Starting phenix.real_space_refine on Sat Dec 9 10:11:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ele_31182/12_2023/7ele_31182.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ele_31182/12_2023/7ele_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_2023/7ele_31182.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ele_31182/12_2023/7ele_31182.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ele_31182/12_2023/7ele_31182.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ele_31182/12_2023/7ele_31182.pdb" } resolution = 4.9 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= 0.000 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 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. 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 6.37, per 1000 atoms: 0.59 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: 5.57 Conformation dependent library (CDL) restraints added in 1.9 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: 3.84 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: 5.14 Time building geometry restraints manager: 5.86 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: 6285 35.91 - 71.82: 432 71.82 - 107.73: 33 107.73 - 143.65: 1 143.65 - 179.56: 3 Dihedral angle restraints: 6754 sinusoidal: 3428 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 6751 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 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: 0.350 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: 2.280 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 38.950 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 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 : 21.162 179.557 4594 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.81 % Allowed : 9.09 % Favored : 90.10 % Rotamer: Outliers : 8.44 % Allowed : 13.63 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 336 HIS 0.010 0.002 HIS A 916 PHE 0.022 0.003 PHE A1392 TYR 0.021 0.003 TYR A 757 ARG 0.010 0.001 ARG A1391 *********************** 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 : 1.207 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: 0.2914 time to fit residues: 75.7273 Evaluate side-chains 107 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 81 time to evaluate : 1.172 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2071 time to fit residues: 9.2996 ------------------------------------------------------------------------------- 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: 4.9990 chunk 70 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- 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 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 569 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** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1317 HIS A1411 GLN A1428 GLN 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11091 Z= 0.222 Angle : 0.736 9.792 15358 Z= 0.383 Chirality : 0.042 0.262 1831 Planarity : 0.005 0.082 1638 Dihedral : 19.787 170.000 2404 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 27.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.56 % Favored : 92.26 % Rotamer: Outliers : 0.31 % Allowed : 7.43 % Favored : 92.27 % 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: -2.48 (0.23), residues: 1111 helix: -0.79 (0.20), residues: 574 sheet: -2.65 (0.49), residues: 87 loop : -2.50 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 341 HIS 0.004 0.001 HIS A 326 PHE 0.019 0.002 PHE A1225 TYR 0.037 0.002 TYR A 757 ARG 0.014 0.001 ARG A 666 *********************** 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 103 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 1.201 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: 3 outliers final: 2 residues processed: 103 average time/residue: 0.2314 time to fit residues: 35.7322 Evaluate side-chains 79 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0961 time to fit residues: 1.8988 ------------------------------------------------------------------------------- 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: 0.8980 chunk 34 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 98 optimal weight: 0.2980 chunk 109 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 overall best weight: 2.8184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1776 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11091 Z= 0.190 Angle : 0.669 11.611 15358 Z= 0.345 Chirality : 0.040 0.201 1831 Planarity : 0.005 0.076 1638 Dihedral : 19.298 170.522 2404 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 25.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.19 % Favored : 91.63 % Rotamer: Outliers : 0.10 % Allowed : 6.31 % Favored : 93.59 % 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: -2.17 (0.24), residues: 1111 helix: -0.40 (0.21), residues: 584 sheet: -2.48 (0.49), residues: 87 loop : -2.62 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 341 HIS 0.009 0.001 HIS A 381 PHE 0.027 0.002 PHE A 889 TYR 0.030 0.002 TYR A 757 ARG 0.006 0.001 ARG A 747 *********************** 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 102 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 1.069 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: 1 outliers final: 1 residues processed: 102 average time/residue: 0.2399 time to fit residues: 35.2613 Evaluate side-chains 75 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1009 time to fit residues: 1.7263 ------------------------------------------------------------------------------- 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: 10.0000 chunk 82 optimal weight: 8.9990 chunk 57 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 52 optimal weight: 30.0000 chunk 73 optimal weight: 30.0000 chunk 110 optimal weight: 0.5980 chunk 116 optimal weight: 20.0000 chunk 104 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11091 Z= 0.235 Angle : 0.699 11.271 15358 Z= 0.364 Chirality : 0.040 0.186 1831 Planarity : 0.005 0.044 1638 Dihedral : 19.382 170.685 2404 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 34.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.64 % Favored : 91.18 % Rotamer: Outliers : 0.10 % Allowed : 6.21 % Favored : 93.69 % 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: -2.02 (0.24), residues: 1111 helix: -0.32 (0.21), residues: 578 sheet: -2.52 (0.50), residues: 87 loop : -2.43 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 341 HIS 0.006 0.002 HIS A 326 PHE 0.015 0.002 PHE A 556 TYR 0.027 0.002 TYR A 757 ARG 0.008 0.001 ARG A1564 *********************** 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 95 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 1.217 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: 95 average time/residue: 0.2468 time to fit residues: 34.4708 Evaluate side-chains 71 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.238 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3748 ------------------------------------------------------------------------------- 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: 2.9990 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 48 optimal weight: 40.0000 chunk 99 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 59 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1722 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11091 Z= 0.190 Angle : 0.676 12.045 15358 Z= 0.346 Chirality : 0.039 0.170 1831 Planarity : 0.005 0.060 1638 Dihedral : 19.149 171.265 2404 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 28.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.64 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % 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: -1.90 (0.24), residues: 1111 helix: -0.21 (0.21), residues: 582 sheet: -2.26 (0.52), residues: 82 loop : -2.45 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1104 HIS 0.004 0.001 HIS A 475 PHE 0.016 0.002 PHE A1225 TYR 0.024 0.002 TYR A 757 ARG 0.017 0.001 ARG A1391 *********************** 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 : 1.123 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: 97 average time/residue: 0.2320 time to fit residues: 33.1077 Evaluate side-chains 75 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.143 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5308 ------------------------------------------------------------------------------- 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: 10.0000 chunk 23 optimal weight: 30.0000 chunk 68 optimal weight: 40.0000 chunk 28 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 overall best weight: 5.3792 ------------------------------------------------------------------------------- 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 417 ASN ** 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 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN ** 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 ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11091 Z= 0.229 Angle : 0.700 11.738 15358 Z= 0.361 Chirality : 0.040 0.196 1831 Planarity : 0.005 0.049 1638 Dihedral : 19.199 172.438 2404 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 32.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.27 % Favored : 90.55 % Rotamer: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.95 (0.24), residues: 1111 helix: -0.22 (0.21), residues: 584 sheet: -2.36 (0.51), residues: 82 loop : -2.53 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1104 HIS 0.007 0.001 HIS A 382 PHE 0.013 0.002 PHE A 556 TYR 0.025 0.002 TYR A 397 ARG 0.009 0.001 ARG A1391 *********************** 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 92 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.271 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: 92 average time/residue: 0.2432 time to fit residues: 33.3078 Evaluate side-chains 71 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.615 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5134 ------------------------------------------------------------------------------- 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: 0.9990 chunk 98 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 116 optimal weight: 20.0000 chunk 72 optimal weight: 30.0000 chunk 71 optimal weight: 0.4980 chunk 53 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 69 optimal weight: 0.6980 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 333 GLN ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.4789 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= 0.166 Angle : 0.657 14.233 15358 Z= 0.330 Chirality : 0.039 0.205 1831 Planarity : 0.004 0.039 1638 Dihedral : 18.748 173.485 2404 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.46 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % 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: -1.63 (0.24), residues: 1111 helix: 0.02 (0.21), residues: 592 sheet: -1.99 (0.59), residues: 68 loop : -2.44 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 341 HIS 0.004 0.001 HIS A 398 PHE 0.016 0.001 PHE A 889 TYR 0.017 0.001 TYR A 757 ARG 0.005 0.000 ARG A1564 *********************** 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 105 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2313 time to fit residues: 35.8598 Evaluate side-chains 79 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.258 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5461 ------------------------------------------------------------------------------- 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: 0.0870 chunk 22 optimal weight: 8.9990 chunk 74 optimal weight: 50.0000 chunk 79 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 111 optimal weight: 50.0000 chunk 101 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 overall best weight: 3.7964 ------------------------------------------------------------------------------- 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 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 904 GLN ** 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** ** A1652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.5013 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= 0.197 Angle : 0.682 13.465 15358 Z= 0.342 Chirality : 0.040 0.162 1831 Planarity : 0.004 0.052 1638 Dihedral : 18.796 174.618 2404 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 27.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.82 % Favored : 91.00 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: -1.61 (0.24), residues: 1111 helix: 0.09 (0.21), residues: 588 sheet: -2.04 (0.56), residues: 74 loop : -2.50 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 341 HIS 0.012 0.001 HIS A1652 PHE 0.019 0.002 PHE A1637 TYR 0.023 0.001 TYR A 757 ARG 0.009 0.001 ARG A1564 *********************** 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 94 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.188 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: 94 average time/residue: 0.2310 time to fit residues: 32.1126 Evaluate side-chains 72 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.221 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5739 ------------------------------------------------------------------------------- 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: 50.0000 chunk 65 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 108 optimal weight: 0.4980 chunk 71 optimal weight: 0.6980 chunk 114 optimal weight: 30.0000 chunk 70 optimal weight: 0.7980 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 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** ** A1652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.5363 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= 0.169 Angle : 0.668 13.719 15358 Z= 0.334 Chirality : 0.039 0.177 1831 Planarity : 0.004 0.034 1638 Dihedral : 18.536 175.324 2404 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.01 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: -1.36 (0.25), residues: 1111 helix: 0.26 (0.22), residues: 587 sheet: -1.55 (0.63), residues: 68 loop : -2.38 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 341 HIS 0.004 0.001 HIS A 398 PHE 0.017 0.001 PHE A 889 TYR 0.021 0.001 TYR A 757 ARG 0.009 0.001 ARG A1564 *********************** 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 100 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.229 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: 100 average time/residue: 0.2375 time to fit residues: 34.9869 Evaluate side-chains 75 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.143 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5149 ------------------------------------------------------------------------------- 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: 0.2980 chunk 79 optimal weight: 7.9990 chunk 120 optimal weight: 30.0000 chunk 110 optimal weight: 8.9990 chunk 95 optimal weight: 50.0000 chunk 9 optimal weight: 0.4980 chunk 74 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 GLN ** 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** ** A1669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.5572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11091 Z= 0.172 Angle : 0.670 13.340 15358 Z= 0.332 Chirality : 0.039 0.162 1831 Planarity : 0.004 0.046 1638 Dihedral : 18.485 175.969 2404 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 22.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.28 % Favored : 91.54 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: -1.33 (0.25), residues: 1111 helix: 0.29 (0.22), residues: 588 sheet: -1.49 (0.62), residues: 72 loop : -2.39 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 341 HIS 0.004 0.001 HIS A 984 PHE 0.020 0.001 PHE A1637 TYR 0.020 0.001 TYR A 757 ARG 0.008 0.000 ARG A1564 ********************** 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 93 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.083 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: 93 average time/residue: 0.2347 time to fit residues: 31.9634 Evaluate side-chains 70 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.127 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5132 ------------------------------------------------------------------------------- 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: 5.9990 chunk 14 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 40.0000 chunk 98 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 GLN ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1103 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.059251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.046113 restraints weight = 153615.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.047150 restraints weight = 111596.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.047902 restraints weight = 88435.557| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.5630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11091 Z= 0.231 Angle : 0.722 12.474 15358 Z= 0.368 Chirality : 0.040 0.178 1831 Planarity : 0.005 0.041 1638 Dihedral : 18.695 176.746 2404 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 31.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.81 % Favored : 90.01 % Rotamer: Outliers : 0.10 % Allowed : 0.51 % Favored : 99.39 % 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: -1.69 (0.24), residues: 1111 helix: -0.04 (0.21), residues: 581 sheet: -1.48 (0.55), residues: 82 loop : -2.52 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1528 HIS 0.005 0.002 HIS A1524 PHE 0.034 0.002 PHE A1637 TYR 0.023 0.002 TYR A 757 ARG 0.009 0.001 ARG A1595 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2001.13 seconds wall clock time: 37 minutes 58.37 seconds (2278.37 seconds total)