Starting phenix.real_space_refine on Wed Jan 17 23:37:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwp_35776/01_2024/8iwp_35776.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwp_35776/01_2024/8iwp_35776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwp_35776/01_2024/8iwp_35776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwp_35776/01_2024/8iwp_35776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwp_35776/01_2024/8iwp_35776.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwp_35776/01_2024/8iwp_35776.pdb" } resolution = 3.59 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 52 5.16 5 C 4372 2.51 5 N 1147 2.21 5 O 1289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "A PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A ASP 172": "OD1" <-> "OD2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 369": "OD1" <-> "OD2" Residue "A TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 546": "OD1" <-> "OD2" Residue "A ASP 572": "OD1" <-> "OD2" Residue "A TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 648": "OD1" <-> "OD2" Residue "A ASP 667": "OD1" <-> "OD2" Residue "A PHE 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 860": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 877": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6861 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 896, 6860 Classifications: {'peptide': 896} Link IDs: {'PTRANS': 35, 'TRANS': 860} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.62, per 1000 atoms: 0.67 Number of scatterers: 6861 At special positions: 0 Unit cell: (86.52, 99.96, 134.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 52 16.00 O 1289 8.00 N 1147 7.00 C 4372 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: 3.29 Conformation dependent library (CDL) restraints added in 1.4 seconds 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1670 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 7 sheets defined 54.4% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 22 through 29 Processing helix chain 'A' and resid 30 through 39 Processing helix chain 'A' and resid 47 through 58 Processing helix chain 'A' and resid 70 through 78 removed outlier: 3.645A pdb=" N LYS A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 97 Processing helix chain 'A' and resid 99 through 131 Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 256 through 287 removed outlier: 3.648A pdb=" N LEU A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 305 Processing helix chain 'A' and resid 309 through 328 Processing helix chain 'A' and resid 334 through 341 removed outlier: 3.601A pdb=" N ILE A 337 " --> pdb=" O LYS A 334 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 338 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU A 339 " --> pdb=" O PRO A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 411 Processing helix chain 'A' and resid 424 through 437 removed outlier: 4.006A pdb=" N MET A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 5.529A pdb=" N GLY A 441 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN A 443 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 503 through 520 Processing helix chain 'A' and resid 551 through 563 Processing helix chain 'A' and resid 573 through 585 Processing helix chain 'A' and resid 596 through 602 Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 621 through 636 removed outlier: 3.736A pdb=" N ASN A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 683 through 723 removed outlier: 4.203A pdb=" N SER A 687 " --> pdb=" O GLN A 683 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 688 " --> pdb=" O THR A 684 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N MET A 723 " --> pdb=" O LEU A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 742 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 757 through 761 removed outlier: 3.526A pdb=" N ARG A 760 " --> pdb=" O ASP A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 798 Processing helix chain 'A' and resid 804 through 826 removed outlier: 4.279A pdb=" N THR A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 837 removed outlier: 3.709A pdb=" N ILE A 836 " --> pdb=" O SER A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 861 Processing helix chain 'A' and resid 861 through 869 Processing helix chain 'A' and resid 874 through 885 Processing helix chain 'A' and resid 888 through 910 Processing sheet with id=AA1, first strand: chain 'A' and resid 146 through 151 removed outlier: 3.550A pdb=" N THR A 150 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS A 139 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N HIS A 140 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER A 182 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 226 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ASP A 180 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA A 228 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA A 178 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N GLY A 230 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE A 176 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL A 232 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG A 174 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY A 234 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 172 " --> pdb=" O GLY A 234 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU A 181 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A 197 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 183 " --> pdb=" O CYS A 195 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS A 195 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 151 removed outlier: 3.550A pdb=" N THR A 150 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS A 139 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N HIS A 140 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER A 182 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 226 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ASP A 180 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA A 228 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA A 178 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N GLY A 230 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE A 176 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL A 232 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG A 174 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY A 234 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 172 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 350 removed outlier: 6.629A pdb=" N GLN A 592 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL A 616 " --> pdb=" O GLN A 592 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 594 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR A 618 " --> pdb=" O VAL A 594 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 391 through 392 removed outlier: 5.040A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL A 362 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 545 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS A 364 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N PHE A 538 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N SER A 529 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 540 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 463 " --> pdb=" O PHE A 478 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 480 " --> pdb=" O MET A 461 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA A 462 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLU A 451 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS A 464 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 392 removed outlier: 5.040A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL A 362 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 545 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS A 364 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N CYS A 490 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE A 538 " --> pdb=" O CYS A 490 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N THR A 492 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N GLY A 540 " --> pdb=" O THR A 492 " (cutoff:3.500A) removed outlier: 10.699A pdb=" N GLN A 494 " --> pdb=" O GLY A 540 " (cutoff:3.500A) removed outlier: 14.335A pdb=" N VAL A 542 " --> pdb=" O GLN A 494 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 415 through 417 removed outlier: 4.370A pdb=" N VAL A 415 " --> pdb=" O MET A 422 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N MET A 422 " --> pdb=" O VAL A 415 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 660 through 661 removed outlier: 6.517A pdb=" N ALA A 660 " --> pdb=" O LEU A 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 412 hydrogen bonds defined for protein. 1194 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: 2.76 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2230 1.34 - 1.46: 1366 1.46 - 1.58: 3290 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 6970 Sorted by residual: bond pdb=" CA GLU A 62 " pdb=" CB GLU A 62 " ideal model delta sigma weight residual 1.535 1.562 -0.027 1.58e-02 4.01e+03 2.98e+00 bond pdb=" CB PRO A 744 " pdb=" CG PRO A 744 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.94e+00 bond pdb=" CA THR A 590 " pdb=" CB THR A 590 " ideal model delta sigma weight residual 1.528 1.565 -0.037 2.61e-02 1.47e+03 1.99e+00 bond pdb=" CG1 ILE A 431 " pdb=" CD1 ILE A 431 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.68e+00 bond pdb=" C THR A 804 " pdb=" N PRO A 805 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.57e+00 ... (remaining 6965 not shown) Histogram of bond angle deviations from ideal: 99.44 - 106.38: 175 106.38 - 113.32: 3940 113.32 - 120.26: 2402 120.26 - 127.20: 2867 127.20 - 134.14: 54 Bond angle restraints: 9438 Sorted by residual: angle pdb=" CA PRO A 744 " pdb=" N PRO A 744 " pdb=" CD PRO A 744 " ideal model delta sigma weight residual 112.00 106.71 5.29 1.40e+00 5.10e-01 1.43e+01 angle pdb=" CA GLN A 512 " pdb=" CB GLN A 512 " pdb=" CG GLN A 512 " ideal model delta sigma weight residual 114.10 121.37 -7.27 2.00e+00 2.50e-01 1.32e+01 angle pdb=" CB LYS A 756 " pdb=" CG LYS A 756 " pdb=" CD LYS A 756 " ideal model delta sigma weight residual 111.30 118.84 -7.54 2.30e+00 1.89e-01 1.08e+01 angle pdb=" CA LYS A 424 " pdb=" CB LYS A 424 " pdb=" CG LYS A 424 " ideal model delta sigma weight residual 114.10 120.66 -6.56 2.00e+00 2.50e-01 1.08e+01 angle pdb=" C VAL A 346 " pdb=" CA VAL A 346 " pdb=" CB VAL A 346 " ideal model delta sigma weight residual 111.29 116.55 -5.26 1.64e+00 3.72e-01 1.03e+01 ... (remaining 9433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3711 17.97 - 35.93: 422 35.93 - 53.90: 100 53.90 - 71.87: 21 71.87 - 89.84: 7 Dihedral angle restraints: 4261 sinusoidal: 1680 harmonic: 2581 Sorted by residual: dihedral pdb=" CA ASN A 81 " pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta harmonic sigma weight residual -180.00 -152.52 -27.48 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA MET A 602 " pdb=" C MET A 602 " pdb=" N ASP A 603 " pdb=" CA ASP A 603 " ideal model delta harmonic sigma weight residual -180.00 -156.17 -23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLY A 208 " pdb=" C GLY A 208 " pdb=" N ASP A 209 " pdb=" CA ASP A 209 " ideal model delta harmonic sigma weight residual 180.00 157.72 22.28 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 4258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 829 0.039 - 0.078: 219 0.078 - 0.116: 78 0.116 - 0.155: 6 0.155 - 0.194: 3 Chirality restraints: 1135 Sorted by residual: chirality pdb=" CG LEU A 780 " pdb=" CB LEU A 780 " pdb=" CD1 LEU A 780 " pdb=" CD2 LEU A 780 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.40e-01 chirality pdb=" CA THR A 804 " pdb=" N THR A 804 " pdb=" C THR A 804 " pdb=" CB THR A 804 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CG LEU A 29 " pdb=" CB LEU A 29 " pdb=" CD1 LEU A 29 " pdb=" CD2 LEU A 29 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.18e-01 ... (remaining 1132 not shown) Planarity restraints: 1193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 743 " -0.079 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO A 744 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO A 744 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 744 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 60 " 0.014 2.00e-02 2.50e+03 1.54e-02 5.93e+00 pdb=" CG TRP A 60 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 60 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 60 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 60 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 60 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 60 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 60 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 60 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 60 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 72 " -0.013 2.00e-02 2.50e+03 1.17e-02 3.43e+00 pdb=" CG TRP A 72 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 72 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 72 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 72 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 72 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 72 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 72 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 72 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 72 " -0.002 2.00e-02 2.50e+03 ... (remaining 1190 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2013 2.82 - 3.34: 6677 3.34 - 3.86: 11234 3.86 - 4.38: 11909 4.38 - 4.90: 21428 Nonbonded interactions: 53261 Sorted by model distance: nonbonded pdb=" OG1 THR A 570 " pdb=" OD2 ASP A 572 " model vdw 2.301 2.440 nonbonded pdb=" N GLN A 829 " pdb=" OE1 GLN A 829 " model vdw 2.351 2.520 nonbonded pdb=" NZ LYS A 333 " pdb=" O ALA A 673 " model vdw 2.351 2.520 nonbonded pdb=" ND2 ASN A 61 " pdb=" O ALA A 152 " model vdw 2.357 2.520 nonbonded pdb=" N THR A 503 " pdb=" OE1 GLN A 506 " model vdw 2.362 2.520 ... (remaining 53256 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 10.010 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 24.810 Find NCS groups from input model: 0.220 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: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 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 0.086 6970 Z= 0.204 Angle : 0.688 10.214 9438 Z= 0.365 Chirality : 0.041 0.194 1135 Planarity : 0.005 0.117 1193 Dihedral : 16.146 89.836 2591 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.92 % Favored : 94.97 % Rotamer: Outliers : 0.39 % Allowed : 25.03 % Favored : 74.58 % 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: 1.35 (0.30), residues: 894 helix: 2.02 (0.24), residues: 461 sheet: -0.49 (0.56), residues: 99 loop : -0.19 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 60 HIS 0.002 0.000 HIS A 149 PHE 0.020 0.001 PHE A 241 TYR 0.010 0.001 TYR A 618 ARG 0.002 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 134 time to evaluate : 0.966 Fit side-chains REVERT: A 71 LEU cc_start: 0.7714 (pp) cc_final: 0.7415 (pp) REVERT: A 797 GLU cc_start: 0.6317 (tm-30) cc_final: 0.5636 (tm-30) outliers start: 3 outliers final: 3 residues processed: 134 average time/residue: 0.1809 time to fit residues: 33.4884 Evaluate side-chains 132 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 739 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.0980 chunk 36 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 51 optimal weight: 9.9990 chunk 80 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6970 Z= 0.213 Angle : 0.588 8.393 9438 Z= 0.294 Chirality : 0.041 0.201 1135 Planarity : 0.004 0.074 1193 Dihedral : 4.557 58.835 950 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.59 % Favored : 95.30 % Rotamer: Outliers : 2.98 % Allowed : 21.92 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.29), residues: 894 helix: 2.03 (0.24), residues: 467 sheet: 0.44 (0.63), residues: 76 loop : -0.49 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 72 HIS 0.004 0.001 HIS A 58 PHE 0.013 0.001 PHE A 812 TYR 0.014 0.001 TYR A 122 ARG 0.002 0.000 ARG A 806 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 0.783 Fit side-chains REVERT: A 138 GLU cc_start: 0.7829 (tp30) cc_final: 0.7611 (tt0) REVERT: A 306 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8388 (mt) REVERT: A 635 ASN cc_start: 0.7341 (OUTLIER) cc_final: 0.7123 (p0) REVERT: A 780 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8392 (mm) outliers start: 23 outliers final: 10 residues processed: 147 average time/residue: 0.1619 time to fit residues: 33.0535 Evaluate side-chains 135 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 790 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7424 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6970 Z= 0.212 Angle : 0.590 9.591 9438 Z= 0.294 Chirality : 0.041 0.201 1135 Planarity : 0.004 0.064 1193 Dihedral : 4.050 27.194 946 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.47 % Favored : 95.30 % Rotamer: Outliers : 3.89 % Allowed : 22.18 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.30), residues: 894 helix: 2.00 (0.24), residues: 467 sheet: -0.43 (0.66), residues: 80 loop : -0.31 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 60 HIS 0.003 0.001 HIS A 58 PHE 0.016 0.001 PHE A 118 TYR 0.012 0.001 TYR A 618 ARG 0.002 0.000 ARG A 796 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 281 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7505 (tmt) REVERT: A 679 ASP cc_start: 0.8288 (t0) cc_final: 0.7861 (t0) REVERT: A 757 ASP cc_start: 0.7737 (t0) cc_final: 0.7372 (t70) REVERT: A 780 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8399 (mm) outliers start: 30 outliers final: 22 residues processed: 146 average time/residue: 0.1888 time to fit residues: 39.6193 Evaluate side-chains 148 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 888 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.7980 chunk 42 optimal weight: 0.0980 chunk 8 optimal weight: 0.1980 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7455 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6970 Z= 0.199 Angle : 0.570 9.597 9438 Z= 0.285 Chirality : 0.040 0.194 1135 Planarity : 0.004 0.060 1193 Dihedral : 4.043 29.247 946 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.15 % Favored : 94.74 % Rotamer: Outliers : 5.06 % Allowed : 21.66 % Favored : 73.28 % 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: 1.39 (0.30), residues: 894 helix: 2.06 (0.24), residues: 468 sheet: 0.17 (0.70), residues: 73 loop : -0.43 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 795 HIS 0.003 0.000 HIS A 58 PHE 0.012 0.001 PHE A 702 TYR 0.010 0.001 TYR A 618 ARG 0.001 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 124 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 281 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7618 (tmt) REVERT: A 306 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8649 (mt) REVERT: A 679 ASP cc_start: 0.8264 (t0) cc_final: 0.7844 (t70) REVERT: A 757 ASP cc_start: 0.7832 (t0) cc_final: 0.7505 (t70) REVERT: A 780 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8401 (mm) outliers start: 39 outliers final: 27 residues processed: 151 average time/residue: 0.2086 time to fit residues: 44.2317 Evaluate side-chains 145 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 115 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 888 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 73 optimal weight: 0.0170 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 0.0020 chunk 77 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 overall best weight: 0.5826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6970 Z= 0.209 Angle : 0.600 9.741 9438 Z= 0.295 Chirality : 0.042 0.197 1135 Planarity : 0.004 0.057 1193 Dihedral : 4.109 27.183 946 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.70 % Favored : 95.19 % Rotamer: Outliers : 5.06 % Allowed : 22.05 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.30), residues: 894 helix: 2.03 (0.24), residues: 468 sheet: -0.03 (0.68), residues: 76 loop : -0.42 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 795 HIS 0.003 0.000 HIS A 58 PHE 0.013 0.001 PHE A 702 TYR 0.010 0.001 TYR A 618 ARG 0.002 0.000 ARG A 796 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 124 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 281 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7657 (tmt) REVERT: A 587 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.6500 (m-80) REVERT: A 679 ASP cc_start: 0.8370 (t0) cc_final: 0.8044 (t70) REVERT: A 757 ASP cc_start: 0.7942 (t0) cc_final: 0.7711 (t70) REVERT: A 780 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8342 (mm) outliers start: 39 outliers final: 30 residues processed: 147 average time/residue: 0.1792 time to fit residues: 35.9555 Evaluate side-chains 152 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 119 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 888 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6970 Z= 0.293 Angle : 0.659 10.597 9438 Z= 0.330 Chirality : 0.043 0.202 1135 Planarity : 0.004 0.057 1193 Dihedral : 4.447 30.727 946 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.37 % Favored : 94.52 % Rotamer: Outliers : 5.58 % Allowed : 22.44 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 1.08 (0.30), residues: 894 helix: 1.79 (0.24), residues: 470 sheet: -0.30 (0.67), residues: 76 loop : -0.49 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP A 72 HIS 0.002 0.001 HIS A 140 PHE 0.016 0.002 PHE A 725 TYR 0.012 0.001 TYR A 618 ARG 0.003 0.000 ARG A 796 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 123 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 281 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7875 (tmt) REVERT: A 306 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8686 (mt) REVERT: A 312 ILE cc_start: 0.8937 (mm) cc_final: 0.8699 (mt) REVERT: A 435 MET cc_start: 0.6941 (tmm) cc_final: 0.6551 (tmm) REVERT: A 594 VAL cc_start: 0.8410 (t) cc_final: 0.8206 (t) REVERT: A 679 ASP cc_start: 0.8565 (t0) cc_final: 0.8139 (t70) REVERT: A 780 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8334 (mm) outliers start: 43 outliers final: 32 residues processed: 148 average time/residue: 0.1770 time to fit residues: 35.6351 Evaluate side-chains 155 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 120 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 85 optimal weight: 0.3980 chunk 53 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 39 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6970 Z= 0.231 Angle : 0.631 11.009 9438 Z= 0.311 Chirality : 0.042 0.195 1135 Planarity : 0.004 0.058 1193 Dihedral : 4.405 30.067 946 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.03 % Favored : 94.85 % Rotamer: Outliers : 5.06 % Allowed : 22.70 % Favored : 72.24 % 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: 1.16 (0.30), residues: 894 helix: 1.90 (0.24), residues: 469 sheet: -0.79 (0.64), residues: 82 loop : -0.37 (0.36), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 72 HIS 0.002 0.000 HIS A 140 PHE 0.022 0.001 PHE A 861 TYR 0.021 0.001 TYR A 483 ARG 0.003 0.000 ARG A 900 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 122 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 306 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8737 (mt) REVERT: A 312 ILE cc_start: 0.8905 (mm) cc_final: 0.8660 (mt) REVERT: A 435 MET cc_start: 0.7057 (tmm) cc_final: 0.6591 (tmm) REVERT: A 613 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8261 (ttpp) REVERT: A 679 ASP cc_start: 0.8498 (t0) cc_final: 0.8105 (t70) REVERT: A 780 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8350 (mm) outliers start: 39 outliers final: 33 residues processed: 146 average time/residue: 0.1789 time to fit residues: 36.0962 Evaluate side-chains 151 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 115 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 0.0470 chunk 74 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 20.0000 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6970 Z= 0.197 Angle : 0.648 11.738 9438 Z= 0.313 Chirality : 0.041 0.188 1135 Planarity : 0.004 0.057 1193 Dihedral : 4.319 29.561 946 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.37 % Favored : 94.52 % Rotamer: Outliers : 4.93 % Allowed : 22.83 % Favored : 72.24 % 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: 1.25 (0.30), residues: 894 helix: 2.01 (0.24), residues: 469 sheet: -0.81 (0.64), residues: 82 loop : -0.37 (0.36), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 72 HIS 0.002 0.000 HIS A 58 PHE 0.017 0.001 PHE A 861 TYR 0.019 0.001 TYR A 483 ARG 0.004 0.000 ARG A 900 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 119 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: A 281 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7736 (tmt) REVERT: A 312 ILE cc_start: 0.8859 (mm) cc_final: 0.8613 (mt) REVERT: A 435 MET cc_start: 0.6941 (tmm) cc_final: 0.6435 (tmm) REVERT: A 613 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8243 (ttpp) REVERT: A 679 ASP cc_start: 0.8462 (t0) cc_final: 0.7966 (t70) REVERT: A 780 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8313 (mm) outliers start: 38 outliers final: 32 residues processed: 142 average time/residue: 0.1649 time to fit residues: 32.2506 Evaluate side-chains 152 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 117 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 79 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6970 Z= 0.228 Angle : 0.683 15.399 9438 Z= 0.327 Chirality : 0.042 0.192 1135 Planarity : 0.004 0.057 1193 Dihedral : 4.361 29.464 946 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.59 % Favored : 94.30 % Rotamer: Outliers : 5.19 % Allowed : 23.87 % Favored : 70.95 % 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: 1.26 (0.30), residues: 894 helix: 2.04 (0.24), residues: 469 sheet: -0.90 (0.65), residues: 82 loop : -0.38 (0.36), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 72 HIS 0.004 0.001 HIS A 58 PHE 0.017 0.001 PHE A 861 TYR 0.017 0.001 TYR A 122 ARG 0.003 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 120 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 312 ILE cc_start: 0.8888 (mm) cc_final: 0.8641 (mt) REVERT: A 337 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7019 (tp) REVERT: A 435 MET cc_start: 0.6995 (tmm) cc_final: 0.6485 (tmm) REVERT: A 594 VAL cc_start: 0.8383 (t) cc_final: 0.8170 (t) REVERT: A 679 ASP cc_start: 0.8485 (t0) cc_final: 0.7966 (t70) REVERT: A 780 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8283 (mm) outliers start: 40 outliers final: 34 residues processed: 144 average time/residue: 0.1813 time to fit residues: 35.6134 Evaluate side-chains 154 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 118 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 467 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6970 Z= 0.262 Angle : 0.715 15.955 9438 Z= 0.343 Chirality : 0.042 0.200 1135 Planarity : 0.004 0.060 1193 Dihedral : 4.482 34.091 946 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.59 % Favored : 94.30 % Rotamer: Outliers : 4.93 % Allowed : 24.51 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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 (0.30), residues: 894 helix: 2.08 (0.24), residues: 463 sheet: -0.69 (0.68), residues: 68 loop : -0.40 (0.36), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 72 HIS 0.004 0.001 HIS A 58 PHE 0.017 0.002 PHE A 861 TYR 0.013 0.001 TYR A 122 ARG 0.004 0.000 ARG A 523 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 123 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: A 306 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8715 (mt) REVERT: A 312 ILE cc_start: 0.8946 (mm) cc_final: 0.8696 (mt) REVERT: A 337 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7135 (tp) REVERT: A 435 MET cc_start: 0.7024 (tmm) cc_final: 0.6538 (tmm) REVERT: A 679 ASP cc_start: 0.8408 (t0) cc_final: 0.7982 (t0) REVERT: A 780 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8312 (mm) outliers start: 38 outliers final: 33 residues processed: 144 average time/residue: 0.1619 time to fit residues: 32.2506 Evaluate side-chains 155 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 800 ASP Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 0.0270 chunk 29 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.194133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.149782 restraints weight = 9263.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.147515 restraints weight = 8470.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.149620 restraints weight = 8157.448| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6970 Z= 0.200 Angle : 0.688 15.194 9438 Z= 0.329 Chirality : 0.041 0.204 1135 Planarity : 0.004 0.059 1193 Dihedral : 4.369 31.333 946 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.26 % Favored : 94.63 % Rotamer: Outliers : 4.54 % Allowed : 24.77 % Favored : 70.69 % 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: 1.41 (0.30), residues: 894 helix: 2.19 (0.24), residues: 463 sheet: -0.46 (0.67), residues: 73 loop : -0.42 (0.36), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 72 HIS 0.004 0.001 HIS A 58 PHE 0.016 0.001 PHE A 861 TYR 0.011 0.001 TYR A 618 ARG 0.004 0.000 ARG A 900 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1822.65 seconds wall clock time: 33 minutes 48.57 seconds (2028.57 seconds total)