Starting phenix.real_space_refine on Sat Jul 20 17:30:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm4_37640/07_2024/8wm4_37640_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm4_37640/07_2024/8wm4_37640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm4_37640/07_2024/8wm4_37640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm4_37640/07_2024/8wm4_37640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm4_37640/07_2024/8wm4_37640_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wm4_37640/07_2024/8wm4_37640_neut.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 38 5.49 5 S 53 5.16 5 C 7151 2.51 5 N 2037 2.21 5 O 2247 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 350": "OE1" <-> "OE2" Residue "A GLU 573": "OE1" <-> "OE2" Residue "A GLU 1267": "OE1" <-> "OE2" Residue "A PHE 1348": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11530 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1331, 10722 Classifications: {'peptide': 1331} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 75, 'TRANS': 1255} Chain breaks: 11 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 804 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 9, 'rna3p_pur': 5, 'rna3p_pyr': 12} Link IDs: {'rna2p': 21, 'rna3p': 16} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 704 SG CYS A 86 38.454 69.978 17.430 1.00163.97 S ATOM 950 SG CYS A 115 37.638 71.529 14.053 1.00166.94 S ATOM 1012 SG CYS A 123 35.076 71.742 16.908 1.00160.83 S ATOM 1036 SG CYS A 126 38.245 73.748 16.992 1.00162.01 S ATOM 3123 SG CYS A 463 47.884 48.549 43.963 1.00141.67 S ATOM 3221 SG CYS A 477 45.686 49.972 40.258 1.00100.77 S ATOM 5038 SG CYS A 706 59.479 38.249 68.581 1.00153.32 S ATOM 5053 SG CYS A 708 56.771 35.686 69.491 1.00124.76 S ATOM 5075 SG CYS A 711 55.779 39.247 68.454 1.00109.54 S ATOM 6938 SG CYS A 965 54.096 40.179 107.956 1.00 57.21 S ATOM 8561 SG CYS A1312 56.829 40.755 105.371 1.00112.45 S ATOM 8624 SG CYS A1342 55.453 37.220 106.081 1.00 60.94 S ATOM 8642 SG CYS A1345 53.393 39.494 104.170 1.00 93.73 S Time building chain proxies: 8.22, per 1000 atoms: 0.71 Number of scatterers: 11530 At special positions: 0 Unit cell: (78.2, 101.15, 171.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 53 16.00 P 38 15.00 O 2247 8.00 N 2037 7.00 C 7151 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: 5.04 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 126 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 115 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 86 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 123 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 477 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 463 " pdb=" ZN A1703 " pdb="ZN ZN A1703 " - pdb=" ND1 HIS A 703 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 711 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 708 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 706 " pdb=" ZN A1704 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1342 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1345 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 965 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1312 " Number of angles added : 15 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2468 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 19 sheets defined 28.9% alpha, 15.7% beta 0 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 57 through 76 removed outlier: 4.282A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.808A pdb=" N ILE A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 225 removed outlier: 4.255A pdb=" N ALA A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 276 Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.864A pdb=" N VAL A 299 " --> pdb=" O SER A 296 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 300 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 340 through 344 removed outlier: 3.681A pdb=" N LYS A 343 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN A 344 " --> pdb=" O GLU A 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 340 through 344' Processing helix chain 'A' and resid 345 through 364 Processing helix chain 'A' and resid 443 through 460 removed outlier: 3.835A pdb=" N VAL A 447 " --> pdb=" O PRO A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 Processing helix chain 'A' and resid 542 through 555 Processing helix chain 'A' and resid 584 through 595 Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 599 through 610 removed outlier: 4.033A pdb=" N LYS A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 648 Processing helix chain 'A' and resid 675 through 691 Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 780 through 785 Processing helix chain 'A' and resid 785 through 801 Processing helix chain 'A' and resid 829 through 833 Processing helix chain 'A' and resid 946 through 962 removed outlier: 4.032A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1247 Processing helix chain 'A' and resid 1300 through 1305 removed outlier: 3.695A pdb=" N MET A1305 " --> pdb=" O GLY A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1395 through 1400 removed outlier: 4.123A pdb=" N SER A1399 " --> pdb=" O ARG A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1426 removed outlier: 3.972A pdb=" N ASP A1426 " --> pdb=" O LYS A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1477 Processing helix chain 'A' and resid 1488 through 1492 Processing helix chain 'A' and resid 1518 through 1534 Processing helix chain 'A' and resid 1538 through 1548 removed outlier: 3.778A pdb=" N GLU A1542 " --> pdb=" O LEU A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1569 removed outlier: 4.206A pdb=" N ASP A1568 " --> pdb=" O ARG A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1581 removed outlier: 3.956A pdb=" N ASP A1581 " --> pdb=" O GLU A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1588 through 1593 Processing sheet with id=AA1, first strand: chain 'A' and resid 199 through 202 Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 17 removed outlier: 3.769A pdb=" N TYR A 190 " --> pdb=" O MET A 17 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP A 185 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 149 through 150 removed outlier: 3.518A pdb=" N HIS A 149 " --> pdb=" O THR A 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 483 through 485 removed outlier: 6.600A pdb=" N GLU A 403 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR A 579 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 405 " --> pdb=" O TYR A 577 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR A 577 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N CYS A 407 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA A 575 " --> pdb=" O CYS A 407 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AA7, first strand: chain 'A' and resid 497 through 501 removed outlier: 3.921A pdb=" N GLU A 497 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 521 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 517 " --> pdb=" O ARG A 501 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 659 through 664 removed outlier: 3.746A pdb=" N GLU A 667 " --> pdb=" O GLU A 664 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 659 through 664 removed outlier: 3.746A pdb=" N GLU A 667 " --> pdb=" O GLU A 664 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A 819 " --> pdb=" O GLU A 633 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 692 through 693 Processing sheet with id=AB2, first strand: chain 'A' and resid 739 through 741 Processing sheet with id=AB3, first strand: chain 'A' and resid 861 through 862 Processing sheet with id=AB4, first strand: chain 'A' and resid 866 through 867 Processing sheet with id=AB5, first strand: chain 'A' and resid 944 through 945 Processing sheet with id=AB6, first strand: chain 'A' and resid 944 through 945 removed outlier: 5.530A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS A 898 " --> pdb=" O VAL A1500 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL A1500 " --> pdb=" O LYS A 898 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE A 900 " --> pdb=" O ILE A1498 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE A1498 " --> pdb=" O ILE A 900 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 908 through 909 removed outlier: 3.773A pdb=" N ALA A 935 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 976 through 978 Processing sheet with id=AB9, first strand: chain 'A' and resid 1276 through 1280 removed outlier: 6.798A pdb=" N TYR A1276 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE A1287 " --> pdb=" O TYR A1276 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LYS A1278 " --> pdb=" O GLU A1285 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1386 through 1387 342 hydrogen bonds defined for protein. 948 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 4.54 Time building geometry restraints manager: 5.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2883 1.33 - 1.46: 2714 1.46 - 1.58: 6120 1.58 - 1.70: 75 1.70 - 1.83: 76 Bond restraints: 11868 Sorted by residual: bond pdb=" N PRO A1253 " pdb=" CD PRO A1253 " ideal model delta sigma weight residual 1.473 1.524 -0.051 1.40e-02 5.10e+03 1.32e+01 bond pdb=" N VAL A1011 " pdb=" CA VAL A1011 " ideal model delta sigma weight residual 1.462 1.490 -0.028 8.70e-03 1.32e+04 1.05e+01 bond pdb=" N VAL A 817 " pdb=" CA VAL A 817 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.15e-02 7.56e+03 8.19e+00 bond pdb=" N GLU A1227 " pdb=" CA GLU A1227 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.27e-02 6.20e+03 7.66e+00 bond pdb=" N ASP A 160 " pdb=" CA ASP A 160 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.27e-02 6.20e+03 7.59e+00 ... (remaining 11863 not shown) Histogram of bond angle deviations from ideal: 98.42 - 106.47: 580 106.47 - 114.52: 6729 114.52 - 122.58: 7032 122.58 - 130.63: 1763 130.63 - 138.68: 63 Bond angle restraints: 16167 Sorted by residual: angle pdb=" CB LYS A 216 " pdb=" CG LYS A 216 " pdb=" CD LYS A 216 " ideal model delta sigma weight residual 111.30 124.30 -13.00 2.30e+00 1.89e-01 3.20e+01 angle pdb=" CB LYS A 297 " pdb=" CG LYS A 297 " pdb=" CD LYS A 297 " ideal model delta sigma weight residual 111.30 123.80 -12.50 2.30e+00 1.89e-01 2.95e+01 angle pdb=" N ASP A1298 " pdb=" CA ASP A1298 " pdb=" C ASP A1298 " ideal model delta sigma weight residual 113.97 107.10 6.87 1.28e+00 6.10e-01 2.88e+01 angle pdb=" CA TRP A1180 " pdb=" CB TRP A1180 " pdb=" CG TRP A1180 " ideal model delta sigma weight residual 113.60 122.66 -9.06 1.90e+00 2.77e-01 2.27e+01 angle pdb=" CA ILE A1236 " pdb=" CB ILE A1236 " pdb=" CG1 ILE A1236 " ideal model delta sigma weight residual 110.40 118.43 -8.03 1.70e+00 3.46e-01 2.23e+01 ... (remaining 16162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 6236 17.87 - 35.75: 739 35.75 - 53.62: 195 53.62 - 71.50: 64 71.50 - 89.37: 21 Dihedral angle restraints: 7255 sinusoidal: 3430 harmonic: 3825 Sorted by residual: dihedral pdb=" CA TYR A1208 " pdb=" C TYR A1208 " pdb=" N TYR A1209 " pdb=" CA TYR A1209 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA THR A1217 " pdb=" C THR A1217 " pdb=" N PHE A1218 " pdb=" CA PHE A1218 " ideal model delta harmonic sigma weight residual -180.00 -160.25 -19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA PRO A 198 " pdb=" C PRO A 198 " pdb=" N ARG A 199 " pdb=" CA ARG A 199 " ideal model delta harmonic sigma weight residual -180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 7252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1486 0.067 - 0.134: 212 0.134 - 0.201: 21 0.201 - 0.268: 3 0.268 - 0.335: 5 Chirality restraints: 1727 Sorted by residual: chirality pdb=" CA ARG A 535 " pdb=" N ARG A 535 " pdb=" C ARG A 535 " pdb=" CB ARG A 535 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA MET A1211 " pdb=" N MET A1211 " pdb=" C MET A1211 " pdb=" CB MET A1211 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA LYS A1223 " pdb=" N LYS A1223 " pdb=" C LYS A1223 " pdb=" CB LYS A1223 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 1724 not shown) Planarity restraints: 1963 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 20 " 0.018 2.00e-02 2.50e+03 2.39e-02 1.42e+01 pdb=" CG TRP A 20 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP A 20 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A 20 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 20 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 20 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 20 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 20 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 20 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 20 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A1439 " -0.051 5.00e-02 4.00e+02 7.80e-02 9.74e+00 pdb=" N PRO A1440 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A1440 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A1440 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 350 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.02e+00 pdb=" CD GLU A 350 " 0.052 2.00e-02 2.50e+03 pdb=" OE1 GLU A 350 " -0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU A 350 " -0.018 2.00e-02 2.50e+03 ... (remaining 1960 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3100 2.81 - 3.33: 9309 3.33 - 3.86: 18342 3.86 - 4.38: 20769 4.38 - 4.90: 36164 Nonbonded interactions: 87684 Sorted by model distance: nonbonded pdb=" O THR A1185 " pdb=" OH TYR A1214 " model vdw 2.291 2.440 nonbonded pdb=" OE1 GLN A 21 " pdb=" CD2 PHE A 33 " model vdw 2.303 3.340 nonbonded pdb=" OG SER A 154 " pdb=" OP2 U R 0 " model vdw 2.323 2.440 nonbonded pdb=" OH TYR A 863 " pdb=" OP2 A R 29 " model vdw 2.340 2.440 nonbonded pdb=" OD2 ASP A 193 " pdb=" OG1 THR A 195 " model vdw 2.360 2.440 ... (remaining 87679 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 40.710 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 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:11.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 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 : 0.004 0.057 11868 Z= 0.282 Angle : 0.866 13.682 16167 Z= 0.465 Chirality : 0.050 0.335 1727 Planarity : 0.007 0.078 1963 Dihedral : 17.050 89.371 4787 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.78 % Allowed : 18.72 % Favored : 80.50 % 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: -2.05 (0.20), residues: 1307 helix: -0.78 (0.25), residues: 335 sheet: -0.23 (0.35), residues: 190 loop : -2.00 (0.19), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 20 HIS 0.005 0.001 HIS A 865 PHE 0.028 0.002 PHE A 197 TYR 0.038 0.002 TYR A1228 ARG 0.016 0.001 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 1.222 Fit side-chains revert: symmetry clash REVERT: A 184 HIS cc_start: 0.6969 (OUTLIER) cc_final: 0.6726 (t-170) REVERT: A 199 ARG cc_start: 0.7057 (ttm110) cc_final: 0.6653 (ttt-90) REVERT: A 236 ARG cc_start: 0.6391 (OUTLIER) cc_final: 0.6124 (ttp-110) REVERT: A 771 MET cc_start: 0.6966 (mmm) cc_final: 0.6710 (mmm) outliers start: 9 outliers final: 4 residues processed: 112 average time/residue: 1.4781 time to fit residues: 178.1798 Evaluate side-chains 93 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 834 ASN Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain A residue 1156 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 626 HIS A 816 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11868 Z= 0.233 Angle : 0.584 6.931 16167 Z= 0.302 Chirality : 0.041 0.209 1727 Planarity : 0.005 0.062 1963 Dihedral : 13.929 87.359 2062 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.03 % Allowed : 19.32 % Favored : 77.64 % 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: -1.30 (0.21), residues: 1307 helix: 0.47 (0.28), residues: 328 sheet: -0.22 (0.34), residues: 205 loop : -1.72 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 595 HIS 0.008 0.001 HIS A 865 PHE 0.016 0.002 PHE A1456 TYR 0.017 0.002 TYR A 958 ARG 0.006 0.001 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 100 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7220 (mppt) cc_final: 0.6644 (mtpt) REVERT: A 201 GLU cc_start: 0.5264 (mm-30) cc_final: 0.4990 (mm-30) REVERT: A 519 MET cc_start: 0.7839 (ttp) cc_final: 0.7600 (ttp) REVERT: A 538 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6134 (mt-10) REVERT: A 692 MET cc_start: 0.5354 (mmm) cc_final: 0.4384 (tmm) REVERT: A 827 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7484 (mptp) REVERT: A 1162 LYS cc_start: 0.5722 (OUTLIER) cc_final: 0.5394 (mttm) REVERT: A 1395 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7482 (mmm160) REVERT: A 1403 SER cc_start: 0.8423 (m) cc_final: 0.7879 (t) outliers start: 35 outliers final: 14 residues processed: 127 average time/residue: 1.2423 time to fit residues: 171.5480 Evaluate side-chains 107 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 1162 LYS Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1472 ILE Chi-restraints excluded: chain A residue 1571 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 0.7980 chunk 38 optimal weight: 0.0870 chunk 102 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11868 Z= 0.183 Angle : 0.531 6.829 16167 Z= 0.273 Chirality : 0.039 0.162 1727 Planarity : 0.004 0.050 1963 Dihedral : 13.703 87.382 2049 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.21 % Allowed : 19.84 % Favored : 76.95 % 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: -1.00 (0.22), residues: 1307 helix: 0.98 (0.29), residues: 328 sheet: -0.09 (0.35), residues: 198 loop : -1.63 (0.20), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 20 HIS 0.006 0.001 HIS A 865 PHE 0.012 0.001 PHE A1456 TYR 0.017 0.001 TYR A1228 ARG 0.005 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 93 time to evaluate : 1.545 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.7627 (mppt) cc_final: 0.6904 (mtpt) REVERT: A 184 HIS cc_start: 0.7007 (OUTLIER) cc_final: 0.6694 (t70) REVERT: A 201 GLU cc_start: 0.5472 (mm-30) cc_final: 0.5254 (mm-30) REVERT: A 538 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6219 (mt-10) REVERT: A 827 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7536 (mptp) REVERT: A 1395 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7360 (mmm160) outliers start: 37 outliers final: 19 residues processed: 121 average time/residue: 1.2627 time to fit residues: 166.4723 Evaluate side-chains 111 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 733 ASP Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1279 HIS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1432 THR Chi-restraints excluded: chain A residue 1472 ILE Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1571 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 13 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 131 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11868 Z= 0.208 Angle : 0.550 7.592 16167 Z= 0.283 Chirality : 0.040 0.223 1727 Planarity : 0.004 0.044 1963 Dihedral : 13.734 87.298 2049 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.29 % Allowed : 20.02 % Favored : 76.69 % 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: -0.93 (0.22), residues: 1307 helix: 1.10 (0.29), residues: 330 sheet: -0.04 (0.36), residues: 202 loop : -1.64 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 315 HIS 0.007 0.001 HIS A 865 PHE 0.014 0.001 PHE A1456 TYR 0.014 0.001 TYR A 958 ARG 0.005 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 92 time to evaluate : 1.318 Fit side-chains REVERT: A 6 LYS cc_start: 0.7631 (mppt) cc_final: 0.6837 (mtpt) REVERT: A 62 ARG cc_start: 0.6446 (OUTLIER) cc_final: 0.5742 (mmm-85) REVERT: A 184 HIS cc_start: 0.6991 (OUTLIER) cc_final: 0.6556 (t70) REVERT: A 201 GLU cc_start: 0.5588 (mm-30) cc_final: 0.5320 (mm-30) REVERT: A 538 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6196 (mt-10) REVERT: A 827 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7553 (mptp) REVERT: A 1162 LYS cc_start: 0.5748 (OUTLIER) cc_final: 0.5408 (mttm) REVERT: A 1395 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7296 (mmm160) outliers start: 38 outliers final: 22 residues processed: 123 average time/residue: 1.2969 time to fit residues: 173.7667 Evaluate side-chains 113 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 85 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 733 ASP Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 1162 LYS Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1279 HIS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1472 ILE Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1571 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 0.5980 chunk 117 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11868 Z= 0.160 Angle : 0.526 8.943 16167 Z= 0.268 Chirality : 0.039 0.185 1727 Planarity : 0.004 0.041 1963 Dihedral : 13.669 87.306 2049 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.03 % Allowed : 20.62 % Favored : 76.34 % 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: -0.74 (0.22), residues: 1307 helix: 1.33 (0.30), residues: 330 sheet: 0.09 (0.36), residues: 202 loop : -1.56 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 20 HIS 0.005 0.001 HIS A 865 PHE 0.015 0.001 PHE A 237 TYR 0.013 0.001 TYR A1238 ARG 0.006 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 92 time to evaluate : 1.389 Fit side-chains REVERT: A 6 LYS cc_start: 0.7587 (mppt) cc_final: 0.6790 (mtpt) REVERT: A 44 ARG cc_start: 0.7245 (mmm-85) cc_final: 0.7018 (mmt90) REVERT: A 62 ARG cc_start: 0.6370 (OUTLIER) cc_final: 0.5793 (mmm-85) REVERT: A 184 HIS cc_start: 0.6951 (OUTLIER) cc_final: 0.6514 (t70) REVERT: A 201 GLU cc_start: 0.5729 (mm-30) cc_final: 0.5427 (mm-30) REVERT: A 538 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6198 (mt-10) REVERT: A 827 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7517 (mptp) REVERT: A 1162 LYS cc_start: 0.5756 (OUTLIER) cc_final: 0.5443 (mttm) REVERT: A 1395 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7259 (mmm160) outliers start: 35 outliers final: 19 residues processed: 121 average time/residue: 1.3412 time to fit residues: 176.2607 Evaluate side-chains 110 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 85 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 733 ASP Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 1162 LYS Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1279 HIS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1571 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 43 optimal weight: 0.0070 chunk 69 optimal weight: 0.0770 chunk 126 optimal weight: 4.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11868 Z= 0.182 Angle : 0.537 10.425 16167 Z= 0.273 Chirality : 0.039 0.139 1727 Planarity : 0.004 0.040 1963 Dihedral : 13.717 87.204 2049 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.55 % Allowed : 20.71 % Favored : 75.74 % 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: -0.70 (0.22), residues: 1307 helix: 1.38 (0.30), residues: 330 sheet: 0.17 (0.36), residues: 202 loop : -1.56 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 20 HIS 0.006 0.001 HIS A 865 PHE 0.018 0.001 PHE A 39 TYR 0.020 0.001 TYR A1228 ARG 0.007 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 93 time to evaluate : 1.375 Fit side-chains REVERT: A 6 LYS cc_start: 0.7556 (mppt) cc_final: 0.6770 (mtpt) REVERT: A 44 ARG cc_start: 0.7258 (mmm-85) cc_final: 0.7017 (mmt90) REVERT: A 62 ARG cc_start: 0.6573 (OUTLIER) cc_final: 0.6047 (mmm-85) REVERT: A 184 HIS cc_start: 0.6998 (OUTLIER) cc_final: 0.6552 (t70) REVERT: A 201 GLU cc_start: 0.5767 (mm-30) cc_final: 0.5461 (mm-30) REVERT: A 538 GLU cc_start: 0.6929 (tt0) cc_final: 0.6188 (mt-10) REVERT: A 692 MET cc_start: 0.5119 (mmm) cc_final: 0.4615 (ptm) REVERT: A 827 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7530 (mptp) REVERT: A 1162 LYS cc_start: 0.5747 (OUTLIER) cc_final: 0.5417 (mttm) REVERT: A 1300 MET cc_start: 0.5992 (mmm) cc_final: 0.5706 (mmp) REVERT: A 1395 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7242 (mmm160) outliers start: 41 outliers final: 21 residues processed: 127 average time/residue: 1.3241 time to fit residues: 182.6053 Evaluate side-chains 115 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 89 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 733 ASP Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 1162 LYS Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1279 HIS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1472 ILE Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1571 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 110 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11868 Z= 0.168 Angle : 0.547 11.706 16167 Z= 0.276 Chirality : 0.039 0.292 1727 Planarity : 0.004 0.040 1963 Dihedral : 13.681 87.144 2049 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.86 % Allowed : 21.92 % Favored : 75.22 % 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: -0.63 (0.23), residues: 1307 helix: 1.46 (0.30), residues: 330 sheet: 0.13 (0.36), residues: 206 loop : -1.50 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 20 HIS 0.006 0.001 HIS A 865 PHE 0.017 0.001 PHE A 237 TYR 0.017 0.001 TYR A1238 ARG 0.007 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 91 time to evaluate : 1.349 Fit side-chains REVERT: A 6 LYS cc_start: 0.7565 (mppt) cc_final: 0.6805 (mtpt) REVERT: A 62 ARG cc_start: 0.6537 (OUTLIER) cc_final: 0.6072 (mmm-85) REVERT: A 184 HIS cc_start: 0.6996 (OUTLIER) cc_final: 0.6554 (t70) REVERT: A 201 GLU cc_start: 0.5792 (mm-30) cc_final: 0.5454 (mm-30) REVERT: A 538 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6285 (mt-10) REVERT: A 593 LYS cc_start: 0.8560 (tptt) cc_final: 0.7694 (ptpp) REVERT: A 692 MET cc_start: 0.5172 (mmm) cc_final: 0.4625 (ptm) REVERT: A 827 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7536 (mptp) REVERT: A 1162 LYS cc_start: 0.5821 (OUTLIER) cc_final: 0.5438 (mttm) REVERT: A 1300 MET cc_start: 0.6011 (mmm) cc_final: 0.5758 (mmp) REVERT: A 1395 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7195 (mmm160) outliers start: 33 outliers final: 20 residues processed: 119 average time/residue: 1.3385 time to fit residues: 172.5121 Evaluate side-chains 110 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 84 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 733 ASP Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 1162 LYS Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1279 HIS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1571 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 GLN A1452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11868 Z= 0.231 Angle : 0.583 11.671 16167 Z= 0.296 Chirality : 0.041 0.286 1727 Planarity : 0.004 0.042 1963 Dihedral : 13.856 86.682 2049 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.47 % Allowed : 21.49 % Favored : 75.04 % 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: -0.78 (0.22), residues: 1307 helix: 1.28 (0.30), residues: 330 sheet: 0.02 (0.35), residues: 212 loop : -1.57 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 20 HIS 0.008 0.001 HIS A 865 PHE 0.015 0.002 PHE A1456 TYR 0.024 0.002 TYR A1238 ARG 0.005 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 88 time to evaluate : 1.396 Fit side-chains REVERT: A 6 LYS cc_start: 0.7501 (mppt) cc_final: 0.6745 (mtpt) REVERT: A 184 HIS cc_start: 0.7072 (OUTLIER) cc_final: 0.6610 (t70) REVERT: A 201 GLU cc_start: 0.5843 (mm-30) cc_final: 0.5495 (mm-30) REVERT: A 538 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6301 (mt-10) REVERT: A 593 LYS cc_start: 0.8599 (tptt) cc_final: 0.7742 (ptpp) REVERT: A 692 MET cc_start: 0.5224 (mmm) cc_final: 0.4693 (ptm) REVERT: A 827 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7615 (mptp) REVERT: A 1162 LYS cc_start: 0.5876 (OUTLIER) cc_final: 0.5481 (mttm) REVERT: A 1300 MET cc_start: 0.5978 (mmm) cc_final: 0.5706 (mmp) REVERT: A 1395 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7198 (mmm160) outliers start: 40 outliers final: 22 residues processed: 122 average time/residue: 1.1853 time to fit residues: 158.5588 Evaluate side-chains 114 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 87 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 733 ASP Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 1162 LYS Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1279 HIS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1472 ILE Chi-restraints excluded: chain A residue 1499 ASP Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1571 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 110 optimal weight: 0.0010 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 80 optimal weight: 6.9990 chunk 129 optimal weight: 0.6980 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11868 Z= 0.173 Angle : 0.559 11.681 16167 Z= 0.282 Chirality : 0.039 0.261 1727 Planarity : 0.004 0.040 1963 Dihedral : 13.759 86.764 2049 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.12 % Allowed : 22.18 % Favored : 74.70 % 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: -0.65 (0.23), residues: 1307 helix: 1.41 (0.30), residues: 329 sheet: -0.01 (0.35), residues: 221 loop : -1.47 (0.21), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 20 HIS 0.006 0.001 HIS A 865 PHE 0.021 0.001 PHE A 517 TYR 0.019 0.001 TYR A1238 ARG 0.006 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 87 time to evaluate : 1.355 Fit side-chains REVERT: A 5 MET cc_start: 0.5898 (pmm) cc_final: 0.4555 (tpt) REVERT: A 6 LYS cc_start: 0.7498 (mppt) cc_final: 0.6565 (mtpt) REVERT: A 184 HIS cc_start: 0.7017 (OUTLIER) cc_final: 0.6561 (t70) REVERT: A 201 GLU cc_start: 0.5815 (mm-30) cc_final: 0.5463 (mm-30) REVERT: A 538 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6304 (mt-10) REVERT: A 593 LYS cc_start: 0.8607 (tptt) cc_final: 0.7771 (ptpp) REVERT: A 692 MET cc_start: 0.5234 (mmm) cc_final: 0.4748 (ptm) REVERT: A 827 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7549 (mptp) REVERT: A 1162 LYS cc_start: 0.5836 (OUTLIER) cc_final: 0.5463 (mttm) REVERT: A 1300 MET cc_start: 0.5908 (mmm) cc_final: 0.5693 (mmp) REVERT: A 1395 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7234 (mmm160) outliers start: 36 outliers final: 21 residues processed: 115 average time/residue: 1.2417 time to fit residues: 155.5091 Evaluate side-chains 111 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 85 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 733 ASP Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 1162 LYS Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1279 HIS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1499 ASP Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1571 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 124 optimal weight: 0.0060 chunk 107 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11868 Z= 0.170 Angle : 0.554 11.642 16167 Z= 0.279 Chirality : 0.039 0.241 1727 Planarity : 0.004 0.039 1963 Dihedral : 13.732 87.031 2049 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.51 % Allowed : 22.70 % Favored : 74.78 % 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: -0.62 (0.23), residues: 1307 helix: 1.44 (0.30), residues: 329 sheet: 0.03 (0.35), residues: 216 loop : -1.45 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 20 HIS 0.006 0.001 HIS A 865 PHE 0.022 0.001 PHE A 517 TYR 0.020 0.001 TYR A1228 ARG 0.007 0.000 ARG A 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 87 time to evaluate : 1.305 Fit side-chains REVERT: A 5 MET cc_start: 0.5926 (pmm) cc_final: 0.4577 (tpt) REVERT: A 6 LYS cc_start: 0.7461 (mppt) cc_final: 0.6526 (mtpt) REVERT: A 184 HIS cc_start: 0.7008 (OUTLIER) cc_final: 0.6554 (t70) REVERT: A 201 GLU cc_start: 0.5863 (mm-30) cc_final: 0.5485 (mm-30) REVERT: A 538 GLU cc_start: 0.6885 (tt0) cc_final: 0.6313 (mt-10) REVERT: A 593 LYS cc_start: 0.8578 (tptt) cc_final: 0.7763 (ptpp) REVERT: A 692 MET cc_start: 0.5215 (mmm) cc_final: 0.4754 (ptm) REVERT: A 827 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7532 (mptp) REVERT: A 1162 LYS cc_start: 0.5767 (OUTLIER) cc_final: 0.5456 (mttm) REVERT: A 1300 MET cc_start: 0.6047 (mmm) cc_final: 0.5758 (mmp) REVERT: A 1395 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7256 (mmm160) outliers start: 29 outliers final: 22 residues processed: 110 average time/residue: 1.2567 time to fit residues: 150.9505 Evaluate side-chains 110 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 84 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 733 ASP Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 1162 LYS Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1279 HIS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1499 ASP Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1571 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.0000 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 110 optimal weight: 0.0000 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 0.0670 chunk 94 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.3926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.181201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.138499 restraints weight = 15755.457| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 2.90 r_work: 0.3970 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11868 Z= 0.152 Angle : 0.544 11.727 16167 Z= 0.272 Chirality : 0.039 0.258 1727 Planarity : 0.004 0.042 1963 Dihedral : 13.590 87.254 2049 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.51 % Allowed : 22.88 % Favored : 74.61 % 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: -0.46 (0.23), residues: 1307 helix: 1.61 (0.30), residues: 329 sheet: 0.19 (0.35), residues: 206 loop : -1.38 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 20 HIS 0.004 0.000 HIS A 865 PHE 0.023 0.001 PHE A 517 TYR 0.016 0.001 TYR A1238 ARG 0.008 0.000 ARG A 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3840.27 seconds wall clock time: 68 minutes 45.31 seconds (4125.31 seconds total)