Starting phenix.real_space_refine on Fri Feb 14 03:17:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rgh_19133/02_2025/8rgh_19133.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rgh_19133/02_2025/8rgh_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/cci-nas-00/data/ceres_data/8rgh_19133/02_2025/8rgh_19133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rgh_19133/02_2025/8rgh_19133.map" model { file = "/net/cci-nas-00/data/ceres_data/8rgh_19133/02_2025/8rgh_19133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rgh_19133/02_2025/8rgh_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. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.14, per 1000 atoms: 0.63 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.2 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: 1.02 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: 3.53 Time building geometry restraints manager: 3.02 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: 0.00 - 1.81: 9316 1.81 - 3.61: 3263 3.61 - 5.42: 710 5.42 - 7.23: 103 7.23 - 9.03: 12 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: 1.120 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.490 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.260 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.979 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: 0.3068 time to fit residues: 57.1486 Evaluate side-chains 83 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.096367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.080363 restraints weight = 47618.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.082220 restraints weight = 29969.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.083414 restraints weight = 22104.517| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 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 to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 THR cc_start: 0.9139 (p) cc_final: 0.8493 (p) REVERT: A 222 ASP cc_start: 0.8595 (t70) cc_final: 0.8340 (t70) REVERT: A 707 MET cc_start: 0.7990 (ttt) cc_final: 0.7653 (ttt) REVERT: C 792 MET cc_start: 0.2367 (pmm) cc_final: 0.1483 (ptt) REVERT: C 1008 VAL cc_start: 0.7374 (t) cc_final: 0.7073 (t) outliers start: 11 outliers final: 2 residues processed: 103 average time/residue: 0.2510 time to fit residues: 35.7059 Evaluate side-chains 82 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 74 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN ** 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 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.097018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.081396 restraints weight = 49583.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.083218 restraints weight = 31178.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.084482 restraints weight = 22943.847| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9864 Z= 0.196 Angle : 0.614 7.530 13404 Z= 0.328 Chirality : 0.042 0.170 1542 Planarity : 0.004 0.052 1742 Dihedral : 5.748 31.716 1359 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.36 % Allowed : 8.28 % Favored : 90.36 % 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: 0.78 (0.23), residues: 1267 helix: 1.90 (0.19), residues: 620 sheet: -0.76 (0.32), residues: 232 loop : -0.79 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 273 HIS 0.009 0.002 HIS A 759 PHE 0.019 0.002 PHE C 970 TYR 0.021 0.002 TYR A 388 ARG 0.004 0.000 ARG A 713 *********************** 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 to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 PHE cc_start: 0.8044 (m-80) cc_final: 0.7840 (m-80) REVERT: A 222 ASP cc_start: 0.8352 (t70) cc_final: 0.8055 (t70) REVERT: A 493 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6870 (pp20) REVERT: A 707 MET cc_start: 0.7963 (ttt) cc_final: 0.7738 (ttt) REVERT: C 599 MET cc_start: 0.7827 (tpp) cc_final: 0.7545 (mtp) REVERT: C 1008 VAL cc_start: 0.7050 (t) cc_final: 0.6738 (t) outliers start: 13 outliers final: 9 residues processed: 98 average time/residue: 0.2509 time to fit residues: 33.8522 Evaluate side-chains 90 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 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 6 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 44 optimal weight: 0.0470 chunk 63 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 28 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.2282 ------------------------------------------------------------------------------- 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 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** 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 = 0.4228 r_free = 0.4228 target = 0.097248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.081855 restraints weight = 48889.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.083694 restraints weight = 30961.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.084955 restraints weight = 22804.339| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.4247 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= 0.180 Angle : 0.572 6.824 13404 Z= 0.303 Chirality : 0.041 0.167 1542 Planarity : 0.004 0.051 1742 Dihedral : 5.253 31.014 1359 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.78 % Allowed : 10.06 % Favored : 88.16 % 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: 0.97 (0.24), residues: 1267 helix: 2.08 (0.20), residues: 634 sheet: -0.76 (0.32), residues: 232 loop : -0.77 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 273 HIS 0.009 0.001 HIS A 184 PHE 0.017 0.002 PHE C 970 TYR 0.014 0.001 TYR A 761 ARG 0.004 0.000 ARG C 731 *********************** 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 105 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 PHE cc_start: 0.8143 (m-80) cc_final: 0.7810 (m-80) REVERT: A 638 MET cc_start: 0.8330 (mtt) cc_final: 0.8081 (mtt) REVERT: C 1008 VAL cc_start: 0.6850 (t) cc_final: 0.6549 (t) REVERT: E 317 TYR cc_start: 0.8017 (m-10) cc_final: 0.7788 (m-10) REVERT: E 334 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8868 (pt0) outliers start: 17 outliers final: 9 residues processed: 100 average time/residue: 0.2638 time to fit residues: 36.3517 Evaluate side-chains 89 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 341 HIS 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 848 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 93 optimal weight: 0.0010 chunk 73 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 38 optimal weight: 0.0040 chunk 78 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 115 optimal weight: 20.0000 chunk 110 optimal weight: 30.0000 overall best weight: 2.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 517 HIS ** A 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.094656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.079195 restraints weight = 49359.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.080929 restraints weight = 31952.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.082121 restraints weight = 23873.839| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9864 Z= 0.246 Angle : 0.616 6.676 13404 Z= 0.327 Chirality : 0.043 0.170 1542 Planarity : 0.004 0.046 1742 Dihedral : 5.412 30.901 1359 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.68 % Allowed : 10.48 % Favored : 87.84 % 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: 0.75 (0.24), residues: 1267 helix: 1.88 (0.20), residues: 637 sheet: -0.92 (0.32), residues: 225 loop : -0.82 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 273 HIS 0.011 0.002 HIS A 184 PHE 0.026 0.002 PHE A 347 TYR 0.021 0.002 TYR A 761 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 98 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 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: A 209 PHE cc_start: 0.8200 (m-80) cc_final: 0.7857 (m-80) REVERT: A 274 GLU cc_start: 0.8004 (mp0) cc_final: 0.7802 (mp0) REVERT: A 438 MET cc_start: 0.6594 (OUTLIER) cc_final: 0.6272 (mtp) REVERT: A 638 MET cc_start: 0.8477 (mtt) cc_final: 0.7958 (mtt) REVERT: A 711 LEU cc_start: 0.8192 (tp) cc_final: 0.7825 (mp) REVERT: C 1008 VAL cc_start: 0.7085 (t) cc_final: 0.6733 (t) REVERT: E 317 TYR cc_start: 0.8203 (m-10) cc_final: 0.7973 (m-10) REVERT: E 325 MET cc_start: 0.8822 (ttm) cc_final: 0.8578 (ttp) outliers start: 16 outliers final: 12 residues processed: 91 average time/residue: 0.2598 time to fit residues: 32.9152 Evaluate side-chains 91 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 MET 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 848 ASP 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 911 LYS Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1005 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 48 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 116 optimal weight: 40.0000 chunk 112 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 762 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.096599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.081315 restraints weight = 49298.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.083123 restraints weight = 31625.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.084350 restraints weight = 23352.570| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9864 Z= 0.168 Angle : 0.562 7.556 13404 Z= 0.294 Chirality : 0.041 0.142 1542 Planarity : 0.004 0.044 1742 Dihedral : 5.021 29.426 1359 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.57 % Allowed : 11.84 % Favored : 86.58 % 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: 0.91 (0.24), residues: 1267 helix: 2.04 (0.20), residues: 637 sheet: -0.97 (0.33), residues: 223 loop : -0.72 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 273 HIS 0.009 0.002 HIS A 184 PHE 0.017 0.002 PHE C 970 TYR 0.015 0.001 TYR A 761 ARG 0.004 0.000 ARG A 717 *********************** 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 100 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.6403 (mtp) REVERT: A 711 LEU cc_start: 0.8054 (tp) cc_final: 0.7661 (mp) REVERT: C 1008 VAL cc_start: 0.6800 (t) cc_final: 0.6418 (t) REVERT: E 338 ARG cc_start: 0.8587 (ttp-110) cc_final: 0.8084 (ptp90) outliers start: 15 outliers final: 9 residues processed: 96 average time/residue: 0.2463 time to fit residues: 33.0510 Evaluate side-chains 86 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 632 ILE 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 857 PHE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 978 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 109 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 61 optimal weight: 0.0970 chunk 52 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.095327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.079818 restraints weight = 49758.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.081578 restraints weight = 32061.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.082772 restraints weight = 23856.935| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.5115 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= 0.205 Angle : 0.592 7.112 13404 Z= 0.310 Chirality : 0.042 0.175 1542 Planarity : 0.004 0.045 1742 Dihedral : 5.083 30.334 1359 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.36 % Allowed : 13.52 % Favored : 85.12 % 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: 0.84 (0.24), residues: 1267 helix: 1.99 (0.20), residues: 637 sheet: -1.14 (0.32), residues: 227 loop : -0.68 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 273 HIS 0.009 0.002 HIS A 184 PHE 0.014 0.002 PHE C 970 TYR 0.012 0.001 TYR A 761 ARG 0.004 0.000 ARG A 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 94 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 MET cc_start: 0.6850 (tpt) cc_final: 0.6570 (mtp) REVERT: A 707 MET cc_start: 0.8625 (tmm) cc_final: 0.8305 (tmm) REVERT: C 1005 MET cc_start: 0.7711 (ppp) cc_final: 0.7231 (tmm) REVERT: C 1008 VAL cc_start: 0.6748 (OUTLIER) cc_final: 0.6320 (t) REVERT: E 335 GLN cc_start: 0.9128 (tp40) cc_final: 0.8896 (mm-40) outliers start: 13 outliers final: 10 residues processed: 90 average time/residue: 0.2655 time to fit residues: 33.1236 Evaluate side-chains 87 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 LEU 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 857 PHE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1008 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 78 optimal weight: 0.3980 chunk 71 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 123 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 39 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.096690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.081296 restraints weight = 49915.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.083146 restraints weight = 31946.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.084373 restraints weight = 23526.625| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9864 Z= 0.164 Angle : 0.562 7.461 13404 Z= 0.292 Chirality : 0.041 0.161 1542 Planarity : 0.004 0.043 1742 Dihedral : 4.854 29.233 1359 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.68 % Allowed : 13.52 % Favored : 84.80 % 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: 0.90 (0.24), residues: 1267 helix: 2.07 (0.20), residues: 637 sheet: -1.13 (0.33), residues: 224 loop : -0.69 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 273 HIS 0.007 0.001 HIS C 840 PHE 0.036 0.002 PHE A 347 TYR 0.013 0.001 TYR E 336 ARG 0.007 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 97 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 707 MET cc_start: 0.8626 (tmm) cc_final: 0.8391 (tmm) REVERT: C 884 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7002 (mt) REVERT: C 1005 MET cc_start: 0.7612 (ppp) cc_final: 0.7078 (tmm) REVERT: C 1008 VAL cc_start: 0.6735 (t) cc_final: 0.6278 (t) outliers start: 16 outliers final: 10 residues processed: 92 average time/residue: 0.2311 time to fit residues: 30.2757 Evaluate side-chains 86 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 632 ILE 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 857 PHE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 978 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 112 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 100 optimal weight: 0.4980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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** E 335 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.095613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.080176 restraints weight = 48802.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.081945 restraints weight = 31718.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.083163 restraints weight = 23629.160| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9864 Z= 0.202 Angle : 0.592 7.414 13404 Z= 0.308 Chirality : 0.042 0.177 1542 Planarity : 0.004 0.044 1742 Dihedral : 4.932 29.072 1359 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.47 % Allowed : 14.15 % Favored : 84.38 % 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: 0.88 (0.24), residues: 1267 helix: 2.07 (0.20), residues: 637 sheet: -1.20 (0.33), residues: 224 loop : -0.69 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 273 HIS 0.010 0.002 HIS A 184 PHE 0.028 0.002 PHE A 347 TYR 0.010 0.001 TYR A 761 ARG 0.007 0.000 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 89 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 707 MET cc_start: 0.8618 (tmm) cc_final: 0.8369 (tmm) REVERT: C 884 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.6985 (mt) REVERT: C 1005 MET cc_start: 0.7728 (ppp) cc_final: 0.7267 (tmm) REVERT: C 1008 VAL cc_start: 0.6873 (t) cc_final: 0.6456 (t) outliers start: 14 outliers final: 11 residues processed: 87 average time/residue: 0.2439 time to fit residues: 29.8849 Evaluate side-chains 84 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 632 ILE 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 857 PHE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 978 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 120 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 80 optimal weight: 0.2980 chunk 121 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.096614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.081455 restraints weight = 48861.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.083266 restraints weight = 31636.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.084515 restraints weight = 23489.284| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.5651 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 : 0.567 7.538 13404 Z= 0.293 Chirality : 0.041 0.164 1542 Planarity : 0.004 0.041 1742 Dihedral : 4.688 27.154 1359 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.05 % Allowed : 14.47 % Favored : 84.49 % 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: 1.01 (0.24), residues: 1267 helix: 2.20 (0.20), residues: 636 sheet: -1.05 (0.34), residues: 210 loop : -0.76 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 273 HIS 0.011 0.001 HIS A 184 PHE 0.028 0.001 PHE A 347 TYR 0.012 0.001 TYR E 336 ARG 0.006 0.000 ARG A 462 ********************** 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 90 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 PHE cc_start: 0.8839 (t80) cc_final: 0.8531 (t80) REVERT: A 707 MET cc_start: 0.8530 (tmm) cc_final: 0.8230 (tmm) REVERT: C 1005 MET cc_start: 0.7643 (ppp) cc_final: 0.7224 (tmm) REVERT: E 334 GLU cc_start: 0.8937 (pt0) cc_final: 0.8637 (pp20) outliers start: 10 outliers final: 8 residues processed: 88 average time/residue: 0.2295 time to fit residues: 29.2284 Evaluate side-chains 79 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 LEU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 88 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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** ** C 955 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 = 0.4193 r_free = 0.4193 target = 0.095850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.080531 restraints weight = 48791.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.082327 restraints weight = 31570.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.083529 restraints weight = 23419.675| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.5738 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= 0.179 Angle : 0.577 7.963 13404 Z= 0.296 Chirality : 0.041 0.169 1542 Planarity : 0.004 0.044 1742 Dihedral : 4.714 27.369 1359 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.05 % Allowed : 15.51 % Favored : 83.44 % 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: 1.00 (0.24), residues: 1267 helix: 2.20 (0.20), residues: 636 sheet: -1.02 (0.35), residues: 208 loop : -0.80 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 273 HIS 0.010 0.002 HIS A 184 PHE 0.016 0.002 PHE A 347 TYR 0.013 0.001 TYR A 346 ARG 0.004 0.000 ARG A 462 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2816.17 seconds wall clock time: 51 minutes 26.98 seconds (3086.98 seconds total)