** 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 189 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.266 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 outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2811 time to fit residues: 72.7505 Evaluate side-chains 131 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6892 ------------------------------------------------------------------------------- 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: 0.9990 chunk 1 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 GLN A 633 HIS ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 HIS A1325 HIS A1339 HIS A1660 ASN A1726 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11332 Z= 0.273 Angle : 0.945 14.311 15323 Z= 0.482 Chirality : 0.050 0.216 1747 Planarity : 0.007 0.092 1954 Dihedral : 7.426 31.434 1519 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 31.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.65 % Favored : 83.35 % Rotamer: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.60 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -3.24 (0.21), residues: 1369 helix: -0.81 (0.19), residues: 623 sheet: -3.11 (0.42), residues: 112 loop : -3.43 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 133 HIS 0.006 0.002 HIS A 633 PHE 0.026 0.002 PHE A 347 TYR 0.034 0.003 TYR A 637 ARG 0.006 0.001 ARG A 307 *********************** 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 173 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.317 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 outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2878 time to fit residues: 69.0393 Evaluate side-chains 133 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.320 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8315 ------------------------------------------------------------------------------- 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: 0.5980 chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 70 optimal weight: 0.4980 chunk 128 optimal weight: 0.0070 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.5302 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= 0.205 Angle : 0.881 12.830 15323 Z= 0.450 Chirality : 0.048 0.198 1747 Planarity : 0.006 0.082 1954 Dihedral : 6.990 31.779 1519 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 24.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.12 % Favored : 84.88 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: -2.95 (0.22), residues: 1369 helix: -0.53 (0.20), residues: 621 sheet: -3.26 (0.43), residues: 101 loop : -3.28 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 133 HIS 0.006 0.001 HIS A1693 PHE 0.035 0.002 PHE A1669 TYR 0.024 0.002 TYR A1834 ARG 0.006 0.000 ARG B 353 *********************** 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 186 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.369 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 outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2769 time to fit residues: 71.6587 Evaluate side-chains 128 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.349 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7639 ------------------------------------------------------------------------------- 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: 1.9990 chunk 76 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 74 optimal weight: 30.0000 chunk 133 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1726 GLN A1727 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11332 Z= 0.237 Angle : 0.897 12.734 15323 Z= 0.459 Chirality : 0.049 0.231 1747 Planarity : 0.006 0.082 1954 Dihedral : 6.982 31.017 1519 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 28.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.85 % Favored : 84.15 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: -2.78 (0.22), residues: 1369 helix: -0.47 (0.20), residues: 625 sheet: -2.56 (0.50), residues: 86 loop : -3.23 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP A 138 HIS 0.006 0.001 HIS A 633 PHE 0.016 0.002 PHE A 816 TYR 0.017 0.002 TYR A 972 ARG 0.003 0.000 ARG A 790 *********************** 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 167 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.422 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 outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2892 time to fit residues: 66.4366 Evaluate side-chains 127 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.273 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8881 ------------------------------------------------------------------------------- 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: 6.9990 chunk 79 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 65 optimal weight: 0.0870 chunk 12 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 120 optimal weight: 0.0980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 84 GLN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN A 559 ASN ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1668 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.5897 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= 0.201 Angle : 0.872 12.608 15323 Z= 0.444 Chirality : 0.048 0.199 1747 Planarity : 0.006 0.068 1954 Dihedral : 6.735 32.168 1519 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 24.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.27 % Favored : 84.73 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: -2.59 (0.22), residues: 1369 helix: -0.29 (0.20), residues: 626 sheet: -3.02 (0.53), residues: 67 loop : -3.10 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP A 138 HIS 0.007 0.001 HIS A 633 PHE 0.017 0.002 PHE B 307 TYR 0.025 0.002 TYR A1834 ARG 0.004 0.000 ARG A1703 *********************** 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 180 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.176 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 outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2884 time to fit residues: 71.6688 Evaluate side-chains 132 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.414 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8900 ------------------------------------------------------------------------------- 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: 10.0000 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 38 optimal weight: 0.0030 chunk 112 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 overall best weight: 1.3996 ------------------------------------------------------------------------------- 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 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN ** A 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.6026 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= 0.214 Angle : 0.880 12.491 15323 Z= 0.450 Chirality : 0.048 0.180 1747 Planarity : 0.006 0.067 1954 Dihedral : 6.715 31.419 1519 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 26.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.12 % Favored : 84.88 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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: -2.65 (0.22), residues: 1369 helix: -0.27 (0.20), residues: 627 sheet: -2.62 (0.52), residues: 92 loop : -3.25 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP A 138 HIS 0.008 0.001 HIS A 633 PHE 0.027 0.002 PHE A 347 TYR 0.039 0.002 TYR A1692 ARG 0.003 0.000 ARG A 450 *********************** 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 163 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.283 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 outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2726 time to fit residues: 61.7094 Evaluate side-chains 126 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.334 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9055 ------------------------------------------------------------------------------- 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: 0.7980 chunk 62 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 137 optimal weight: 30.0000 chunk 126 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 116 optimal weight: 0.0770 overall best weight: 2.9744 ------------------------------------------------------------------------------- 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 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 GLN A 157 ASN ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1031 GLN ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11332 Z= 0.271 Angle : 0.949 12.274 15323 Z= 0.486 Chirality : 0.051 0.205 1747 Planarity : 0.006 0.073 1954 Dihedral : 7.006 29.942 1519 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 32.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 16.14 % Favored : 83.78 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.60 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.22), residues: 1369 helix: -0.42 (0.20), residues: 619 sheet: -2.37 (0.46), residues: 106 loop : -3.31 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP A 138 HIS 0.009 0.001 HIS A 850 PHE 0.026 0.002 PHE A 347 TYR 0.019 0.002 TYR A 972 ARG 0.005 0.001 ARG A 450 ********************** 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 162 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.221 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 outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2728 time to fit residues: 61.8426 Evaluate side-chains 124 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.237 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8252 ------------------------------------------------------------------------------- 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: 7.9990 chunk 100 optimal weight: 7.9990 chunk 16 optimal weight: 0.1980 chunk 30 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 112 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 ASN ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1668 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.088241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.070164 restraints weight = 78580.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.072061 restraints weight = 56735.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.073521 restraints weight = 44253.189| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.6051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11332 Z= 0.227 Angle : 0.909 11.554 15323 Z= 0.466 Chirality : 0.049 0.194 1747 Planarity : 0.006 0.070 1954 Dihedral : 6.847 30.472 1519 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 28.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.63 % Favored : 84.37 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -2.75 (0.22), residues: 1369 helix: -0.44 (0.20), residues: 625 sheet: -2.18 (0.52), residues: 93 loop : -3.29 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP A 138 HIS 0.007 0.001 HIS A 633 PHE 0.025 0.002 PHE A 347 TYR 0.025 0.002 TYR A1834 ARG 0.003 0.000 ARG A 450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2406.18 seconds wall clock time: 44 minutes 56.80 seconds (2696.80 seconds total)