Starting phenix.real_space_refine (version: dev) on Mon Dec 12 14:32:15 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ele_31182/12_2022/7ele_31182.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ele_31182/12_2022/7ele_31182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ele_31182/12_2022/7ele_31182.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ele_31182/12_2022/7ele_31182.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ele_31182/12_2022/7ele_31182.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ele_31182/12_2022/7ele_31182.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 270": "OE1" <-> "OE2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A ARG 666": "NH1" <-> "NH2" Residue "A GLU 1016": "OE1" <-> "OE2" Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1105": "OE1" <-> "OE2" Residue "A PHE 1225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1244": "OE1" <-> "OE2" Residue "A TYR 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1312": "OE1" <-> "OE2" Residue "A ARG 1628": "NH1" <-> "NH2" Residue "A GLU 1667": "OE1" <-> "OE2" Residue "A GLU 1740": "OE1" <-> "OE2" Residue "A ARG 1755": "NH1" <-> "NH2" Residue "A ARG 1788": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 10733 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1137, 8976 Classifications: {'peptide': 1137} Link IDs: {'PTRANS': 38, 'TRANS': 1098} Chain breaks: 12 Chain: "G" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1757 Classifications: {'RNA': 83} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 39, 'rna3p_pyr': 42} Link IDs: {'rna2p': 1, 'rna3p': 81} Chain breaks: 3 Time building chain proxies: 6.45, per 1000 atoms: 0.60 Number of scatterers: 10733 At special positions: 0 Unit cell: (161.226, 129.792, 93.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 83 15.00 O 2227 8.00 N 1851 7.00 C 6512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 5.11 Conformation dependent library (CDL) restraints added in 1.5 seconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 5 sheets defined 54.4% alpha, 6.6% beta 35 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 3.67 Creating SS restraints... Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.828A pdb=" N LEU A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 289 Processing helix chain 'A' and resid 305 through 319 Processing helix chain 'A' and resid 335 through 348 removed outlier: 4.055A pdb=" N ARG A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLU A 346 " --> pdb=" O GLN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 363 Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.739A pdb=" N ILE A 372 " --> pdb=" O MET A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 383 Processing helix chain 'A' and resid 387 through 396 removed outlier: 3.887A pdb=" N LEU A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 438 Processing helix chain 'A' and resid 473 through 493 removed outlier: 3.912A pdb=" N THR A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 567 removed outlier: 3.612A pdb=" N GLY A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLN A 546 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 9.610A pdb=" N TRP A 547 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N CYS A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A 549 " --> pdb=" O GLY A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 593 removed outlier: 3.752A pdb=" N GLU A 592 " --> pdb=" O CYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 659 Processing helix chain 'A' and resid 673 through 687 Proline residue: A 681 - end of helix Processing helix chain 'A' and resid 708 through 721 Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 753 through 763 Processing helix chain 'A' and resid 781 through 801 Processing helix chain 'A' and resid 823 through 826 removed outlier: 3.956A pdb=" N TYR A 826 " --> pdb=" O GLY A 823 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 823 through 826' Processing helix chain 'A' and resid 827 through 849 removed outlier: 3.810A pdb=" N THR A 831 " --> pdb=" O LYS A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 918 Processing helix chain 'A' and resid 1049 through 1066 Processing helix chain 'A' and resid 1103 through 1113 Processing helix chain 'A' and resid 1254 through 1264 Processing helix chain 'A' and resid 1301 through 1307 removed outlier: 4.085A pdb=" N VAL A1307 " --> pdb=" O LYS A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1348 Proline residue: A1331 - end of helix removed outlier: 3.565A pdb=" N ASN A1348 " --> pdb=" O VAL A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1364 removed outlier: 3.508A pdb=" N THR A1364 " --> pdb=" O LEU A1360 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1397 Processing helix chain 'A' and resid 1401 through 1413 Processing helix chain 'A' and resid 1414 through 1426 removed outlier: 3.589A pdb=" N LEU A1418 " --> pdb=" O SER A1414 " (cutoff:3.500A) Processing helix chain 'A' and resid 1427 through 1430 Processing helix chain 'A' and resid 1501 through 1517 removed outlier: 3.753A pdb=" N GLY A1517 " --> pdb=" O TYR A1513 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1530 removed outlier: 3.740A pdb=" N ALA A1522 " --> pdb=" O GLY A1518 " (cutoff:3.500A) Processing helix chain 'A' and resid 1559 through 1566 Processing helix chain 'A' and resid 1572 through 1581 removed outlier: 3.696A pdb=" N LEU A1576 " --> pdb=" O GLU A1572 " (cutoff:3.500A) Processing helix chain 'A' and resid 1593 through 1615 Processing helix chain 'A' and resid 1620 through 1632 Processing helix chain 'A' and resid 1633 through 1645 removed outlier: 3.548A pdb=" N PHE A1637 " --> pdb=" O ASN A1633 " (cutoff:3.500A) Processing helix chain 'A' and resid 1654 through 1668 removed outlier: 3.628A pdb=" N GLU A1658 " --> pdb=" O SER A1654 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A1668 " --> pdb=" O PHE A1664 " (cutoff:3.500A) Processing helix chain 'A' and resid 1690 through 1706 Processing helix chain 'A' and resid 1710 through 1722 removed outlier: 3.512A pdb=" N VAL A1716 " --> pdb=" O ALA A1712 " (cutoff:3.500A) Proline residue: A1719 - end of helix Processing helix chain 'A' and resid 1723 through 1725 No H-bonds generated for 'chain 'A' and resid 1723 through 1725' Processing helix chain 'A' and resid 1733 through 1742 Processing helix chain 'A' and resid 1781 through 1794 Processing sheet with id=AA1, first strand: chain 'A' and resid 300 through 302 removed outlier: 5.618A pdb=" N VAL A 300 " --> pdb=" O ILE A 376 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ASP A 378 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU A 302 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LEU A 375 " --> pdb=" O PHE A 409 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N MET A 411 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU A 377 " --> pdb=" O MET A 411 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR A 265 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE A 266 " --> pdb=" O CYS A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 459 through 463 removed outlier: 5.835A pdb=" N SER A 459 " --> pdb=" O TYR A 771 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU A 773 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A 461 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL A 745 " --> pdb=" O ILE A 772 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N MET A 774 " --> pdb=" O VAL A 745 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE A 668 " --> pdb=" O MET A 746 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 667 " --> pdb=" O ALA A 729 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 862 through 867 Processing sheet with id=AA4, first strand: chain 'A' and resid 1026 through 1029 removed outlier: 4.882A pdb=" N SER A 979 " --> pdb=" O ILE A1011 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A1011 " --> pdb=" O SER A 979 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A1086 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1308 through 1309 removed outlier: 6.431A pdb=" N LEU A1274 " --> pdb=" O ILE A1230 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE A1230 " --> pdb=" O LEU A1274 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LYS A1276 " --> pdb=" O ASP A1228 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP A1228 " --> pdb=" O LYS A1276 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A1211 " --> pdb=" O HIS A1317 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A1315 " --> pdb=" O GLY A1213 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 6.47 Time building geometry restraints manager: 5.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1869 1.33 - 1.45: 3078 1.45 - 1.57: 5886 1.57 - 1.69: 162 1.69 - 1.81: 96 Bond restraints: 11091 Sorted by residual: bond pdb=" N ILE A 693 " pdb=" CA ILE A 693 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.11e-02 8.12e+03 1.45e+01 bond pdb=" N VAL A 728 " pdb=" CA VAL A 728 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.24e+01 bond pdb=" N ILE A 367 " pdb=" CA ILE A 367 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.11e+01 bond pdb=" N VAL A 669 " pdb=" CA VAL A 669 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" N ILE A 858 " pdb=" CA ILE A 858 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 1.01e+01 ... (remaining 11086 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.88: 730 106.88 - 113.96: 6431 113.96 - 121.03: 5280 121.03 - 128.10: 2742 128.10 - 135.18: 175 Bond angle restraints: 15358 Sorted by residual: angle pdb=" N LEU A1427 " pdb=" CA LEU A1427 " pdb=" C LEU A1427 " ideal model delta sigma weight residual 113.19 105.76 7.43 1.19e+00 7.06e-01 3.90e+01 angle pdb=" C4' U G 49 " pdb=" C3' U G 49 " pdb=" O3' U G 49 " ideal model delta sigma weight residual 113.00 121.48 -8.48 1.50e+00 4.44e-01 3.20e+01 angle pdb=" N GLU A 799 " pdb=" CA GLU A 799 " pdb=" C GLU A 799 " ideal model delta sigma weight residual 112.89 106.12 6.77 1.24e+00 6.50e-01 2.98e+01 angle pdb=" N THR A1501 " pdb=" CA THR A1501 " pdb=" C THR A1501 " ideal model delta sigma weight residual 113.02 106.92 6.10 1.20e+00 6.94e-01 2.58e+01 angle pdb=" N THR A 412 " pdb=" CA THR A 412 " pdb=" C THR A 412 " ideal model delta sigma weight residual 113.30 106.50 6.80 1.34e+00 5.57e-01 2.57e+01 ... (remaining 15353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 6197 35.91 - 71.82: 345 71.82 - 107.73: 14 107.73 - 143.65: 1 143.65 - 179.56: 3 Dihedral angle restraints: 6560 sinusoidal: 3234 harmonic: 3326 Sorted by residual: dihedral pdb=" CA GLN A1722 " pdb=" C GLN A1722 " pdb=" N PRO A1723 " pdb=" CA PRO A1723 " ideal model delta harmonic sigma weight residual -180.00 -151.75 -28.25 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA TYR A 327 " pdb=" C TYR A 327 " pdb=" N CYS A 328 " pdb=" CA CYS A 328 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA TYR A1374 " pdb=" C TYR A1374 " pdb=" N GLU A1375 " pdb=" CA GLU A1375 " ideal model delta harmonic sigma weight residual -180.00 -152.83 -27.17 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 6557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1537 0.087 - 0.173: 253 0.173 - 0.260: 38 0.260 - 0.346: 2 0.346 - 0.433: 1 Chirality restraints: 1831 Sorted by residual: chirality pdb=" C3' U G 49 " pdb=" C4' U G 49 " pdb=" O3' U G 49 " pdb=" C2' U G 49 " both_signs ideal model delta sigma weight residual False -2.48 -2.04 -0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" C2' G G 36 " pdb=" C3' G G 36 " pdb=" O2' G G 36 " pdb=" C1' G G 36 " both_signs ideal model delta sigma weight residual False -2.75 -2.43 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C3' U G 25 " pdb=" C4' U G 25 " pdb=" O3' U G 25 " pdb=" C2' U G 25 " both_signs ideal model delta sigma weight residual False -2.48 -2.22 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 1828 not shown) Planarity restraints: 1638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 663 " 0.012 2.00e-02 2.50e+03 2.54e-02 6.48e+00 pdb=" C ALA A 663 " -0.044 2.00e-02 2.50e+03 pdb=" O ALA A 663 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP A 664 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 387 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO A 388 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 388 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 388 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1426 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" C GLY A1426 " 0.040 2.00e-02 2.50e+03 pdb=" O GLY A1426 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU A1427 " -0.014 2.00e-02 2.50e+03 ... (remaining 1635 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1544 2.75 - 3.29: 11596 3.29 - 3.82: 21135 3.82 - 4.36: 24828 4.36 - 4.90: 34960 Nonbonded interactions: 94063 Sorted by model distance: nonbonded pdb=" O ALA A 789 " pdb=" OG SER A 792 " model vdw 2.210 2.440 nonbonded pdb=" O PHE A 846 " pdb=" OG SER A 849 " model vdw 2.222 2.440 nonbonded pdb=" O2 U G 26 " pdb=" N2 G G 62 " model vdw 2.231 2.496 nonbonded pdb=" O LEU A 391 " pdb=" OG SER A 394 " model vdw 2.238 2.440 nonbonded pdb=" O LEU A1301 " pdb=" OG1 THR A1304 " model vdw 2.239 2.440 ... (remaining 94058 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 83 5.49 5 S 60 5.16 5 C 6512 2.51 5 N 1851 2.21 5 O 2227 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.410 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: 2.510 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.080 Process input model: 37.360 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 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 : 0.007 0.051 11091 Z= 0.460 Angle : 1.164 10.177 15358 Z= 0.721 Chirality : 0.065 0.433 1831 Planarity : 0.006 0.063 1638 Dihedral : 19.443 179.557 4400 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.81 % Allowed : 9.09 % Favored : 90.10 % Rotamer Outliers : 8.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.21), residues: 1111 helix: -1.87 (0.18), residues: 568 sheet: -2.57 (0.51), residues: 75 loop : -2.84 (0.25), residues: 468 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 122 time to evaluate : 1.219 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 outliers start: 83 outliers final: 26 residues processed: 193 average time/residue: 0.2677 time to fit residues: 69.7374 Evaluate side-chains 107 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 81 time to evaluate : 1.203 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1982 time to fit residues: 8.9592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 30.0000 chunk 94 optimal weight: 30.0000 chunk 36 optimal weight: 0.1980 chunk 57 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 319 GLN ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1268 ASN ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1317 HIS A1411 GLN ** A1428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1523 ASN A1582 HIS ** A1647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1789 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 11091 Z= 0.228 Angle : 0.737 10.007 15358 Z= 0.383 Chirality : 0.042 0.262 1831 Planarity : 0.006 0.081 1638 Dihedral : 15.736 168.816 2210 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 28.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.11 % Favored : 92.71 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.23), residues: 1111 helix: -0.77 (0.20), residues: 580 sheet: -2.70 (0.45), residues: 99 loop : -2.55 (0.27), residues: 432 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 1.293 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 outliers start: 2 outliers final: 2 residues processed: 104 average time/residue: 0.2001 time to fit residues: 31.1427 Evaluate side-chains 79 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0965 time to fit residues: 1.7776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 chunk 98 optimal weight: 0.0020 chunk 109 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1268 ASN ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1524 HIS A1647 HIS A1669 GLN A1776 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 11091 Z= 0.192 Angle : 0.670 11.587 15358 Z= 0.344 Chirality : 0.039 0.196 1831 Planarity : 0.005 0.046 1638 Dihedral : 15.145 169.281 2210 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 25.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.37 % Favored : 91.45 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.24), residues: 1111 helix: -0.38 (0.21), residues: 585 sheet: -2.47 (0.49), residues: 87 loop : -2.61 (0.26), residues: 439 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 1.142 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: 1 outliers final: 1 residues processed: 103 average time/residue: 0.2273 time to fit residues: 33.8766 Evaluate side-chains 72 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 1.199 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0942 time to fit residues: 1.7860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 52 optimal weight: 30.0000 chunk 73 optimal weight: 30.0000 chunk 110 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 97 optimal weight: 0.9980 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 GLN ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1103 ASN ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1669 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 11091 Z= 0.219 Angle : 0.688 11.490 15358 Z= 0.356 Chirality : 0.040 0.186 1831 Planarity : 0.005 0.079 1638 Dihedral : 15.095 168.574 2210 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 31.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.64 % Favored : 91.18 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.24), residues: 1111 helix: -0.26 (0.21), residues: 580 sheet: -2.25 (0.52), residues: 82 loop : -2.51 (0.27), residues: 449 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 1.192 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: 1 outliers final: 0 residues processed: 93 average time/residue: 0.2261 time to fit residues: 31.1488 Evaluate side-chains 69 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 20.0000 chunk 99 optimal weight: 0.9990 chunk 80 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 59 optimal weight: 0.0770 chunk 104 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1060 HIS ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1268 ASN ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1669 GLN A1722 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 11091 Z= 0.196 Angle : 0.669 9.439 15358 Z= 0.344 Chirality : 0.039 0.168 1831 Planarity : 0.005 0.067 1638 Dihedral : 14.866 168.625 2210 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 28.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.91 % Favored : 90.91 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.24), residues: 1111 helix: -0.20 (0.21), residues: 583 sheet: -2.23 (0.52), residues: 82 loop : -2.41 (0.28), residues: 446 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.963 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 outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2341 time to fit residues: 32.7465 Evaluate side-chains 70 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.153 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 68 optimal weight: 30.0000 chunk 28 optimal weight: 8.9990 chunk 117 optimal weight: 20.0000 chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.0000 chunk 112 optimal weight: 20.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1268 ASN ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1523 ASN A1669 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 11091 Z= 0.194 Angle : 0.668 13.816 15358 Z= 0.341 Chirality : 0.039 0.185 1831 Planarity : 0.005 0.054 1638 Dihedral : 14.627 169.029 2210 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 28.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.09 % Favored : 90.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.24), residues: 1111 helix: -0.08 (0.21), residues: 584 sheet: -2.24 (0.51), residues: 82 loop : -2.48 (0.27), residues: 445 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.173 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 outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2182 time to fit residues: 31.5619 Evaluate side-chains 71 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.175 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 72 optimal weight: 30.0000 chunk 71 optimal weight: 0.5980 chunk 53 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 69 optimal weight: 0.0270 overall best weight: 2.7244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1268 ASN ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1669 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 11091 Z= 0.180 Angle : 0.655 14.063 15358 Z= 0.334 Chirality : 0.040 0.197 1831 Planarity : 0.004 0.048 1638 Dihedral : 14.375 169.612 2210 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 24.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.73 % Favored : 91.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.24), residues: 1111 helix: 0.01 (0.21), residues: 585 sheet: -2.05 (0.52), residues: 82 loop : -2.46 (0.27), residues: 444 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.173 Fit side-chains 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: 98 average time/residue: 0.2256 time to fit residues: 32.6253 Evaluate side-chains 70 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.113 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 HIS ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1103 ASN ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1523 ASN A1669 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 11091 Z= 0.245 Angle : 0.731 13.102 15358 Z= 0.376 Chirality : 0.041 0.175 1831 Planarity : 0.005 0.054 1638 Dihedral : 14.729 170.351 2210 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 35.81 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.99 % Favored : 89.74 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.24), residues: 1111 helix: -0.26 (0.21), residues: 585 sheet: -2.30 (0.51), residues: 82 loop : -2.57 (0.27), residues: 444 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 1.239 Fit side-chains 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: 92 average time/residue: 0.2218 time to fit residues: 30.4114 Evaluate side-chains 69 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 30.0000 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 30.0000 chunk 85 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 71 optimal weight: 0.0770 chunk 114 optimal weight: 30.0000 chunk 70 optimal weight: 7.9990 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN A1103 ASN A1268 ASN ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.5198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11091 Z= 0.212 Angle : 0.697 12.583 15358 Z= 0.358 Chirality : 0.040 0.160 1831 Planarity : 0.005 0.069 1638 Dihedral : 14.574 170.658 2210 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 31.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.90 % Favored : 89.92 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.24), residues: 1111 helix: -0.25 (0.20), residues: 592 sheet: -1.95 (0.58), residues: 68 loop : -2.50 (0.27), residues: 451 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 1.139 Fit side-chains 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: 95 average time/residue: 0.2167 time to fit residues: 30.9085 Evaluate side-chains 65 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 120 optimal weight: 30.0000 chunk 110 optimal weight: 30.0000 chunk 95 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 chunk 58 optimal weight: 0.6980 chunk 76 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1669 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 11091 Z= 0.208 Angle : 0.700 12.155 15358 Z= 0.358 Chirality : 0.040 0.182 1831 Planarity : 0.005 0.070 1638 Dihedral : 14.465 171.440 2210 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 30.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.99 % Favored : 89.83 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.24), residues: 1111 helix: -0.19 (0.21), residues: 590 sheet: -1.77 (0.61), residues: 68 loop : -2.52 (0.27), residues: 453 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 1.251 Fit side-chains 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: 90 average time/residue: 0.2237 time to fit residues: 29.8289 Evaluate side-chains 66 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 98 optimal weight: 0.0670 chunk 12 optimal weight: 30.0000 chunk 17 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN A1268 ASN ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1523 ASN A1669 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.063878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.050296 restraints weight = 147043.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.051446 restraints weight = 104806.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.052203 restraints weight = 81421.111| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 11091 Z= 0.169 Angle : 0.670 12.899 15358 Z= 0.336 Chirality : 0.040 0.192 1831 Planarity : 0.005 0.075 1638 Dihedral : 13.834 172.211 2210 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.73 % Favored : 91.09 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.25), residues: 1111 helix: 0.22 (0.21), residues: 585 sheet: -1.84 (0.54), residues: 84 loop : -2.44 (0.28), residues: 442 =============================================================================== Job complete usr+sys time: 1794.15 seconds wall clock time: 34 minutes 12.73 seconds (2052.73 seconds total)