Starting phenix.real_space_refine on Wed Sep 17 16:24:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rgh_19133/09_2025/8rgh_19133.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rgh_19133/09_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_19133/09_2025/8rgh_19133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rgh_19133/09_2025/8rgh_19133.map" model { file = "/net/cci-nas-00/data/ceres_data/8rgh_19133/09_2025/8rgh_19133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rgh_19133/09_2025/8rgh_19133.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 2, 'ARG:plan': 4, 'PHE:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1} 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: {'GLU:plan': 5, 'ARG:plan': 5, 'GLN:plan1': 6, 'ASN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3} 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: {'GLU:plan': 5, 'ARG:plan': 5, 'GLN:plan1': 6, 'ASN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 139 Time building chain proxies: 2.45, per 1000 atoms: 0.25 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: 0.94 Conformation dependent library (CDL) restraints added in 402.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.33 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: 1.78 Time building geometry restraints manager: 1.23 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: 1.840 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.910 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.560 ------------------------------------------------------------------------------- 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= 0.741 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.021 0.002 ARG C 731 TYR 0.149 0.024 TYR A 197 PHE 0.082 0.018 PHE A 344 TRP 0.130 0.033 TRP C 982 HIS 0.020 0.004 HIS C 648 Details of bonding type rmsd covalent geometry : bond 0.01185 ( 9864) covalent geometry : angle 1.87663 (13404) hydrogen bonds : bond 0.16445 ( 628) hydrogen bonds : angle 7.26594 ( 1845) *********************** 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 : 0.407 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: 0.1438 time to fit residues: 26.6574 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 : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 312 HIS A 641 GLN A 714 GLN C 648 HIS C 690 GLN C 733 HIS C 973 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.098224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.082086 restraints weight = 47569.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.084053 restraints weight = 29758.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.085388 restraints weight = 21751.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.086268 restraints weight = 17592.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.086842 restraints weight = 15192.250| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9864 Z= 0.158 Angle : 0.674 8.448 13404 Z= 0.365 Chirality : 0.043 0.162 1542 Planarity : 0.004 0.046 1742 Dihedral : 6.285 32.569 1359 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.84 % Favored : 97.00 % Rotamer: Outliers : 0.63 % Allowed : 6.29 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.23), residues: 1267 helix: 1.72 (0.19), residues: 619 sheet: -0.51 (0.34), residues: 214 loop : -0.94 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 338 TYR 0.014 0.002 TYR A 761 PHE 0.020 0.002 PHE C 943 TRP 0.028 0.002 TRP A 273 HIS 0.011 0.002 HIS A 759 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9864) covalent geometry : angle 0.67382 (13404) hydrogen bonds : bond 0.05330 ( 628) hydrogen bonds : angle 5.17498 ( 1845) *********************** 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 107 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 THR cc_start: 0.9107 (p) cc_final: 0.8420 (p) REVERT: A 209 PHE cc_start: 0.7909 (m-80) cc_final: 0.7656 (m-80) REVERT: A 222 ASP cc_start: 0.8505 (t70) cc_final: 0.8192 (t70) REVERT: A 330 ARG cc_start: 0.7859 (tpt170) cc_final: 0.7408 (tpt170) REVERT: A 707 MET cc_start: 0.7953 (ttt) cc_final: 0.7639 (ttt) REVERT: C 792 MET cc_start: 0.2427 (pmm) cc_final: 0.1527 (ptt) REVERT: C 848 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7420 (t0) REVERT: C 1008 VAL cc_start: 0.7127 (t) cc_final: 0.6840 (t) REVERT: E 335 GLN cc_start: 0.9080 (tp40) cc_final: 0.8353 (tp40) outliers start: 6 outliers final: 1 residues processed: 104 average time/residue: 0.1162 time to fit residues: 16.8640 Evaluate side-chains 79 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain C residue 848 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 34 optimal weight: 9.9990 chunk 110 optimal weight: 30.0000 chunk 40 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 114 optimal weight: 0.0470 chunk 77 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.7884 ------------------------------------------------------------------------------- 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 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 GLN C 619 GLN C 631 GLN ** C 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 862 GLN C 973 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.094541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.078677 restraints weight = 48480.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.080526 restraints weight = 30850.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.081767 restraints weight = 22703.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.082631 restraints weight = 18477.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.083184 restraints weight = 15998.447| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9864 Z= 0.199 Angle : 0.674 9.166 13404 Z= 0.361 Chirality : 0.044 0.165 1542 Planarity : 0.004 0.051 1742 Dihedral : 6.012 32.359 1359 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.47 % Allowed : 8.70 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.23), residues: 1267 helix: 1.71 (0.20), residues: 619 sheet: -0.87 (0.32), residues: 237 loop : -0.81 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 338 TYR 0.022 0.002 TYR A 388 PHE 0.018 0.002 PHE A 347 TRP 0.038 0.002 TRP A 273 HIS 0.010 0.002 HIS A 622 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 9864) covalent geometry : angle 0.67385 (13404) hydrogen bonds : bond 0.05082 ( 628) hydrogen bonds : angle 5.11441 ( 1845) *********************** 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 98 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 PHE cc_start: 0.8096 (m-80) cc_final: 0.7890 (m-80) REVERT: A 222 ASP cc_start: 0.8540 (t70) cc_final: 0.8291 (t70) REVERT: A 293 GLN cc_start: 0.9220 (pt0) cc_final: 0.8893 (pm20) REVERT: A 493 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7029 (pp20) REVERT: A 707 MET cc_start: 0.8062 (ttt) cc_final: 0.7834 (ttt) REVERT: C 599 MET cc_start: 0.7749 (tpp) cc_final: 0.7508 (mtp) REVERT: C 1008 VAL cc_start: 0.7267 (t) cc_final: 0.6980 (t) outliers start: 14 outliers final: 8 residues processed: 92 average time/residue: 0.1244 time to fit residues: 15.7693 Evaluate side-chains 79 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 848 ASP Chi-restraints excluded: chain C residue 884 LEU 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 1005 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 125 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 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 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 = 0.4181 r_free = 0.4181 target = 0.095297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.079631 restraints weight = 48218.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.081421 restraints weight = 31049.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.082650 restraints weight = 23014.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.083504 restraints weight = 18713.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.084030 restraints weight = 16220.380| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.4238 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= 0.160 Angle : 0.602 7.009 13404 Z= 0.321 Chirality : 0.042 0.142 1542 Planarity : 0.004 0.052 1742 Dihedral : 5.481 31.072 1359 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.78 % Allowed : 10.27 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.24), residues: 1267 helix: 1.86 (0.20), residues: 627 sheet: -0.70 (0.33), residues: 222 loop : -0.82 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 835 TYR 0.019 0.002 TYR A 761 PHE 0.017 0.002 PHE C 970 TRP 0.036 0.002 TRP A 273 HIS 0.008 0.002 HIS A 759 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9864) covalent geometry : angle 0.60166 (13404) hydrogen bonds : bond 0.04471 ( 628) hydrogen bonds : angle 4.85722 ( 1845) *********************** 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 97 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 PHE cc_start: 0.7987 (m-80) cc_final: 0.7676 (m-80) REVERT: A 493 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6960 (pp20) REVERT: A 644 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8799 (mm) REVERT: C 1008 VAL cc_start: 0.6954 (t) cc_final: 0.6660 (t) REVERT: E 317 TYR cc_start: 0.8144 (m-10) cc_final: 0.7890 (m-10) REVERT: E 334 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8942 (mm-30) outliers start: 17 outliers final: 10 residues processed: 91 average time/residue: 0.1308 time to fit residues: 16.2846 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 : 0.400 ------------------------------------------------------------------------------- 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 644 LEU Chi-restraints excluded: chain C residue 596 CYS 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 978 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 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 = 0.4207 r_free = 0.4207 target = 0.096541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.080977 restraints weight = 49269.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.082838 restraints weight = 31545.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.084072 restraints weight = 23289.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.084932 restraints weight = 18952.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.085399 restraints weight = 16459.107| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.4675 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= 0.130 Angle : 0.558 7.411 13404 Z= 0.295 Chirality : 0.041 0.138 1542 Planarity : 0.004 0.046 1742 Dihedral : 5.104 30.787 1359 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.99 % Allowed : 10.06 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.24), residues: 1267 helix: 1.97 (0.20), residues: 637 sheet: -0.87 (0.33), residues: 221 loop : -0.64 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 717 TYR 0.017 0.001 TYR A 761 PHE 0.026 0.002 PHE A 347 TRP 0.040 0.002 TRP A 273 HIS 0.009 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9864) covalent geometry : angle 0.55810 (13404) hydrogen bonds : bond 0.04166 ( 628) hydrogen bonds : angle 4.63604 ( 1845) *********************** 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 103 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 PHE cc_start: 0.7987 (m-80) cc_final: 0.7690 (m-80) REVERT: A 222 ASP cc_start: 0.8299 (t0) cc_final: 0.8074 (t70) REVERT: A 711 LEU cc_start: 0.8062 (tp) cc_final: 0.7792 (mp) REVERT: C 924 ILE cc_start: 0.7490 (pt) cc_final: 0.7274 (pt) REVERT: C 1008 VAL cc_start: 0.6735 (t) cc_final: 0.6381 (t) REVERT: E 317 TYR cc_start: 0.8121 (m-10) cc_final: 0.7884 (m-10) REVERT: E 325 MET cc_start: 0.8839 (ttm) cc_final: 0.8596 (ttp) REVERT: E 334 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8711 (pt0) outliers start: 19 outliers final: 11 residues processed: 96 average time/residue: 0.1143 time to fit residues: 15.5547 Evaluate side-chains 88 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 582 LEU 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 978 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 109 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 92 optimal weight: 0.2980 chunk 60 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS A 316 ASN ** 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 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 = 0.4178 r_free = 0.4178 target = 0.095035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.079087 restraints weight = 48245.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.080965 restraints weight = 30783.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.082238 restraints weight = 22677.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.083038 restraints weight = 18453.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.083589 restraints weight = 16109.224| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.4919 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= 0.157 Angle : 0.589 7.040 13404 Z= 0.311 Chirality : 0.042 0.190 1542 Planarity : 0.004 0.047 1742 Dihedral : 5.154 30.385 1359 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.99 % Allowed : 11.74 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.24), residues: 1267 helix: 1.94 (0.20), residues: 637 sheet: -1.02 (0.33), residues: 223 loop : -0.72 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 717 TYR 0.016 0.001 TYR A 761 PHE 0.014 0.002 PHE C 970 TRP 0.039 0.002 TRP A 273 HIS 0.011 0.002 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9864) covalent geometry : angle 0.58919 (13404) hydrogen bonds : bond 0.04241 ( 628) hydrogen bonds : angle 4.72978 ( 1845) *********************** 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 97 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 PHE cc_start: 0.8090 (m-80) cc_final: 0.7757 (m-80) REVERT: A 222 ASP cc_start: 0.8585 (t0) cc_final: 0.8284 (t70) REVERT: A 711 LEU cc_start: 0.8123 (tp) cc_final: 0.7731 (mp) REVERT: C 599 MET cc_start: 0.7598 (tpp) cc_final: 0.7358 (mtp) REVERT: C 1008 VAL cc_start: 0.6850 (OUTLIER) cc_final: 0.6432 (t) REVERT: E 317 TYR cc_start: 0.8281 (m-10) cc_final: 0.8071 (m-10) REVERT: E 334 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8913 (pt0) outliers start: 19 outliers final: 11 residues processed: 88 average time/residue: 0.1187 time to fit residues: 14.6823 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 : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Chi-restraints excluded: chain C residue 1053 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 chunk 47 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 overall best weight: 2.2588 ------------------------------------------------------------------------------- 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 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 = 0.4165 r_free = 0.4165 target = 0.094366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.078786 restraints weight = 49234.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.080554 restraints weight = 31796.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.081758 restraints weight = 23762.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.082555 restraints weight = 19536.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.083085 restraints weight = 17043.067| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.5199 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= 0.168 Angle : 0.602 7.256 13404 Z= 0.316 Chirality : 0.042 0.167 1542 Planarity : 0.004 0.043 1742 Dihedral : 5.189 30.062 1359 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.99 % Allowed : 12.58 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.24), residues: 1267 helix: 1.94 (0.20), residues: 631 sheet: -1.26 (0.33), residues: 224 loop : -0.66 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 338 TYR 0.015 0.002 TYR A 761 PHE 0.026 0.002 PHE A 209 TRP 0.041 0.002 TRP A 273 HIS 0.010 0.002 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9864) covalent geometry : angle 0.60233 (13404) hydrogen bonds : bond 0.04253 ( 628) hydrogen bonds : angle 4.80062 ( 1845) *********************** 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 97 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1005 MET cc_start: 0.7657 (ppp) cc_final: 0.7136 (tmm) REVERT: C 1008 VAL cc_start: 0.6745 (OUTLIER) cc_final: 0.6269 (t) REVERT: E 334 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8913 (pt0) outliers start: 19 outliers final: 13 residues processed: 88 average time/residue: 0.1172 time to fit residues: 14.4917 Evaluate side-chains 86 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 949 ASP Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 965 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 37 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 57 optimal weight: 0.0970 chunk 105 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4202 r_free = 0.4202 target = 0.096388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.080921 restraints weight = 49120.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.082776 restraints weight = 31595.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.084049 restraints weight = 23362.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.084871 restraints weight = 18971.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.085432 restraints weight = 16512.484| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.5388 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= 0.118 Angle : 0.564 7.775 13404 Z= 0.290 Chirality : 0.041 0.148 1542 Planarity : 0.004 0.041 1742 Dihedral : 4.829 29.254 1359 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.15 % Allowed : 14.15 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.24), residues: 1267 helix: 2.13 (0.20), residues: 637 sheet: -1.13 (0.34), residues: 216 loop : -0.81 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 338 TYR 0.012 0.001 TYR A 761 PHE 0.015 0.001 PHE C 970 TRP 0.042 0.002 TRP A 294 HIS 0.009 0.001 HIS C 840 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9864) covalent geometry : angle 0.56371 (13404) hydrogen bonds : bond 0.03922 ( 628) hydrogen bonds : angle 4.58114 ( 1845) *********************** 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 90 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 PHE cc_start: 0.7960 (m-10) cc_final: 0.7634 (m-80) REVERT: A 222 ASP cc_start: 0.8406 (t0) cc_final: 0.8096 (t70) REVERT: C 599 MET cc_start: 0.7321 (mtp) cc_final: 0.7096 (ttm) REVERT: C 884 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7062 (mt) REVERT: C 1005 MET cc_start: 0.7622 (ppp) cc_final: 0.6990 (tmm) REVERT: E 334 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8962 (pt0) outliers start: 11 outliers final: 6 residues processed: 86 average time/residue: 0.1140 time to fit residues: 13.8055 Evaluate side-chains 79 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 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 1008 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 HIS C 718 HIS ** 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 = 0.4190 r_free = 0.4190 target = 0.095724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.080166 restraints weight = 48852.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.081923 restraints weight = 31768.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.083142 restraints weight = 23851.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.083895 restraints weight = 19581.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.084472 restraints weight = 17186.221| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.5533 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= 0.137 Angle : 0.583 7.897 13404 Z= 0.300 Chirality : 0.041 0.183 1542 Planarity : 0.004 0.042 1742 Dihedral : 4.831 28.753 1359 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.15 % Allowed : 14.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.24), residues: 1267 helix: 2.16 (0.20), residues: 637 sheet: -1.16 (0.34), residues: 214 loop : -0.78 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 338 TYR 0.014 0.001 TYR A 761 PHE 0.042 0.002 PHE A 347 TRP 0.027 0.002 TRP A 273 HIS 0.009 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9864) covalent geometry : angle 0.58273 (13404) hydrogen bonds : bond 0.03969 ( 628) hydrogen bonds : angle 4.58265 ( 1845) *********************** 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 85 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 PHE cc_start: 0.8813 (t80) cc_final: 0.8534 (t80) REVERT: A 222 ASP cc_start: 0.8419 (t0) cc_final: 0.8079 (t70) REVERT: C 884 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7047 (mt) REVERT: C 1005 MET cc_start: 0.7639 (ppp) cc_final: 0.7153 (tmm) REVERT: E 334 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8973 (pt0) outliers start: 11 outliers final: 8 residues processed: 83 average time/residue: 0.1190 time to fit residues: 13.9733 Evaluate side-chains 80 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR 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 1008 VAL Chi-restraints excluded: chain C residue 1017 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 98 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 106 optimal weight: 0.0870 chunk 85 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.096678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.081573 restraints weight = 48476.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.083399 restraints weight = 31291.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.084643 restraints weight = 23173.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.085456 restraints weight = 18871.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.086064 restraints weight = 16395.457| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.5728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9864 Z= 0.111 Angle : 0.562 7.957 13404 Z= 0.288 Chirality : 0.041 0.164 1542 Planarity : 0.004 0.041 1742 Dihedral : 4.603 27.057 1359 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.94 % Allowed : 14.88 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.24), residues: 1267 helix: 2.26 (0.20), residues: 637 sheet: -1.06 (0.34), residues: 216 loop : -0.83 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 717 TYR 0.012 0.001 TYR A 346 PHE 0.038 0.001 PHE A 347 TRP 0.026 0.001 TRP A 273 HIS 0.008 0.001 HIS C 840 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 9864) covalent geometry : angle 0.56159 (13404) hydrogen bonds : bond 0.03765 ( 628) hydrogen bonds : angle 4.45260 ( 1845) ********************** 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 88 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 PHE cc_start: 0.8760 (t80) cc_final: 0.8495 (t80) REVERT: A 222 ASP cc_start: 0.8358 (t0) cc_final: 0.8065 (t70) REVERT: C 924 ILE cc_start: 0.7421 (pt) cc_final: 0.7064 (pt) REVERT: C 1005 MET cc_start: 0.7502 (ppp) cc_final: 0.7039 (tmm) REVERT: E 334 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8920 (pt0) outliers start: 9 outliers final: 7 residues processed: 86 average time/residue: 0.1172 time to fit residues: 14.1876 Evaluate side-chains 81 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 848 ASP Chi-restraints excluded: chain C residue 857 PHE Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1017 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 124 optimal weight: 0.5980 chunk 85 optimal weight: 0.0870 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 111 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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** C 955 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.097533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.082411 restraints weight = 48221.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.084195 restraints weight = 31157.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.085457 restraints weight = 23210.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.086344 restraints weight = 18871.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.086938 restraints weight = 16276.106| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.5912 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= 0.107 Angle : 0.560 8.574 13404 Z= 0.284 Chirality : 0.041 0.171 1542 Planarity : 0.004 0.049 1742 Dihedral : 4.486 27.036 1359 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.94 % Allowed : 14.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.24), residues: 1267 helix: 2.40 (0.20), residues: 637 sheet: -0.89 (0.35), residues: 207 loop : -0.81 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 717 TYR 0.011 0.001 TYR A 761 PHE 0.035 0.001 PHE A 347 TRP 0.028 0.001 TRP A 294 HIS 0.008 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 9864) covalent geometry : angle 0.56042 (13404) hydrogen bonds : bond 0.03642 ( 628) hydrogen bonds : angle 4.36273 ( 1845) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1752.37 seconds wall clock time: 31 minutes 12.03 seconds (1872.03 seconds total)