Starting phenix.real_space_refine on Fri Mar 15 05:37:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ele_31182/03_2024/7ele_31182.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ele_31182/03_2024/7ele_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_31182/03_2024/7ele_31182.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ele_31182/03_2024/7ele_31182.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ele_31182/03_2024/7ele_31182.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ele_31182/03_2024/7ele_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.02, per 1000 atoms: 0.56 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: 5.31 Conformation dependent library (CDL) restraints added in 1.8 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: 4.06 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: 5.10 Time building geometry restraints manager: 5.69 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: 6330 35.91 - 71.82: 483 71.82 - 107.73: 33 107.73 - 143.65: 1 143.65 - 179.56: 3 Dihedral angle restraints: 6850 sinusoidal: 3524 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 6847 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: 0.330 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: 0.000 Extract box with map and model: 2.160 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 36.620 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.790 ------------------------------------------------------------------------------- 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 : 21.734 179.557 4690 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 : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 GLN cc_start: 0.9818 (mm-40) cc_final: 0.9533 (tp40) REVERT: A 331 MET cc_start: 0.7068 (mtp) cc_final: 0.6798 (mtm) REVERT: A 352 VAL cc_start: 0.9594 (t) cc_final: 0.9234 (m) REVERT: A 393 MET cc_start: 0.9478 (tpt) cc_final: 0.9058 (tpp) REVERT: A 397 TYR cc_start: 0.9695 (t80) cc_final: 0.9456 (t80) REVERT: A 670 PHE cc_start: 0.9605 (m-80) cc_final: 0.9271 (m-80) REVERT: A 691 SER cc_start: 0.9230 (OUTLIER) cc_final: 0.9010 (p) REVERT: A 746 MET cc_start: 0.9629 (OUTLIER) cc_final: 0.9235 (tpp) REVERT: A 845 HIS cc_start: 0.9006 (t70) cc_final: 0.8765 (t70) REVERT: A 900 MET cc_start: 0.9432 (ttp) cc_final: 0.9207 (tpt) REVERT: A 1087 PHE cc_start: 0.9083 (m-10) cc_final: 0.8761 (p90) REVERT: A 1261 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: A 1408 MET cc_start: 0.9507 (mmm) cc_final: 0.9254 (mtt) REVERT: A 1416 MET cc_start: 0.9634 (mmt) cc_final: 0.9407 (mmp) REVERT: A 1742 CYS cc_start: 0.6261 (OUTLIER) cc_final: 0.5279 (p) REVERT: A 1781 MET cc_start: 0.8569 (mmt) cc_final: 0.8322 (mmp) outliers start: 83 outliers final: 26 residues processed: 193 average time/residue: 0.2723 time to fit residues: 70.5082 Evaluate side-chains 115 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 85 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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: 6.9990 chunk 91 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 94 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 70 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11091 Z= 0.230 Angle : 0.737 10.712 15358 Z= 0.383 Chirality : 0.042 0.260 1831 Planarity : 0.006 0.086 1638 Dihedral : 20.862 170.052 2500 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 28.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.29 % Favored : 92.53 % Rotamer: Outliers : 0.20 % Allowed : 6.61 % Favored : 93.18 % 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: -2.52 (0.23), residues: 1111 helix: -0.82 (0.20), residues: 581 sheet: -2.59 (0.48), residues: 87 loop : -2.57 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 341 HIS 0.005 0.001 HIS A 808 PHE 0.020 0.002 PHE A1225 TYR 0.036 0.002 TYR A 757 ARG 0.012 0.001 ARG A1391 *********************** 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 106 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.9605 (tm-30) cc_final: 0.9262 (mp0) REVERT: A 369 MET cc_start: 0.9483 (mmp) cc_final: 0.9064 (tmm) REVERT: A 393 MET cc_start: 0.9366 (tpt) cc_final: 0.8710 (tpp) REVERT: A 397 TYR cc_start: 0.9674 (t80) cc_final: 0.9454 (t80) REVERT: A 670 PHE cc_start: 0.9573 (m-80) cc_final: 0.9270 (m-80) REVERT: A 746 MET cc_start: 0.9464 (tpt) cc_final: 0.8666 (mmm) REVERT: A 774 MET cc_start: 0.9014 (ttt) cc_final: 0.7551 (tpp) REVERT: A 900 MET cc_start: 0.9659 (ttp) cc_final: 0.9449 (tpp) REVERT: A 1340 MET cc_start: 0.9352 (mmm) cc_final: 0.9032 (mmm) REVERT: A 1408 MET cc_start: 0.9548 (mmm) cc_final: 0.9268 (mtt) REVERT: A 1646 LEU cc_start: 0.9331 (mm) cc_final: 0.8804 (mm) REVERT: A 1704 LEU cc_start: 0.9524 (tt) cc_final: 0.9316 (mt) REVERT: A 1724 MET cc_start: 0.7300 (mpp) cc_final: 0.7033 (mpp) outliers start: 2 outliers final: 1 residues processed: 106 average time/residue: 0.2144 time to fit residues: 34.0356 Evaluate side-chains 81 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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: 20.0000 chunk 34 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 chunk 98 optimal weight: 0.0170 chunk 109 optimal weight: 30.0000 chunk 37 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 overall best weight: 4.8026 ------------------------------------------------------------------------------- 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 741 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** A1103 ASN A1261 GLN ** 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** ** A1647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11091 Z= 0.230 Angle : 0.699 11.046 15358 Z= 0.363 Chirality : 0.040 0.193 1831 Planarity : 0.005 0.047 1638 Dihedral : 20.700 170.711 2500 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 32.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.55 % Favored : 91.27 % Rotamer: Outliers : 0.10 % Allowed : 6.61 % Favored : 93.29 % 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: -2.25 (0.24), residues: 1111 helix: -0.56 (0.20), residues: 585 sheet: -2.48 (0.49), residues: 87 loop : -2.51 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 341 HIS 0.010 0.002 HIS A 381 PHE 0.027 0.002 PHE A 889 TYR 0.027 0.002 TYR A 757 ARG 0.007 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 97 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.948 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: A 346 GLU cc_start: 0.9605 (tm-30) cc_final: 0.9287 (mp0) REVERT: A 369 MET cc_start: 0.9536 (mmp) cc_final: 0.9116 (tmm) REVERT: A 393 MET cc_start: 0.9331 (tpt) cc_final: 0.8699 (tpp) REVERT: A 397 TYR cc_start: 0.9679 (t80) cc_final: 0.9436 (t80) REVERT: A 670 PHE cc_start: 0.9593 (m-80) cc_final: 0.9249 (m-80) REVERT: A 746 MET cc_start: 0.9489 (tpt) cc_final: 0.8630 (mmm) REVERT: A 774 MET cc_start: 0.8796 (ttt) cc_final: 0.7680 (tpp) REVERT: A 900 MET cc_start: 0.9650 (ttp) cc_final: 0.9448 (tpt) REVERT: A 1340 MET cc_start: 0.9404 (mmm) cc_final: 0.9107 (mmm) REVERT: A 1412 MET cc_start: 0.9632 (mmp) cc_final: 0.9399 (mmm) REVERT: A 1724 MET cc_start: 0.7594 (mpp) cc_final: 0.7302 (mpp) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.2235 time to fit residues: 32.3570 Evaluate side-chains 74 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.234 ------------------------------------------------------------------------------- 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: 20.0000 chunk 82 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 52 optimal weight: 50.0000 chunk 73 optimal weight: 40.0000 chunk 110 optimal weight: 40.0000 chunk 116 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 overall best weight: 11.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 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 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 GLN A 575 GLN ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 HIS ** A 886 ASN ** 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** ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1775 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 11091 Z= 0.397 Angle : 0.896 10.170 15358 Z= 0.472 Chirality : 0.047 0.259 1831 Planarity : 0.007 0.092 1638 Dihedral : 21.249 170.240 2500 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 54.78 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.71 % Favored : 89.02 % Rotamer: Outliers : 0.20 % Allowed : 8.14 % Favored : 91.66 % 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: -2.83 (0.22), residues: 1111 helix: -1.13 (0.19), residues: 569 sheet: -2.65 (0.51), residues: 82 loop : -2.62 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A1528 HIS 0.012 0.003 HIS A1401 PHE 0.020 0.003 PHE A1392 TYR 0.024 0.003 TYR A 757 ARG 0.010 0.001 ARG A1391 *********************** 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 89 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.9440 (tpt) cc_final: 0.8892 (tpp) REVERT: A 397 TYR cc_start: 0.9730 (t80) cc_final: 0.9500 (t80) REVERT: A 411 MET cc_start: 0.8027 (mtt) cc_final: 0.7710 (mtt) REVERT: A 670 PHE cc_start: 0.9646 (m-80) cc_final: 0.9404 (m-80) REVERT: A 900 MET cc_start: 0.9621 (ttp) cc_final: 0.9420 (tpt) REVERT: A 1340 MET cc_start: 0.9299 (mmm) cc_final: 0.9075 (mmm) REVERT: A 1412 MET cc_start: 0.9682 (mmp) cc_final: 0.9470 (mmm) REVERT: A 1597 GLU cc_start: 0.8523 (tm-30) cc_final: 0.7785 (mt-10) REVERT: A 1724 MET cc_start: 0.7679 (mpp) cc_final: 0.7433 (mpp) outliers start: 2 outliers final: 1 residues processed: 89 average time/residue: 0.2299 time to fit residues: 29.8695 Evaluate side-chains 69 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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: 4.9990 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 0.2980 chunk 99 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 59 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- 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 538 ASN ** A 660 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 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: 0.7352 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11091 Z= 0.212 Angle : 0.711 11.630 15358 Z= 0.364 Chirality : 0.041 0.181 1831 Planarity : 0.006 0.077 1638 Dihedral : 20.579 170.721 2500 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 32.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.27 % Favored : 90.55 % Rotamer: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.31 (0.23), residues: 1111 helix: -0.61 (0.20), residues: 577 sheet: -2.42 (0.50), residues: 82 loop : -2.54 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1104 HIS 0.004 0.001 HIS A 661 PHE 0.017 0.002 PHE A1225 TYR 0.021 0.002 TYR A 757 ARG 0.020 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 94 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.161 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: A 393 MET cc_start: 0.9422 (tpt) cc_final: 0.8807 (tpp) REVERT: A 397 TYR cc_start: 0.9670 (t80) cc_final: 0.9434 (t80) REVERT: A 411 MET cc_start: 0.7638 (mtt) cc_final: 0.7266 (mtt) REVERT: A 670 PHE cc_start: 0.9550 (m-80) cc_final: 0.9237 (m-80) REVERT: A 695 CYS cc_start: 0.9590 (m) cc_final: 0.9383 (t) REVERT: A 746 MET cc_start: 0.9183 (tpt) cc_final: 0.8808 (tpt) REVERT: A 900 MET cc_start: 0.9615 (ttp) cc_final: 0.9403 (tpt) REVERT: A 1340 MET cc_start: 0.9384 (mmm) cc_final: 0.9046 (mmm) REVERT: A 1412 MET cc_start: 0.9711 (mmp) cc_final: 0.9476 (mmm) REVERT: A 1724 MET cc_start: 0.7711 (mpp) cc_final: 0.7466 (mpp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2345 time to fit residues: 31.7272 Evaluate side-chains 71 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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: 8.9990 chunk 23 optimal weight: 7.9990 chunk 68 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 112 optimal weight: 20.0000 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN ** 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 723 HIS ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** A1647 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: 0.7392 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11091 Z= 0.259 Angle : 0.741 11.689 15358 Z= 0.382 Chirality : 0.042 0.189 1831 Planarity : 0.005 0.063 1638 Dihedral : 20.594 172.582 2500 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 38.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.35 % Favored : 89.47 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % 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: -2.26 (0.24), residues: 1111 helix: -0.59 (0.20), residues: 578 sheet: -2.30 (0.50), residues: 82 loop : -2.50 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1528 HIS 0.006 0.002 HIS A 382 PHE 0.013 0.002 PHE A 889 TYR 0.020 0.002 TYR A 771 ARG 0.011 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 94 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.9318 (mtm) cc_final: 0.8635 (ttp) REVERT: A 393 MET cc_start: 0.9408 (tpt) cc_final: 0.8825 (tpp) REVERT: A 397 TYR cc_start: 0.9671 (t80) cc_final: 0.9435 (t80) REVERT: A 411 MET cc_start: 0.7727 (mtt) cc_final: 0.7503 (mtp) REVERT: A 670 PHE cc_start: 0.9513 (m-80) cc_final: 0.9254 (m-10) REVERT: A 695 CYS cc_start: 0.9566 (m) cc_final: 0.9362 (t) REVERT: A 900 MET cc_start: 0.9585 (ttp) cc_final: 0.9368 (tpt) REVERT: A 1339 SER cc_start: 0.9558 (t) cc_final: 0.9327 (p) REVERT: A 1340 MET cc_start: 0.9400 (mmm) cc_final: 0.8884 (mmm) REVERT: A 1408 MET cc_start: 0.9502 (mmm) cc_final: 0.9208 (mtt) REVERT: A 1412 MET cc_start: 0.9710 (mmp) cc_final: 0.9486 (mmm) REVERT: A 1576 LEU cc_start: 0.9714 (tt) cc_final: 0.9484 (tt) REVERT: A 1597 GLU cc_start: 0.8580 (tm-30) cc_final: 0.7929 (mt-10) REVERT: A 1724 MET cc_start: 0.7835 (mpp) cc_final: 0.7629 (mpp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2455 time to fit residues: 32.8185 Evaluate side-chains 73 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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: 0.0980 chunk 66 optimal weight: 6.9990 chunk 85 optimal weight: 0.0770 chunk 98 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 72 optimal weight: 30.0000 chunk 71 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 overall best weight: 4.0344 ------------------------------------------------------------------------------- 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 660 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 ** A1647 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: 0.7348 moved from start: 0.4577 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= 0.206 Angle : 0.700 14.656 15358 Z= 0.356 Chirality : 0.041 0.201 1831 Planarity : 0.005 0.055 1638 Dihedral : 20.356 173.578 2500 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 31.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.26 % Favored : 89.56 % 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: -1.97 (0.24), residues: 1111 helix: -0.26 (0.21), residues: 573 sheet: -2.27 (0.50), residues: 82 loop : -2.47 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1104 HIS 0.006 0.001 HIS A 382 PHE 0.015 0.002 PHE A 889 TYR 0.027 0.002 TYR A 757 ARG 0.007 0.001 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 95 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.9241 (mtm) cc_final: 0.8429 (ttp) REVERT: A 393 MET cc_start: 0.9379 (tpt) cc_final: 0.9129 (tpp) REVERT: A 397 TYR cc_start: 0.9668 (t80) cc_final: 0.9443 (t80) REVERT: A 411 MET cc_start: 0.7582 (mtt) cc_final: 0.7181 (mtt) REVERT: A 670 PHE cc_start: 0.9344 (m-80) cc_final: 0.8957 (m-80) REVERT: A 695 CYS cc_start: 0.9570 (m) cc_final: 0.9358 (t) REVERT: A 746 MET cc_start: 0.8852 (tpt) cc_final: 0.8378 (tpt) REVERT: A 900 MET cc_start: 0.9579 (ttp) cc_final: 0.9358 (tpt) REVERT: A 1340 MET cc_start: 0.9369 (mmm) cc_final: 0.8981 (mmm) REVERT: A 1412 MET cc_start: 0.9709 (mmp) cc_final: 0.9449 (mmm) REVERT: A 1724 MET cc_start: 0.7737 (mpp) cc_final: 0.7526 (mpp) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2278 time to fit residues: 30.8675 Evaluate side-chains 71 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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: 6.9990 chunk 22 optimal weight: 10.0000 chunk 74 optimal weight: 30.0000 chunk 79 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 106 optimal weight: 0.3980 chunk 111 optimal weight: 40.0000 chunk 101 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 overall best weight: 3.8788 ------------------------------------------------------------------------------- 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 312 GLN ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 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** 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** ** A1647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1776 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4840 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= 0.201 Angle : 0.692 14.062 15358 Z= 0.352 Chirality : 0.041 0.232 1831 Planarity : 0.005 0.063 1638 Dihedral : 20.214 175.313 2500 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 31.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.99 % Favored : 89.83 % 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: -1.86 (0.24), residues: 1111 helix: -0.15 (0.21), residues: 577 sheet: -2.22 (0.50), residues: 82 loop : -2.47 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 341 HIS 0.005 0.001 HIS A1652 PHE 0.018 0.002 PHE A 396 TYR 0.028 0.002 TYR A 757 ARG 0.007 0.001 ARG A 765 *********************** 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 91 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 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 revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.8854 (mtt) cc_final: 0.8544 (mmm) REVERT: A 369 MET cc_start: 0.9278 (mtm) cc_final: 0.8445 (ttp) REVERT: A 393 MET cc_start: 0.9311 (tpt) cc_final: 0.8807 (tpp) REVERT: A 397 TYR cc_start: 0.9619 (t80) cc_final: 0.9393 (t80) REVERT: A 411 MET cc_start: 0.7434 (mtt) cc_final: 0.7030 (mtt) REVERT: A 670 PHE cc_start: 0.9403 (m-80) cc_final: 0.9082 (m-10) REVERT: A 707 MET cc_start: 0.7192 (mmp) cc_final: 0.6979 (tpp) REVERT: A 746 MET cc_start: 0.8839 (tpt) cc_final: 0.8517 (tpt) REVERT: A 900 MET cc_start: 0.9574 (ttp) cc_final: 0.9339 (tpt) REVERT: A 1340 MET cc_start: 0.9206 (mmm) cc_final: 0.8892 (mmm) REVERT: A 1408 MET cc_start: 0.9498 (mmm) cc_final: 0.9218 (mtt) REVERT: A 1412 MET cc_start: 0.9697 (mmp) cc_final: 0.9448 (mmm) REVERT: A 1597 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8350 (tm-30) REVERT: A 1724 MET cc_start: 0.7774 (mpp) cc_final: 0.7558 (mpp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2392 time to fit residues: 31.1953 Evaluate side-chains 71 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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: 8.9990 chunk 33 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 114 optimal weight: 30.0000 chunk 70 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 433 ASN ** 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 ** 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** ** A1647 HIS ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.5095 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= 0.211 Angle : 0.692 13.356 15358 Z= 0.353 Chirality : 0.040 0.175 1831 Planarity : 0.005 0.071 1638 Dihedral : 20.155 176.792 2500 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 34.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.72 % Favored : 90.10 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -1.93 (0.24), residues: 1111 helix: -0.19 (0.21), residues: 581 sheet: -2.37 (0.50), residues: 82 loop : -2.50 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1528 HIS 0.006 0.001 HIS A1652 PHE 0.015 0.002 PHE A 889 TYR 0.028 0.002 TYR A 757 ARG 0.018 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 93 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.8826 (mtt) cc_final: 0.8510 (mmm) REVERT: A 369 MET cc_start: 0.9267 (mtm) cc_final: 0.8417 (ttp) REVERT: A 393 MET cc_start: 0.9383 (tpt) cc_final: 0.8882 (tpp) REVERT: A 397 TYR cc_start: 0.9634 (t80) cc_final: 0.9400 (t80) REVERT: A 670 PHE cc_start: 0.9432 (m-80) cc_final: 0.9130 (m-10) REVERT: A 707 MET cc_start: 0.7505 (mmp) cc_final: 0.7249 (tpp) REVERT: A 746 MET cc_start: 0.8713 (tpt) cc_final: 0.8471 (tpt) REVERT: A 774 MET cc_start: 0.8324 (ttt) cc_final: 0.7726 (tpp) REVERT: A 900 MET cc_start: 0.9563 (ttp) cc_final: 0.9309 (tpt) REVERT: A 1340 MET cc_start: 0.9216 (mmm) cc_final: 0.8904 (mmm) REVERT: A 1408 MET cc_start: 0.9494 (mmm) cc_final: 0.9200 (mtt) REVERT: A 1412 MET cc_start: 0.9698 (mmp) cc_final: 0.9437 (mmm) REVERT: A 1724 MET cc_start: 0.7829 (mpp) cc_final: 0.7412 (mpp) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.2415 time to fit residues: 31.9248 Evaluate side-chains 70 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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: 30.0000 chunk 79 optimal weight: 6.9990 chunk 120 optimal weight: 30.0000 chunk 110 optimal weight: 8.9990 chunk 95 optimal weight: 50.0000 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 58 optimal weight: 30.0000 chunk 76 optimal weight: 40.0000 chunk 102 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 433 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** ** 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** ** A1647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1652 HIS ** A1669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11091 Z= 0.283 Angle : 0.773 12.661 15358 Z= 0.401 Chirality : 0.043 0.233 1831 Planarity : 0.006 0.081 1638 Dihedral : 20.409 177.580 2500 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 42.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.16 % Favored : 88.66 % Rotamer: Outliers : 0.10 % Allowed : 0.31 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -2.22 (0.24), residues: 1111 helix: -0.52 (0.20), residues: 575 sheet: -2.37 (0.51), residues: 82 loop : -2.52 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1528 HIS 0.007 0.002 HIS A 326 PHE 0.016 0.002 PHE A1392 TYR 0.029 0.002 TYR A 757 ARG 0.006 0.001 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 90 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 1.237 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: A 393 MET cc_start: 0.9394 (tpt) cc_final: 0.8909 (tpp) REVERT: A 397 TYR cc_start: 0.9658 (t80) cc_final: 0.9440 (t80) REVERT: A 411 MET cc_start: 0.7554 (mtt) cc_final: 0.7176 (mtt) REVERT: A 670 PHE cc_start: 0.9445 (m-80) cc_final: 0.9152 (m-10) REVERT: A 707 MET cc_start: 0.7757 (mmp) cc_final: 0.7503 (tpp) REVERT: A 774 MET cc_start: 0.8439 (ttt) cc_final: 0.7860 (tpp) REVERT: A 900 MET cc_start: 0.9529 (ttp) cc_final: 0.9278 (tpt) REVERT: A 1340 MET cc_start: 0.9164 (mmm) cc_final: 0.8840 (mmm) REVERT: A 1412 MET cc_start: 0.9711 (mmp) cc_final: 0.9446 (mmm) REVERT: A 1597 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8301 (tm-30) REVERT: A 1724 MET cc_start: 0.7902 (mpp) cc_final: 0.7507 (mpp) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.2423 time to fit residues: 31.3838 Evaluate side-chains 71 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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: 0.4980 chunk 14 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 98 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 17 optimal weight: 30.0000 chunk 84 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 overall best weight: 2.8384 ------------------------------------------------------------------------------- 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 433 ASN A 538 ASN ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 HIS ** 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** ** A1647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1722 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.059935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.046740 restraints weight = 152365.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.047784 restraints weight = 110566.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.048480 restraints weight = 86893.628| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11091 Z= 0.189 Angle : 0.690 12.590 15358 Z= 0.347 Chirality : 0.040 0.165 1831 Planarity : 0.005 0.075 1638 Dihedral : 19.920 177.491 2500 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 28.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.54 % Favored : 90.28 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -1.83 (0.24), residues: 1111 helix: -0.12 (0.21), residues: 580 sheet: -2.30 (0.51), residues: 82 loop : -2.45 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 547 HIS 0.004 0.001 HIS A 382 PHE 0.020 0.002 PHE A 396 TYR 0.028 0.001 TYR A 757 ARG 0.009 0.001 ARG A1564 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1908.39 seconds wall clock time: 35 minutes 57.23 seconds (2157.23 seconds total)