Starting phenix.real_space_refine on Sat Nov 16 03:15:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilv_35547/11_2024/8ilv_35547.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilv_35547/11_2024/8ilv_35547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilv_35547/11_2024/8ilv_35547.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilv_35547/11_2024/8ilv_35547.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilv_35547/11_2024/8ilv_35547.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilv_35547/11_2024/8ilv_35547.cif" } resolution = 3.19 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= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 6508 2.51 5 N 1763 2.21 5 O 1878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10218 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7933 Classifications: {'peptide': 971} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 47, 'TRANS': 923} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2241 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {'L2V': 1} Classifications: {'undetermined': 1, 'water': 4} Link IDs: {None: 4} Time building chain proxies: 6.01, per 1000 atoms: 0.59 Number of scatterers: 10218 At special positions: 0 Unit cell: (85.68, 117.81, 121.023, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 1878 8.00 N 1763 7.00 C 6508 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 - 3.00 Amino acid : True - 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: 2.44 Conformation dependent library (CDL) restraints added in 1.2 seconds 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 11 sheets defined 51.5% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.555A pdb=" N LYS A 51 " --> pdb=" O HIS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 62 removed outlier: 3.875A pdb=" N LEU A 61 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.615A pdb=" N ARG A 93 " --> pdb=" O CYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 122 removed outlier: 3.743A pdb=" N LYS A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 112 " --> pdb=" O ARG A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 130 removed outlier: 3.514A pdb=" N GLU A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.511A pdb=" N PHE A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 157 removed outlier: 3.506A pdb=" N CYS A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASN A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 167 removed outlier: 3.882A pdb=" N ARG A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 184 through 187 removed outlier: 7.738A pdb=" N LYS A 187 " --> pdb=" O LYS A 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 184 through 187' Processing helix chain 'A' and resid 216 through 229 removed outlier: 3.580A pdb=" N THR A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 290 through 297 removed outlier: 3.707A pdb=" N GLN A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 4.252A pdb=" N ARG A 309 " --> pdb=" O PRO A 305 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 305 through 310' Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 488 through 496 Processing helix chain 'A' and resid 526 through 536 removed outlier: 4.065A pdb=" N GLN A 530 " --> pdb=" O ASN A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 564 through 570 removed outlier: 3.731A pdb=" N LEU A 570 " --> pdb=" O PRO A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 589 removed outlier: 3.517A pdb=" N VAL A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 586 " --> pdb=" O GLN A 582 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 600 through 603 Processing helix chain 'A' and resid 608 through 623 removed outlier: 3.781A pdb=" N LYS A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 631 Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 649 through 658 removed outlier: 4.112A pdb=" N LYS A 655 " --> pdb=" O ARG A 651 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 656 " --> pdb=" O PHE A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 674 removed outlier: 3.670A pdb=" N PHE A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 674 " --> pdb=" O HIS A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 695 Processing helix chain 'A' and resid 697 through 721 removed outlier: 4.172A pdb=" N HIS A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 713 " --> pdb=" O MET A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 741 removed outlier: 3.532A pdb=" N GLU A 737 " --> pdb=" O LYS A 733 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 748 removed outlier: 3.524A pdb=" N ALA A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 828 Processing helix chain 'A' and resid 857 through 861 Processing helix chain 'A' and resid 875 through 884 Processing helix chain 'A' and resid 885 through 886 No H-bonds generated for 'chain 'A' and resid 885 through 886' Processing helix chain 'A' and resid 887 through 888 No H-bonds generated for 'chain 'A' and resid 887 through 888' Processing helix chain 'A' and resid 889 through 912 removed outlier: 3.859A pdb=" N ASP A 895 " --> pdb=" O ASP A 891 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 903 " --> pdb=" O ARG A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 965 removed outlier: 3.823A pdb=" N ILE A 962 " --> pdb=" O GLN A 958 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 994 Processing helix chain 'A' and resid 994 through 1003 removed outlier: 3.902A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1020 No H-bonds generated for 'chain 'A' and resid 1018 through 1020' Processing helix chain 'A' and resid 1021 through 1026 Processing helix chain 'A' and resid 1031 through 1048 removed outlier: 3.573A pdb=" N LEU A1036 " --> pdb=" O GLU A1032 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU A1037 " --> pdb=" O GLN A1033 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA A1046 " --> pdb=" O GLN A1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 339 through 345 removed outlier: 3.969A pdb=" N GLU B 345 " --> pdb=" O GLU B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 410 removed outlier: 3.930A pdb=" N ASN B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 437 Processing helix chain 'B' and resid 441 through 505 removed outlier: 3.539A pdb=" N GLY B 446 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS B 450 " --> pdb=" O GLY B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 510 Processing helix chain 'B' and resid 524 through 585 Proline residue: B 568 - end of helix Processing helix chain 'B' and resid 590 through 598 removed outlier: 3.790A pdb=" N LEU B 594 " --> pdb=" O ARG B 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 36 removed outlier: 4.287A pdb=" N ILE A 20 " --> pdb=" O CYS A 36 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 99 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE A 70 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 212 removed outlier: 8.855A pdb=" N LEU A 285 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL A 193 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 250 through 251 Processing sheet with id=AA4, first strand: chain 'A' and resid 324 through 326 Processing sheet with id=AA5, first strand: chain 'A' and resid 382 through 392 removed outlier: 6.741A pdb=" N TRP A 383 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N CYS A 340 " --> pdb=" O TRP A 383 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU A 385 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU A 334 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLU A 474 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA A 341 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N CYS A 472 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.857A pdb=" N GLU A 365 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.857A pdb=" N GLU A 365 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU A 402 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASN A 426 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU A 404 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TRP A 424 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 406 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 751 through 753 removed outlier: 3.531A pdb=" N PHE A 751 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N HIS A 759 " --> pdb=" O SER A 753 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 764 through 771 removed outlier: 7.197A pdb=" N GLU A 768 " --> pdb=" O ASN A 782 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASN A 782 " --> pdb=" O GLU A 768 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 855 through 856 Processing sheet with id=AB2, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.602A pdb=" N ASN B 377 " --> pdb=" O LYS B 374 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1305 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.54 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3341 1.34 - 1.46: 1476 1.46 - 1.57: 5508 1.57 - 1.69: 0 1.69 - 1.81: 106 Bond restraints: 10431 Sorted by residual: bond pdb=" C38 L2V A1101 " pdb=" N39 L2V A1101 " ideal model delta sigma weight residual 1.306 1.361 -0.055 2.00e-02 2.50e+03 7.49e+00 bond pdb=" CA ARG A 777 " pdb=" C ARG A 777 " ideal model delta sigma weight residual 1.534 1.557 -0.023 9.50e-03 1.11e+04 5.81e+00 bond pdb=" C02 L2V A1101 " pdb=" N01 L2V A1101 " ideal model delta sigma weight residual 1.312 1.357 -0.045 2.00e-02 2.50e+03 5.06e+00 bond pdb=" C36 L2V A1101 " pdb=" N35 L2V A1101 " ideal model delta sigma weight residual 1.313 1.356 -0.043 2.00e-02 2.50e+03 4.65e+00 bond pdb=" C ARG A 777 " pdb=" N PRO A 778 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.53e+00 ... (remaining 10426 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 13988 2.66 - 5.32: 76 5.32 - 7.98: 8 7.98 - 10.64: 2 10.64 - 13.29: 1 Bond angle restraints: 14075 Sorted by residual: angle pdb=" N ALA A 775 " pdb=" CA ALA A 775 " pdb=" C ALA A 775 " ideal model delta sigma weight residual 111.40 124.69 -13.29 1.22e+00 6.72e-01 1.19e+02 angle pdb=" C ALA A 775 " pdb=" CA ALA A 775 " pdb=" CB ALA A 775 " ideal model delta sigma weight residual 110.79 101.07 9.72 1.68e+00 3.54e-01 3.35e+01 angle pdb=" N ASN B 324 " pdb=" CA ASN B 324 " pdb=" C ASN B 324 " ideal model delta sigma weight residual 113.38 106.89 6.49 1.23e+00 6.61e-01 2.79e+01 angle pdb=" N LYS A 776 " pdb=" CA LYS A 776 " pdb=" CB LYS A 776 " ideal model delta sigma weight residual 110.49 117.33 -6.84 1.69e+00 3.50e-01 1.64e+01 angle pdb=" C ARG A 777 " pdb=" N PRO A 778 " pdb=" CA PRO A 778 " ideal model delta sigma weight residual 119.84 115.30 4.54 1.25e+00 6.40e-01 1.32e+01 ... (remaining 14070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.99: 5660 23.99 - 47.98: 608 47.98 - 71.96: 85 71.96 - 95.95: 14 95.95 - 119.94: 1 Dihedral angle restraints: 6368 sinusoidal: 2720 harmonic: 3648 Sorted by residual: dihedral pdb=" C09 L2V A1101 " pdb=" C11 L2V A1101 " pdb=" C12 L2V A1101 " pdb=" C13 L2V A1101 " ideal model delta sinusoidal sigma weight residual -170.44 -50.50 -119.94 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" CA LYS B 438 " pdb=" C LYS B 438 " pdb=" N GLU B 439 " pdb=" CA GLU B 439 " ideal model delta harmonic sigma weight residual 180.00 163.00 17.00 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ASP A 725 " pdb=" CB ASP A 725 " pdb=" CG ASP A 725 " pdb=" OD1 ASP A 725 " ideal model delta sinusoidal sigma weight residual -30.00 -88.45 58.45 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 6365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1183 0.043 - 0.086: 251 0.086 - 0.129: 81 0.129 - 0.173: 4 0.173 - 0.216: 2 Chirality restraints: 1521 Sorted by residual: chirality pdb=" CA ALA A 775 " pdb=" N ALA A 775 " pdb=" C ALA A 775 " pdb=" CB ALA A 775 " both_signs ideal model delta sigma weight residual False 2.48 2.27 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ASP B 394 " pdb=" N ASP B 394 " pdb=" C ASP B 394 " pdb=" CB ASP B 394 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB ILE A 543 " pdb=" CA ILE A 543 " pdb=" CG1 ILE A 543 " pdb=" CG2 ILE A 543 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 1518 not shown) Planarity restraints: 1806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 L2V A1101 " -0.074 2.00e-02 2.50e+03 6.28e-02 4.93e+01 pdb=" C27 L2V A1101 " 0.032 2.00e-02 2.50e+03 pdb=" C29 L2V A1101 " -0.060 2.00e-02 2.50e+03 pdb=" N26 L2V A1101 " 0.097 2.00e-02 2.50e+03 pdb=" O28 L2V A1101 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 L2V A1101 " -0.036 2.00e-02 2.50e+03 3.95e-02 3.51e+01 pdb=" C12 L2V A1101 " -0.005 2.00e-02 2.50e+03 pdb=" C13 L2V A1101 " 0.029 2.00e-02 2.50e+03 pdb=" C14 L2V A1101 " 0.072 2.00e-02 2.50e+03 pdb=" C15 L2V A1101 " 0.039 2.00e-02 2.50e+03 pdb=" C16 L2V A1101 " 0.004 2.00e-02 2.50e+03 pdb=" C17 L2V A1101 " -0.019 2.00e-02 2.50e+03 pdb=" C18 L2V A1101 " -0.014 2.00e-02 2.50e+03 pdb=" C19 L2V A1101 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 L2V A1101 " 0.033 2.00e-02 2.50e+03 2.87e-02 2.69e+01 pdb=" C29 L2V A1101 " 0.023 2.00e-02 2.50e+03 pdb=" C30 L2V A1101 " 0.012 2.00e-02 2.50e+03 pdb=" C31 L2V A1101 " 0.003 2.00e-02 2.50e+03 pdb=" C32 L2V A1101 " -0.027 2.00e-02 2.50e+03 pdb=" C33 L2V A1101 " -0.031 2.00e-02 2.50e+03 pdb=" C34 L2V A1101 " -0.021 2.00e-02 2.50e+03 pdb=" C36 L2V A1101 " 0.003 2.00e-02 2.50e+03 pdb=" C37 L2V A1101 " 0.071 2.00e-02 2.50e+03 pdb=" C38 L2V A1101 " -0.012 2.00e-02 2.50e+03 pdb=" C40 L2V A1101 " 0.002 2.00e-02 2.50e+03 pdb=" N35 L2V A1101 " -0.027 2.00e-02 2.50e+03 pdb=" N39 L2V A1101 " -0.031 2.00e-02 2.50e+03 ... (remaining 1803 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 104 2.64 - 3.20: 9038 3.20 - 3.77: 15149 3.77 - 4.33: 20937 4.33 - 4.90: 35193 Nonbonded interactions: 80421 Sorted by model distance: nonbonded pdb=" O VAL B 436 " pdb=" NZ LYS B 438 " model vdw 2.073 3.120 nonbonded pdb=" OG SER A 173 " pdb=" OD2 ASP A 626 " model vdw 2.197 3.040 nonbonded pdb=" O LEU A 367 " pdb=" ND2 ASN A 575 " model vdw 2.199 3.120 nonbonded pdb=" OG SER A 199 " pdb=" OD1 ASN A 201 " model vdw 2.204 3.040 nonbonded pdb=" OD2 ASP A 603 " pdb=" OG SER A1003 " model vdw 2.234 3.040 ... (remaining 80416 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.410 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 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 : 0.003 0.055 10431 Z= 0.210 Angle : 0.526 13.295 14075 Z= 0.283 Chirality : 0.040 0.216 1521 Planarity : 0.004 0.068 1806 Dihedral : 18.372 119.939 3998 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.26 % Allowed : 27.98 % Favored : 71.76 % 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 (0.24), residues: 1218 helix: -0.32 (0.21), residues: 555 sheet: -0.68 (0.50), residues: 121 loop : -0.51 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 479 HIS 0.002 0.000 HIS A 665 PHE 0.016 0.001 PHE A 794 TYR 0.010 0.001 TYR A 392 ARG 0.003 0.000 ARG A 740 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 1.200 Fit side-chains REVERT: A 489 MET cc_start: 0.7663 (tpt) cc_final: 0.7405 (mmt) outliers start: 3 outliers final: 0 residues processed: 136 average time/residue: 0.2665 time to fit residues: 49.9422 Evaluate side-chains 129 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 0.0670 chunk 31 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN A 822 ASN B 579 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10431 Z= 0.185 Angle : 0.521 5.969 14075 Z= 0.273 Chirality : 0.040 0.161 1521 Planarity : 0.004 0.057 1806 Dihedral : 4.036 24.546 1367 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.18 % Allowed : 25.07 % Favored : 71.76 % 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: 0.18 (0.24), residues: 1218 helix: 1.03 (0.22), residues: 569 sheet: -0.80 (0.43), residues: 153 loop : -0.54 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 880 HIS 0.003 0.000 HIS A 665 PHE 0.010 0.001 PHE A 930 TYR 0.013 0.001 TYR B 556 ARG 0.003 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 1.139 Fit side-chains REVERT: A 115 ARG cc_start: 0.7515 (ttt90) cc_final: 0.7098 (ttp-110) REVERT: A 138 ASP cc_start: 0.7907 (m-30) cc_final: 0.7553 (m-30) REVERT: A 262 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8415 (pp) REVERT: A 489 MET cc_start: 0.7466 (tpt) cc_final: 0.7213 (mmt) REVERT: A 781 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8524 (mt) REVERT: B 574 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.6230 (tpt-90) outliers start: 36 outliers final: 19 residues processed: 167 average time/residue: 0.2377 time to fit residues: 55.3713 Evaluate side-chains 148 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 574 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 110 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 89 optimal weight: 0.0370 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10431 Z= 0.185 Angle : 0.507 9.537 14075 Z= 0.258 Chirality : 0.040 0.180 1521 Planarity : 0.004 0.053 1806 Dihedral : 3.944 20.668 1367 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.44 % Allowed : 25.24 % Favored : 71.32 % 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: 0.43 (0.24), residues: 1218 helix: 1.43 (0.22), residues: 576 sheet: -0.90 (0.42), residues: 156 loop : -0.62 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.004 0.000 HIS A 665 PHE 0.012 0.001 PHE A 751 TYR 0.014 0.001 TYR B 556 ARG 0.003 0.000 ARG A 777 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 1.178 Fit side-chains REVERT: A 76 GLU cc_start: 0.6757 (pm20) cc_final: 0.6400 (pm20) REVERT: A 115 ARG cc_start: 0.7478 (ttt90) cc_final: 0.7074 (ttp-110) REVERT: A 138 ASP cc_start: 0.7939 (m-30) cc_final: 0.7546 (m-30) REVERT: A 226 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.5178 (ttm110) REVERT: A 641 TYR cc_start: 0.8419 (m-10) cc_final: 0.7848 (m-80) REVERT: A 654 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7881 (mp) REVERT: A 781 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8598 (mt) REVERT: A 798 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7488 (mm-30) REVERT: A 1040 MET cc_start: 0.7568 (mtm) cc_final: 0.7312 (mtt) REVERT: B 574 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6234 (tpt-90) outliers start: 39 outliers final: 20 residues processed: 164 average time/residue: 0.2453 time to fit residues: 56.1270 Evaluate side-chains 154 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 574 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 8.9990 chunk 84 optimal weight: 0.0050 chunk 58 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 106 optimal weight: 0.0270 chunk 32 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 overall best weight: 0.5252 ------------------------------------------------------------------------------- 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: 0.7570 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10431 Z= 0.157 Angle : 0.488 7.778 14075 Z= 0.250 Chirality : 0.039 0.153 1521 Planarity : 0.003 0.050 1806 Dihedral : 3.826 17.946 1367 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.62 % Allowed : 25.51 % Favored : 70.87 % 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: 0.61 (0.25), residues: 1218 helix: 1.63 (0.22), residues: 576 sheet: -0.83 (0.42), residues: 155 loop : -0.61 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 880 HIS 0.005 0.000 HIS A 665 PHE 0.010 0.001 PHE A 794 TYR 0.013 0.001 TYR B 556 ARG 0.003 0.000 ARG A 740 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.934 Fit side-chains REVERT: A 115 ARG cc_start: 0.7459 (ttt90) cc_final: 0.7021 (ttp-110) REVERT: A 138 ASP cc_start: 0.7962 (m-30) cc_final: 0.7513 (m-30) REVERT: A 226 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.5148 (ttm110) REVERT: A 654 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7876 (mp) REVERT: A 781 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8569 (mt) REVERT: A 798 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7545 (mm-30) REVERT: A 1040 MET cc_start: 0.7566 (mtm) cc_final: 0.7317 (mtt) REVERT: B 574 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6259 (tpt-90) outliers start: 41 outliers final: 22 residues processed: 168 average time/residue: 0.2435 time to fit residues: 57.9239 Evaluate side-chains 159 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 574 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 106 optimal weight: 0.0270 chunk 30 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10431 Z= 0.157 Angle : 0.488 7.778 14075 Z= 0.250 Chirality : 0.039 0.153 1521 Planarity : 0.004 0.052 1806 Dihedral : 3.826 17.946 1367 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.38 % Allowed : 26.83 % Favored : 70.79 % 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: 0.61 (0.25), residues: 1218 helix: 1.63 (0.22), residues: 576 sheet: -0.83 (0.42), residues: 155 loop : -0.61 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 880 HIS 0.005 0.000 HIS A 665 PHE 0.010 0.001 PHE A 794 TYR 0.013 0.001 TYR B 556 ARG 0.003 0.000 ARG A 740 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.114 Fit side-chains REVERT: A 115 ARG cc_start: 0.7461 (ttt90) cc_final: 0.7021 (ttp-110) REVERT: A 138 ASP cc_start: 0.7940 (m-30) cc_final: 0.7512 (m-30) REVERT: A 226 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.5149 (ttm110) REVERT: A 654 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7876 (mp) REVERT: A 781 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8569 (mt) REVERT: A 798 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7545 (mm-30) REVERT: A 1040 MET cc_start: 0.7560 (mtm) cc_final: 0.7317 (mtt) REVERT: B 574 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6259 (tpt-90) outliers start: 27 outliers final: 22 residues processed: 154 average time/residue: 0.2490 time to fit residues: 54.0275 Evaluate side-chains 158 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 574 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 0.0770 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10431 Z= 0.217 Angle : 0.526 9.868 14075 Z= 0.266 Chirality : 0.040 0.155 1521 Planarity : 0.004 0.052 1806 Dihedral : 3.883 18.117 1367 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.35 % Allowed : 26.39 % Favored : 70.26 % 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: 0.55 (0.25), residues: 1218 helix: 1.61 (0.22), residues: 576 sheet: -1.01 (0.43), residues: 146 loop : -0.62 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 880 HIS 0.005 0.001 HIS A 665 PHE 0.011 0.001 PHE A 751 TYR 0.015 0.001 TYR B 556 ARG 0.006 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 1.067 Fit side-chains REVERT: A 108 ARG cc_start: 0.7227 (tpp-160) cc_final: 0.6950 (ttm-80) REVERT: A 115 ARG cc_start: 0.7436 (ttt90) cc_final: 0.7015 (ttp-110) REVERT: A 138 ASP cc_start: 0.8026 (m-30) cc_final: 0.7573 (m-30) REVERT: A 226 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.5188 (ttm110) REVERT: A 641 TYR cc_start: 0.8488 (m-10) cc_final: 0.7914 (m-10) REVERT: A 654 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7892 (mp) REVERT: A 781 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8592 (mt) REVERT: A 798 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7570 (mm-30) REVERT: A 982 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: A 1040 MET cc_start: 0.7585 (mtm) cc_final: 0.7339 (mtt) REVERT: B 333 TRP cc_start: 0.8184 (OUTLIER) cc_final: 0.7984 (p-90) REVERT: B 574 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6238 (tpt-90) outliers start: 38 outliers final: 23 residues processed: 163 average time/residue: 0.2433 time to fit residues: 56.7551 Evaluate side-chains 157 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain B residue 333 TRP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 574 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 0.0570 chunk 54 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10431 Z= 0.217 Angle : 0.526 9.868 14075 Z= 0.266 Chirality : 0.040 0.155 1521 Planarity : 0.004 0.054 1806 Dihedral : 3.883 18.117 1367 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.65 % Allowed : 26.92 % Favored : 70.43 % 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: 0.55 (0.25), residues: 1218 helix: 1.61 (0.22), residues: 576 sheet: -1.01 (0.43), residues: 146 loop : -0.62 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 880 HIS 0.005 0.001 HIS A 665 PHE 0.011 0.001 PHE A 751 TYR 0.015 0.001 TYR B 556 ARG 0.006 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 1.173 Fit side-chains REVERT: A 108 ARG cc_start: 0.7227 (tpp-160) cc_final: 0.6950 (ttm-80) REVERT: A 115 ARG cc_start: 0.7437 (ttt90) cc_final: 0.7015 (ttp-110) REVERT: A 138 ASP cc_start: 0.8024 (m-30) cc_final: 0.7573 (m-30) REVERT: A 226 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.5188 (ttm110) REVERT: A 641 TYR cc_start: 0.8487 (m-10) cc_final: 0.7914 (m-10) REVERT: A 654 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7892 (mp) REVERT: A 781 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8592 (mt) REVERT: A 798 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7571 (mm-30) REVERT: A 982 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: A 1040 MET cc_start: 0.7583 (mtm) cc_final: 0.7339 (mtt) REVERT: B 574 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6238 (tpt-90) outliers start: 30 outliers final: 23 residues processed: 153 average time/residue: 0.2394 time to fit residues: 51.8375 Evaluate side-chains 155 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 574 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 3.9990 chunk 35 optimal weight: 0.0000 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 0.0770 chunk 113 optimal weight: 1.9990 overall best weight: 0.4542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10431 Z= 0.217 Angle : 0.526 9.868 14075 Z= 0.266 Chirality : 0.040 0.155 1521 Planarity : 0.004 0.054 1806 Dihedral : 3.883 18.117 1367 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.56 % Allowed : 27.01 % Favored : 70.43 % 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: 0.55 (0.25), residues: 1218 helix: 1.61 (0.22), residues: 576 sheet: -1.01 (0.43), residues: 146 loop : -0.62 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 880 HIS 0.005 0.001 HIS A 665 PHE 0.011 0.001 PHE A 751 TYR 0.015 0.001 TYR B 556 ARG 0.006 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 1.178 Fit side-chains REVERT: A 108 ARG cc_start: 0.7227 (tpp-160) cc_final: 0.6950 (ttm-80) REVERT: A 115 ARG cc_start: 0.7437 (ttt90) cc_final: 0.7014 (ttp-110) REVERT: A 138 ASP cc_start: 0.8024 (m-30) cc_final: 0.7573 (m-30) REVERT: A 226 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.5186 (ttm110) REVERT: A 641 TYR cc_start: 0.8487 (m-10) cc_final: 0.7914 (m-10) REVERT: A 654 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7891 (mp) REVERT: A 781 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8592 (mt) REVERT: A 798 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7571 (mm-30) REVERT: A 982 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: A 1040 MET cc_start: 0.7582 (mtm) cc_final: 0.7340 (mtt) REVERT: B 574 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6238 (tpt-90) outliers start: 29 outliers final: 23 residues processed: 151 average time/residue: 0.2299 time to fit residues: 49.3801 Evaluate side-chains 154 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 574 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.6980 chunk 110 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 48 optimal weight: 0.0030 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 116 optimal weight: 10.0000 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10431 Z= 0.217 Angle : 0.526 9.868 14075 Z= 0.266 Chirality : 0.040 0.155 1521 Planarity : 0.004 0.054 1806 Dihedral : 3.883 18.117 1367 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.56 % Allowed : 26.92 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1218 helix: 1.61 (0.22), residues: 576 sheet: -1.01 (0.43), residues: 146 loop : -0.62 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 880 HIS 0.005 0.001 HIS A 665 PHE 0.011 0.001 PHE A 751 TYR 0.015 0.001 TYR B 556 ARG 0.006 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 1.218 Fit side-chains REVERT: A 108 ARG cc_start: 0.7227 (tpp-160) cc_final: 0.6950 (ttm-80) REVERT: A 115 ARG cc_start: 0.7436 (ttt90) cc_final: 0.7014 (ttp-110) REVERT: A 138 ASP cc_start: 0.8024 (m-30) cc_final: 0.7573 (m-30) REVERT: A 226 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.5186 (ttm110) REVERT: A 641 TYR cc_start: 0.8488 (m-10) cc_final: 0.7914 (m-10) REVERT: A 654 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7891 (mp) REVERT: A 781 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8592 (mt) REVERT: A 798 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7571 (mm-30) REVERT: A 982 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: A 1040 MET cc_start: 0.7583 (mtm) cc_final: 0.7340 (mtt) REVERT: B 574 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6238 (tpt-90) outliers start: 29 outliers final: 23 residues processed: 150 average time/residue: 0.2273 time to fit residues: 49.1984 Evaluate side-chains 154 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 574 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.0170 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 97 optimal weight: 0.0570 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10431 Z= 0.217 Angle : 0.526 9.868 14075 Z= 0.266 Chirality : 0.040 0.155 1521 Planarity : 0.004 0.054 1806 Dihedral : 3.883 18.117 1367 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.56 % Allowed : 26.92 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1218 helix: 1.61 (0.22), residues: 576 sheet: -1.01 (0.43), residues: 146 loop : -0.62 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 880 HIS 0.005 0.001 HIS A 665 PHE 0.011 0.001 PHE A 751 TYR 0.015 0.001 TYR B 556 ARG 0.006 0.000 ARG A 274 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 1.195 Fit side-chains REVERT: A 108 ARG cc_start: 0.7227 (tpp-160) cc_final: 0.6950 (ttm-80) REVERT: A 115 ARG cc_start: 0.7436 (ttt90) cc_final: 0.7014 (ttp-110) REVERT: A 138 ASP cc_start: 0.8024 (m-30) cc_final: 0.7573 (m-30) REVERT: A 226 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.5186 (ttm110) REVERT: A 641 TYR cc_start: 0.8488 (m-10) cc_final: 0.7914 (m-10) REVERT: A 654 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7891 (mp) REVERT: A 781 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8592 (mt) REVERT: A 798 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7571 (mm-30) REVERT: A 982 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: A 1040 MET cc_start: 0.7583 (mtm) cc_final: 0.7340 (mtt) REVERT: B 574 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6238 (tpt-90) outliers start: 29 outliers final: 23 residues processed: 150 average time/residue: 0.2312 time to fit residues: 49.5497 Evaluate side-chains 154 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 574 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.6980 chunk 89 optimal weight: 0.0030 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 97 optimal weight: 0.0570 chunk 40 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 85 optimal weight: 0.4980 chunk 5 optimal weight: 4.9990 overall best weight: 0.3708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.202426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.162681 restraints weight = 11719.809| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.54 r_work: 0.3800 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10431 Z= 0.217 Angle : 0.526 9.868 14075 Z= 0.266 Chirality : 0.040 0.155 1521 Planarity : 0.004 0.054 1806 Dihedral : 3.883 18.117 1367 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.56 % Allowed : 26.92 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1218 helix: 1.61 (0.22), residues: 576 sheet: -1.01 (0.43), residues: 146 loop : -0.62 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 880 HIS 0.005 0.001 HIS A 665 PHE 0.011 0.001 PHE A 751 TYR 0.015 0.001 TYR B 556 ARG 0.006 0.000 ARG A 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2207.00 seconds wall clock time: 41 minutes 8.54 seconds (2468.54 seconds total)