Starting phenix.real_space_refine on Sun Aug 4 05:08:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgh_19133/08_2024/8rgh_19133.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgh_19133/08_2024/8rgh_19133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgh_19133/08_2024/8rgh_19133.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgh_19133/08_2024/8rgh_19133.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgh_19133/08_2024/8rgh_19133.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rgh_19133/08_2024/8rgh_19133.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.017 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 34 5.16 5 C 6123 2.51 5 N 1711 2.21 5 O 1814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 185": "NH1" <-> "NH2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "A ARG 207": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 430": "NH1" <-> "NH2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A ARG 456": "NH1" <-> "NH2" Residue "A ARG 462": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 490": "NH1" <-> "NH2" Residue "A ARG 514": "NH1" <-> "NH2" Residue "A ARG 540": "NH1" <-> "NH2" Residue "A ARG 550": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A ARG 578": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A ARG 636": "NH1" <-> "NH2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 713": "NH1" <-> "NH2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "A ARG 726": "NH1" <-> "NH2" Residue "C ARG 587": "NH1" <-> "NH2" Residue "C ARG 593": "NH1" <-> "NH2" Residue "C ARG 607": "NH1" <-> "NH2" Residue "C ARG 617": "NH1" <-> "NH2" Residue "C ARG 621": "NH1" <-> "NH2" Residue "C ARG 642": "NH1" <-> "NH2" Residue "C ARG 651": "NH1" <-> "NH2" Residue "C ARG 654": "NH1" <-> "NH2" Residue "C ARG 727": "NH1" <-> "NH2" Residue "C ARG 731": "NH1" <-> "NH2" Residue "C ARG 746": "NH1" <-> "NH2" Residue "C ARG 762": "NH1" <-> "NH2" Residue "C ARG 835": "NH1" <-> "NH2" Residue "C ARG 890": "NH1" <-> "NH2" Residue "C ARG 894": "NH1" <-> "NH2" Residue "C ARG 908": "NH1" <-> "NH2" Residue "C PHE 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 935": "NH1" <-> "NH2" Residue "C ARG 966": "NH1" <-> "NH2" Residue "C ARG 1001": "NH1" <-> "NH2" Residue "C ARG 1025": "NH1" <-> "NH2" Residue "C ARG 1037": "NH1" <-> "NH2" Residue "C ARG 1038": "NH1" <-> "NH2" Residue "C ARG 1049": "NH1" <-> "NH2" Residue "C ARG 1051": "NH1" <-> "NH2" Residue "E ARG 313": "NH1" <-> "NH2" Residue "E ARG 326": "NH1" <-> "NH2" Residue "E ARG 338": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9682 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4757 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 18, 'TRANS': 558} Chain breaks: 3 Chain: "C" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3615 Classifications: {'peptide': 467} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 439} Chain breaks: 1 Chain: "D" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 150 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 1, 'TRANS': 28} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 70 Chain: "E" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 236 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "G" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 462 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 5, 'TRANS': 87} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 139 Chain: "H" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 462 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 5, 'TRANS': 87} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 139 Time building chain proxies: 5.35, per 1000 atoms: 0.55 Number of scatterers: 9682 At special positions: 0 Unit cell: (100.188, 94.392, 129.168, 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 34 16.00 O 1814 8.00 N 1711 7.00 C 6123 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: 3.38 Conformation dependent library (CDL) restraints added in 1.6 seconds 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2466 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 52.9% alpha, 14.1% 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 172 through 186 Processing helix chain 'A' and resid 188 through 211 removed outlier: 3.547A pdb=" N THR A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 216 through 237 removed outlier: 3.523A pdb=" N GLU A 225 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 269 Processing helix chain 'A' and resid 276 through 304 removed outlier: 3.841A pdb=" N VAL A 280 " --> pdb=" O PRO A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 322 through 348 Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.711A pdb=" N ILE A 355 " --> pdb=" O SER A 351 " (cutoff:3.500A) Proline residue: A 364 - end of helix Processing helix chain 'A' and resid 377 through 410 Proline residue: A 394 - end of helix removed outlier: 3.628A pdb=" N LYS A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 430 through 437 Processing helix chain 'A' and resid 437 through 465 Processing helix chain 'A' and resid 481 through 507 Processing helix chain 'A' and resid 512 through 546 Processing helix chain 'A' and resid 576 through 593 removed outlier: 4.112A pdb=" N VAL A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 630 removed outlier: 3.940A pdb=" N ASP A 628 " --> pdb=" O TYR A 624 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN A 629 " --> pdb=" O ASN A 625 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 654 removed outlier: 3.858A pdb=" N MET A 639 " --> pdb=" O GLN A 635 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLN A 641 " --> pdb=" O PRO A 637 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N SER A 642 " --> pdb=" O MET A 638 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 708 Processing helix chain 'A' and resid 711 through 713 No H-bonds generated for 'chain 'A' and resid 711 through 713' Processing helix chain 'A' and resid 714 through 735 Processing helix chain 'A' and resid 738 through 770 removed outlier: 3.870A pdb=" N MET A 742 " --> pdb=" O GLN A 738 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 768 " --> pdb=" O GLY A 764 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN A 769 " --> pdb=" O LEU A 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 585 Processing helix chain 'C' and resid 585 through 611 Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 753 through 755 No H-bonds generated for 'chain 'C' and resid 753 through 755' Processing helix chain 'C' and resid 845 through 850 Processing helix chain 'C' and resid 1036 through 1041 Processing helix chain 'C' and resid 1045 through 1057 Processing helix chain 'D' and resid 105 through 129 Processing helix chain 'E' and resid 319 through 339 Processing helix chain 'G' and resid 4 through 13 Processing helix chain 'G' and resid 35 through 61 Processing helix chain 'H' and resid 4 through 13 Processing helix chain 'H' and resid 35 through 61 Processing sheet with id=AA1, first strand: chain 'A' and resid 562 through 564 Processing sheet with id=AA2, first strand: chain 'C' and resid 629 through 632 removed outlier: 4.521A pdb=" N ILE C1030 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA C1004 " --> pdb=" O ALA C1024 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 644 through 649 removed outlier: 4.060A pdb=" N SER C 646 " --> pdb=" O VAL C 660 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL C 660 " --> pdb=" O SER C 646 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 677 " --> pdb=" O HIS C 661 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 699 through 704 Processing sheet with id=AA5, first strand: chain 'C' and resid 735 through 738 Processing sheet with id=AA6, first strand: chain 'C' and resid 765 through 771 removed outlier: 3.672A pdb=" N ALA C 767 " --> pdb=" O LEU C 802 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN C 809 " --> pdb=" O SER C 801 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 863 through 868 removed outlier: 4.210A pdb=" N ASN C 865 " --> pdb=" O GLY C 879 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 912 through 917 removed outlier: 6.971A pdb=" N GLY C 928 " --> pdb=" O ASN C 913 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ILE C 915 " --> pdb=" O LEU C 926 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU C 926 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE C 917 " --> pdb=" O ILE C 924 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE C 924 " --> pdb=" O PHE C 917 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 957 through 962 removed outlier: 3.595A pdb=" N GLY C 959 " --> pdb=" O GLN C 973 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN C 978 " --> pdb=" O ASP C 974 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.538A pdb=" N VAL G 22 " --> pdb=" O ILE G 30 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER G 32 " --> pdb=" O ILE G 20 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE G 20 " --> pdb=" O SER G 32 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR G 67 " --> pdb=" O PRO G 82 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU G 66 " --> pdb=" O SER H 73 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N SER H 73 " --> pdb=" O LEU G 66 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE G 68 " --> pdb=" O ILE H 71 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE H 71 " --> pdb=" O PHE G 68 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG G 70 " --> pdb=" O LEU H 69 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU H 69 " --> pdb=" O ARG G 70 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG G 72 " --> pdb=" O THR H 67 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N THR H 67 " --> pdb=" O PRO H 82 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1845 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: 2.77 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2569 1.33 - 1.46: 1796 1.46 - 1.58: 5448 1.58 - 1.70: 0 1.70 - 1.82: 51 Bond restraints: 9864 Sorted by residual: bond pdb=" CZ ARG C 966 " pdb=" NH2 ARG C 966 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.73e+00 bond pdb=" CZ ARG C 727 " pdb=" NH2 ARG C 727 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.52e+00 bond pdb=" CZ ARG C 835 " pdb=" NH2 ARG C 835 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.40e+00 bond pdb=" CZ ARG C 731 " pdb=" NH2 ARG C 731 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.26e+00 bond pdb=" CZ ARG C 935 " pdb=" NH2 ARG C 935 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.64e+00 ... (remaining 9859 not shown) Histogram of bond angle deviations from ideal: 97.25 - 104.86: 163 104.86 - 112.47: 4505 112.47 - 120.08: 4498 120.08 - 127.69: 4119 127.69 - 135.30: 119 Bond angle restraints: 13404 Sorted by residual: angle pdb=" CA ASN A 605 " pdb=" CB ASN A 605 " pdb=" CG ASN A 605 " ideal model delta sigma weight residual 112.60 119.19 -6.59 1.00e+00 1.00e+00 4.34e+01 angle pdb=" CA ASP C 803 " pdb=" CB ASP C 803 " pdb=" CG ASP C 803 " ideal model delta sigma weight residual 112.60 119.04 -6.44 1.00e+00 1.00e+00 4.15e+01 angle pdb=" N ALA C 610 " pdb=" CA ALA C 610 " pdb=" C ALA C 610 " ideal model delta sigma weight residual 111.40 119.12 -7.72 1.22e+00 6.72e-01 4.01e+01 angle pdb=" C ALA C 714 " pdb=" N GLY C 715 " pdb=" CA GLY C 715 " ideal model delta sigma weight residual 122.18 126.34 -4.16 6.90e-01 2.10e+00 3.64e+01 angle pdb=" N GLU A 493 " pdb=" CA GLU A 493 " pdb=" CB GLU A 493 " ideal model delta sigma weight residual 110.12 118.72 -8.60 1.47e+00 4.63e-01 3.42e+01 ... (remaining 13399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 5423 17.41 - 34.82: 424 34.82 - 52.22: 77 52.22 - 69.63: 14 69.63 - 87.04: 14 Dihedral angle restraints: 5952 sinusoidal: 2185 harmonic: 3767 Sorted by residual: dihedral pdb=" CA LEU C 765 " pdb=" C LEU C 765 " pdb=" N GLN C 766 " pdb=" CA GLN C 766 " ideal model delta harmonic sigma weight residual 180.00 150.26 29.74 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA LEU C 632 " pdb=" C LEU C 632 " pdb=" N ASN C 633 " pdb=" CA ASN C 633 " ideal model delta harmonic sigma weight residual 180.00 -150.55 -29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA GLY H 19 " pdb=" C GLY H 19 " pdb=" N ILE H 20 " pdb=" CA ILE H 20 " ideal model delta harmonic sigma weight residual 180.00 150.57 29.43 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 5949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1210 0.120 - 0.241: 305 0.241 - 0.361: 24 0.361 - 0.482: 2 0.482 - 0.602: 1 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CA MET A 639 " pdb=" N MET A 639 " pdb=" C MET A 639 " pdb=" CB MET A 639 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.07e+00 chirality pdb=" CA GLU A 274 " pdb=" N GLU A 274 " pdb=" C GLU A 274 " pdb=" CB GLU A 274 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CA ASP A 509 " pdb=" N ASP A 509 " pdb=" C ASP A 509 " pdb=" CB ASP A 509 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.34e+00 ... (remaining 1539 not shown) Planarity restraints: 1742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 197 " 0.149 2.00e-02 2.50e+03 7.82e-02 1.22e+02 pdb=" CG TYR A 197 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR A 197 " -0.059 2.00e-02 2.50e+03 pdb=" CD2 TYR A 197 " -0.076 2.00e-02 2.50e+03 pdb=" CE1 TYR A 197 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR A 197 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR A 197 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 197 " 0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 982 " 0.130 2.00e-02 2.50e+03 6.89e-02 1.19e+02 pdb=" CG TRP C 982 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP C 982 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP C 982 " -0.078 2.00e-02 2.50e+03 pdb=" NE1 TRP C 982 " -0.047 2.00e-02 2.50e+03 pdb=" CE2 TRP C 982 " -0.026 2.00e-02 2.50e+03 pdb=" CE3 TRP C 982 " -0.086 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 982 " 0.079 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 982 " -0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP C 982 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 314 " -0.121 2.00e-02 2.50e+03 6.70e-02 1.12e+02 pdb=" CG TRP A 314 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TRP A 314 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 314 " 0.073 2.00e-02 2.50e+03 pdb=" NE1 TRP A 314 " 0.047 2.00e-02 2.50e+03 pdb=" CE2 TRP A 314 " 0.025 2.00e-02 2.50e+03 pdb=" CE3 TRP A 314 " 0.092 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 314 " -0.073 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 314 " 0.022 2.00e-02 2.50e+03 pdb=" CH2 TRP A 314 " -0.086 2.00e-02 2.50e+03 ... (remaining 1739 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 4555 2.98 - 3.46: 10550 3.46 - 3.94: 15499 3.94 - 4.42: 16937 4.42 - 4.90: 28428 Nonbonded interactions: 75969 Sorted by model distance: nonbonded pdb=" OE2 GLU A 175 " pdb=" OH TYR A 243 " model vdw 2.504 3.040 nonbonded pdb=" OG SER C 763 " pdb=" OD2 ASP C 803 " model vdw 2.551 3.040 nonbonded pdb=" OG SER C 626 " pdb=" O HIS C1034 " model vdw 2.559 3.040 nonbonded pdb=" OG SER A 351 " pdb=" OE1 GLU A 353 " model vdw 2.561 3.040 nonbonded pdb=" O ASN A 211 " pdb=" OG SER A 214 " model vdw 2.572 3.040 ... (remaining 75964 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 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'H' } 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=0.00 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: 1.530 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.600 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 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 : 0.012 0.041 9864 Z= 0.772 Angle : 1.877 9.034 13404 Z= 1.280 Chirality : 0.100 0.602 1542 Planarity : 0.018 0.208 1742 Dihedral : 14.042 87.037 3486 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 3.57 % 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: -1.05 (0.21), residues: 1267 helix: -0.14 (0.17), residues: 620 sheet: -0.28 (0.35), residues: 191 loop : -1.52 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.130 0.033 TRP C 982 HIS 0.020 0.004 HIS C 648 PHE 0.082 0.018 PHE A 344 TYR 0.149 0.024 TYR A 197 ARG 0.021 0.002 ARG C 731 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ILE cc_start: 0.7965 (pt) cc_final: 0.7044 (pt) REVERT: A 222 ASP cc_start: 0.7761 (t70) cc_final: 0.7415 (t70) REVERT: C 1008 VAL cc_start: 0.6972 (t) cc_final: 0.6669 (t) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2823 time to fit residues: 52.4455 Evaluate side-chains 83 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 312 HIS ** A 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 GLN A 762 GLN C 619 GLN C 631 GLN ** C 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 733 HIS ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 862 GLN C 973 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9864 Z= 0.261 Angle : 0.711 8.149 13404 Z= 0.385 Chirality : 0.045 0.170 1542 Planarity : 0.005 0.045 1742 Dihedral : 6.491 33.278 1359 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.08 % Favored : 96.69 % Rotamer: Outliers : 1.15 % Allowed : 7.02 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.23), residues: 1267 helix: 1.53 (0.19), residues: 619 sheet: -0.76 (0.33), residues: 235 loop : -0.90 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 273 HIS 0.012 0.002 HIS A 759 PHE 0.020 0.002 PHE C 970 TYR 0.016 0.002 TYR A 761 ARG 0.006 0.001 ARG E 338 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 THR cc_start: 0.8806 (p) cc_final: 0.8209 (p) REVERT: A 222 ASP cc_start: 0.7848 (t70) cc_final: 0.7574 (t70) REVERT: A 707 MET cc_start: 0.7599 (ttt) cc_final: 0.7317 (ttt) REVERT: C 792 MET cc_start: 0.2183 (pmm) cc_final: 0.1638 (ptt) REVERT: C 882 MET cc_start: 0.7541 (mmm) cc_final: 0.7338 (tpt) REVERT: C 965 THR cc_start: 0.8106 (p) cc_final: 0.7894 (t) REVERT: C 1008 VAL cc_start: 0.6992 (t) cc_final: 0.6728 (t) outliers start: 11 outliers final: 2 residues processed: 103 average time/residue: 0.2374 time to fit residues: 33.7944 Evaluate side-chains 83 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain C residue 958 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 77 optimal weight: 0.0270 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 102 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN A 517 HIS ** A 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 GLN A 747 GLN ** C 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9864 Z= 0.231 Angle : 0.639 7.352 13404 Z= 0.342 Chirality : 0.043 0.167 1542 Planarity : 0.004 0.052 1742 Dihedral : 5.840 31.964 1359 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.47 % Allowed : 8.39 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.24), residues: 1267 helix: 1.78 (0.20), residues: 627 sheet: -0.96 (0.32), residues: 236 loop : -0.77 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 273 HIS 0.010 0.002 HIS A 759 PHE 0.019 0.002 PHE A 347 TYR 0.023 0.002 TYR A 388 ARG 0.004 0.000 ARG C 731 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.7852 (t70) cc_final: 0.7584 (t70) REVERT: A 493 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7009 (pp20) REVERT: C 1008 VAL cc_start: 0.6763 (t) cc_final: 0.6469 (t) outliers start: 14 outliers final: 10 residues processed: 99 average time/residue: 0.2504 time to fit residues: 34.4046 Evaluate side-chains 89 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain C residue 702 CYS Chi-restraints excluded: chain C residue 797 PHE Chi-restraints excluded: chain C residue 803 ASP Chi-restraints excluded: chain C residue 848 ASP Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 973 GLN Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1005 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 109 optimal weight: 40.0000 chunk 32 optimal weight: 8.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9864 Z= 0.231 Angle : 0.614 6.468 13404 Z= 0.329 Chirality : 0.042 0.171 1542 Planarity : 0.004 0.051 1742 Dihedral : 5.596 31.796 1359 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.20 % Allowed : 10.48 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.68 (0.24), residues: 1267 helix: 1.84 (0.20), residues: 628 sheet: -0.96 (0.32), residues: 224 loop : -0.83 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 273 HIS 0.009 0.002 HIS A 184 PHE 0.017 0.002 PHE C 970 TYR 0.021 0.002 TYR A 761 ARG 0.004 0.000 ARG E 338 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 PHE cc_start: 0.8047 (m-80) cc_final: 0.7788 (m-80) REVERT: A 493 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7084 (pp20) REVERT: C 599 MET cc_start: 0.7691 (tpp) cc_final: 0.7399 (mtp) REVERT: C 1008 VAL cc_start: 0.6759 (t) cc_final: 0.6485 (t) REVERT: E 334 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8648 (mm-30) outliers start: 21 outliers final: 12 residues processed: 93 average time/residue: 0.2744 time to fit residues: 34.8375 Evaluate side-chains 88 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain C residue 702 CYS Chi-restraints excluded: chain C residue 797 PHE Chi-restraints excluded: chain C residue 803 ASP Chi-restraints excluded: chain C residue 840 HIS Chi-restraints excluded: chain C residue 848 ASP Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 978 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN ** A 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 798 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9864 Z= 0.349 Angle : 0.724 9.691 13404 Z= 0.383 Chirality : 0.045 0.157 1542 Planarity : 0.005 0.088 1742 Dihedral : 5.996 32.198 1359 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.52 % Allowed : 11.32 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.02 (0.23), residues: 1267 helix: 1.39 (0.20), residues: 620 sheet: -1.56 (0.30), residues: 229 loop : -1.04 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 273 HIS 0.016 0.002 HIS A 622 PHE 0.026 0.003 PHE A 347 TYR 0.022 0.002 TYR A 197 ARG 0.007 0.001 ARG E 338 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 81 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 PHE cc_start: 0.8182 (m-80) cc_final: 0.7866 (m-80) REVERT: A 438 MET cc_start: 0.6943 (tpp) cc_final: 0.6630 (mtp) REVERT: C 599 MET cc_start: 0.8037 (tpp) cc_final: 0.7612 (mtm) REVERT: C 924 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7569 (pt) REVERT: C 1008 VAL cc_start: 0.6943 (OUTLIER) cc_final: 0.6627 (t) REVERT: E 317 TYR cc_start: 0.7707 (m-10) cc_final: 0.7463 (m-10) outliers start: 24 outliers final: 14 residues processed: 94 average time/residue: 0.2963 time to fit residues: 37.0780 Evaluate side-chains 91 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 717 ARG Chi-restraints excluded: chain C residue 694 ILE Chi-restraints excluded: chain C residue 803 ASP Chi-restraints excluded: chain C residue 840 HIS Chi-restraints excluded: chain C residue 857 PHE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 924 ILE Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 973 GLN Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1053 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 ASN C 633 ASN ** C 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9864 Z= 0.257 Angle : 0.648 8.781 13404 Z= 0.341 Chirality : 0.043 0.155 1542 Planarity : 0.004 0.059 1742 Dihedral : 5.627 32.731 1359 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.47 % Allowed : 12.79 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.11 (0.23), residues: 1267 helix: 1.48 (0.20), residues: 631 sheet: -1.74 (0.30), residues: 225 loop : -0.96 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 273 HIS 0.012 0.002 HIS A 622 PHE 0.017 0.002 PHE A 347 TYR 0.018 0.002 TYR A 761 ARG 0.011 0.001 ARG E 338 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 PHE cc_start: 0.8182 (m-80) cc_final: 0.7883 (m-80) REVERT: A 638 MET cc_start: 0.8406 (mtt) cc_final: 0.7954 (mtt) REVERT: C 1008 VAL cc_start: 0.6689 (OUTLIER) cc_final: 0.6349 (t) REVERT: E 317 TYR cc_start: 0.7727 (m-10) cc_final: 0.7507 (m-10) outliers start: 14 outliers final: 11 residues processed: 92 average time/residue: 0.2724 time to fit residues: 33.9446 Evaluate side-chains 89 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain C residue 702 CYS Chi-restraints excluded: chain C residue 797 PHE Chi-restraints excluded: chain C residue 803 ASP Chi-restraints excluded: chain C residue 840 HIS Chi-restraints excluded: chain C residue 857 PHE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1008 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 89 optimal weight: 0.2980 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 76 optimal weight: 0.0980 chunk 74 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9864 Z= 0.157 Angle : 0.581 8.021 13404 Z= 0.303 Chirality : 0.041 0.168 1542 Planarity : 0.004 0.041 1742 Dihedral : 5.026 30.752 1359 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.15 % Allowed : 14.26 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.59 (0.24), residues: 1267 helix: 1.87 (0.20), residues: 634 sheet: -1.33 (0.32), residues: 221 loop : -0.89 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 273 HIS 0.008 0.001 HIS A 184 PHE 0.016 0.002 PHE C 970 TYR 0.013 0.001 TYR A 761 ARG 0.005 0.000 ARG E 338 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 GLU cc_start: 0.7789 (mp0) cc_final: 0.7489 (mp0) REVERT: A 638 MET cc_start: 0.8094 (mtt) cc_final: 0.7705 (mtt) REVERT: C 882 MET cc_start: 0.7582 (tpt) cc_final: 0.6942 (tpp) REVERT: C 1008 VAL cc_start: 0.6281 (t) cc_final: 0.5913 (t) outliers start: 11 outliers final: 5 residues processed: 97 average time/residue: 0.2300 time to fit residues: 31.4397 Evaluate side-chains 80 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain C residue 797 PHE Chi-restraints excluded: chain C residue 803 ASP Chi-restraints excluded: chain C residue 857 PHE Chi-restraints excluded: chain C residue 978 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 77 optimal weight: 0.0270 chunk 82 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 HIS ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9864 Z= 0.218 Angle : 0.617 8.371 13404 Z= 0.320 Chirality : 0.043 0.185 1542 Planarity : 0.004 0.050 1742 Dihedral : 5.142 30.858 1359 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.47 % Allowed : 14.68 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.59 (0.24), residues: 1267 helix: 1.88 (0.20), residues: 635 sheet: -1.43 (0.32), residues: 221 loop : -0.85 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 273 HIS 0.011 0.002 HIS A 184 PHE 0.015 0.002 PHE A 347 TYR 0.019 0.002 TYR E 317 ARG 0.008 0.000 ARG E 338 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 763 MET cc_start: 0.5108 (mmm) cc_final: 0.4887 (mmp) REVERT: C 1008 VAL cc_start: 0.6371 (t) cc_final: 0.6014 (t) outliers start: 14 outliers final: 7 residues processed: 89 average time/residue: 0.2526 time to fit residues: 31.2577 Evaluate side-chains 81 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 797 PHE Chi-restraints excluded: chain C residue 803 ASP Chi-restraints excluded: chain C residue 857 PHE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 981 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 8.9990 chunk 116 optimal weight: 30.0000 chunk 68 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 102 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 119 optimal weight: 30.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 689 ASN ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9864 Z= 0.223 Angle : 0.633 7.931 13404 Z= 0.328 Chirality : 0.043 0.177 1542 Planarity : 0.004 0.043 1742 Dihedral : 5.198 30.427 1359 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.15 % Allowed : 15.09 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.50 (0.24), residues: 1267 helix: 1.83 (0.20), residues: 635 sheet: -1.50 (0.32), residues: 223 loop : -0.91 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 273 HIS 0.010 0.002 HIS A 184 PHE 0.016 0.002 PHE A 347 TYR 0.023 0.002 TYR E 317 ARG 0.010 0.001 ARG E 338 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ILE cc_start: 0.8149 (pt) cc_final: 0.7348 (pt) REVERT: C 1008 VAL cc_start: 0.6362 (t) cc_final: 0.5988 (t) outliers start: 11 outliers final: 9 residues processed: 89 average time/residue: 0.2642 time to fit residues: 32.3343 Evaluate side-chains 82 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain C residue 797 PHE Chi-restraints excluded: chain C residue 803 ASP Chi-restraints excluded: chain C residue 857 PHE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 981 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 83 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 115 optimal weight: 20.0000 chunk 99 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 77 optimal weight: 0.0870 chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9864 Z= 0.164 Angle : 0.608 12.443 13404 Z= 0.317 Chirality : 0.043 0.169 1542 Planarity : 0.004 0.051 1742 Dihedral : 4.886 28.415 1359 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.84 % Allowed : 16.25 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.67 (0.24), residues: 1267 helix: 1.94 (0.20), residues: 638 sheet: -1.26 (0.33), residues: 221 loop : -0.93 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 273 HIS 0.010 0.001 HIS C 840 PHE 0.047 0.002 PHE A 209 TYR 0.022 0.001 TYR E 317 ARG 0.009 0.000 ARG E 338 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 MET cc_start: 0.6424 (tpt) cc_final: 0.6181 (mtp) REVERT: A 638 MET cc_start: 0.7941 (mtt) cc_final: 0.7653 (mtt) REVERT: A 742 MET cc_start: 0.8357 (mpp) cc_final: 0.8110 (pmm) REVERT: C 599 MET cc_start: 0.6899 (ttt) cc_final: 0.6684 (mtm) REVERT: C 882 MET cc_start: 0.7573 (tpt) cc_final: 0.6810 (tpp) REVERT: C 884 LEU cc_start: 0.7884 (mp) cc_final: 0.7173 (mt) REVERT: C 1008 VAL cc_start: 0.6071 (t) cc_final: 0.5820 (t) outliers start: 8 outliers final: 6 residues processed: 88 average time/residue: 0.2464 time to fit residues: 30.2721 Evaluate side-chains 80 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain C residue 797 PHE Chi-restraints excluded: chain C residue 857 PHE Chi-restraints excluded: chain C residue 965 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 HIS ** 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 = 0.4147 r_free = 0.4147 target = 0.093624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.078289 restraints weight = 49115.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.080028 restraints weight = 31890.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.081191 restraints weight = 23819.822| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.5838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9864 Z= 0.250 Angle : 0.667 10.242 13404 Z= 0.348 Chirality : 0.044 0.193 1542 Planarity : 0.004 0.059 1742 Dihedral : 5.168 30.553 1359 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.47 % Allowed : 15.09 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.50 (0.24), residues: 1267 helix: 1.82 (0.20), residues: 638 sheet: -1.48 (0.32), residues: 221 loop : -0.93 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 273 HIS 0.011 0.002 HIS A 184 PHE 0.039 0.002 PHE A 209 TYR 0.025 0.002 TYR E 317 ARG 0.009 0.000 ARG E 338 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1767.57 seconds wall clock time: 32 minutes 31.81 seconds (1951.81 seconds total)