Starting phenix.real_space_refine on Wed Apr 30 16:41:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rgh_19133/04_2025/8rgh_19133.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rgh_19133/04_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_19133/04_2025/8rgh_19133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rgh_19133/04_2025/8rgh_19133.map" model { file = "/net/cci-nas-00/data/ceres_data/8rgh_19133/04_2025/8rgh_19133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rgh_19133/04_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-5669/modules/chem_data/mon_lib" Total number of atoms: 9682 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4757 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 18, 'TRANS': 558} Chain breaks: 3 Chain: "C" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3615 Classifications: {'peptide': 467} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 439} Chain breaks: 1 Chain: "D" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 150 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 1, 'TRANS': 28} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 70 Chain: "E" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 236 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "G" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 462 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 5, 'TRANS': 87} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 139 Chain: "H" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 462 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 5, 'TRANS': 87} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 139 Time building chain proxies: 5.69, per 1000 atoms: 0.59 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: 2.28 Conformation dependent library (CDL) restraints added in 1.1 seconds 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2466 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 52.9% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 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: 3.07 Time building geometry restraints manager: 2.73 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: 0.010 Normalize map: mean=0, sd=1: 1.440 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.920 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.880 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.16445 ( 628) hydrogen bonds : angle 7.26594 ( 1845) covalent geometry : bond 0.01185 ( 9864) covalent geometry : angle 1.87663 (13404) *********************** 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 : 1.196 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: 0.2969 time to fit residues: 55.1873 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 : 1.212 ------------------------------------------------------------------------------- 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 = 0.4207 r_free = 0.4207 target = 0.096390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.080403 restraints weight = 47686.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.082253 restraints weight = 30130.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.083501 restraints weight = 22174.283| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 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= 0.192 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 Details of bonding type rmsd hydrogen bonds : bond 0.05526 ( 628) hydrogen bonds : angle 5.31817 ( 1845) covalent geometry : bond 0.00400 ( 9864) covalent geometry : angle 0.71085 (13404) *********************** 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 : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 THR cc_start: 0.9130 (p) cc_final: 0.8488 (p) REVERT: A 222 ASP cc_start: 0.8568 (t70) cc_final: 0.8312 (t70) REVERT: A 707 MET cc_start: 0.7980 (ttt) cc_final: 0.7646 (ttt) REVERT: C 792 MET cc_start: 0.2364 (pmm) cc_final: 0.1484 (ptt) REVERT: C 965 THR cc_start: 0.8443 (p) cc_final: 0.8243 (t) REVERT: C 1008 VAL cc_start: 0.7363 (t) cc_final: 0.7064 (t) outliers start: 11 outliers final: 2 residues processed: 103 average time/residue: 0.2491 time to fit residues: 35.8785 Evaluate side-chains 83 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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: 0.9980 chunk 7 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 117 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 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 242 HIS 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.097614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.082017 restraints weight = 49277.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.083903 restraints weight = 30781.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.085175 restraints weight = 22488.659| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9864 Z= 0.140 Angle : 0.605 7.796 13404 Z= 0.323 Chirality : 0.042 0.167 1542 Planarity : 0.004 0.053 1742 Dihedral : 5.624 31.338 1359 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.47 % Allowed : 8.39 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.23), residues: 1267 helix: 1.94 (0.19), residues: 621 sheet: -0.70 (0.32), residues: 231 loop : -0.80 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 273 HIS 0.009 0.002 HIS A 759 PHE 0.020 0.002 PHE A 347 TYR 0.023 0.002 TYR A 388 ARG 0.004 0.000 ARG C 731 Details of bonding type rmsd hydrogen bonds : bond 0.04662 ( 628) hydrogen bonds : angle 4.81880 ( 1845) covalent geometry : bond 0.00287 ( 9864) covalent geometry : angle 0.60477 (13404) *********************** 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 108 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 PHE cc_start: 0.8020 (m-80) cc_final: 0.7569 (m-80) REVERT: A 222 ASP cc_start: 0.8344 (t70) cc_final: 0.8048 (t70) REVERT: A 493 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6875 (pp20) REVERT: A 707 MET cc_start: 0.7961 (ttt) cc_final: 0.7735 (ttt) REVERT: C 1008 VAL cc_start: 0.6966 (t) cc_final: 0.6656 (t) REVERT: E 334 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8987 (mm-30) outliers start: 14 outliers final: 8 residues processed: 102 average time/residue: 0.2564 time to fit residues: 36.3805 Evaluate side-chains 87 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 79 optimal weight: 3.9990 chunk 114 optimal weight: 0.1980 chunk 44 optimal weight: 0.9990 chunk 63 optimal weight: 0.0040 chunk 88 optimal weight: 0.0870 chunk 28 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.4572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 648 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.099539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.084156 restraints weight = 48729.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.086102 restraints weight = 30263.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.087449 restraints weight = 21936.403| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9864 Z= 0.113 Angle : 0.555 6.965 13404 Z= 0.296 Chirality : 0.041 0.171 1542 Planarity : 0.004 0.050 1742 Dihedral : 5.045 30.015 1359 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.57 % Allowed : 9.96 % Favored : 88.47 % 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: 1.08 (0.24), residues: 1267 helix: 2.14 (0.19), residues: 637 sheet: -0.66 (0.32), residues: 231 loop : -0.74 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 273 HIS 0.008 0.001 HIS A 184 PHE 0.017 0.001 PHE C 970 TYR 0.014 0.001 TYR A 761 ARG 0.006 0.000 ARG E 338 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 628) hydrogen bonds : angle 4.51036 ( 1845) covalent geometry : bond 0.00226 ( 9864) covalent geometry : angle 0.55510 (13404) *********************** 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 108 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 PHE cc_start: 0.8132 (m-80) cc_final: 0.7769 (m-80) REVERT: A 638 MET cc_start: 0.8248 (mtt) cc_final: 0.7922 (mtt) REVERT: A 707 MET cc_start: 0.7932 (ttt) cc_final: 0.7686 (ttt) REVERT: C 882 MET cc_start: 0.7514 (tpt) cc_final: 0.6657 (tpp) REVERT: C 1005 MET cc_start: 0.7401 (tmm) cc_final: 0.7122 (tmm) REVERT: C 1008 VAL cc_start: 0.6738 (t) cc_final: 0.6430 (t) REVERT: E 334 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8739 (pt0) REVERT: E 338 ARG cc_start: 0.8712 (ttp-110) cc_final: 0.8241 (ptp-110) outliers start: 15 outliers final: 6 residues processed: 102 average time/residue: 0.2454 time to fit residues: 34.7756 Evaluate side-chains 88 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain C residue 797 PHE Chi-restraints excluded: chain C residue 848 ASP 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 93 optimal weight: 0.2980 chunk 73 optimal weight: 9.9990 chunk 124 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 115 optimal weight: 20.0000 chunk 110 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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** A 747 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.099436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.084528 restraints weight = 48379.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.086329 restraints weight = 31383.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.087549 restraints weight = 23284.703| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9864 Z= 0.111 Angle : 0.535 6.787 13404 Z= 0.283 Chirality : 0.041 0.173 1542 Planarity : 0.004 0.046 1742 Dihedral : 4.787 29.167 1359 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.15 % Allowed : 11.22 % Favored : 87.63 % 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: 1.22 (0.24), residues: 1267 helix: 2.27 (0.19), residues: 637 sheet: -0.61 (0.32), residues: 229 loop : -0.67 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 273 HIS 0.010 0.001 HIS A 184 PHE 0.025 0.002 PHE A 347 TYR 0.016 0.001 TYR A 761 ARG 0.002 0.000 ARG C 835 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 628) hydrogen bonds : angle 4.40229 ( 1845) covalent geometry : bond 0.00224 ( 9864) covalent geometry : angle 0.53484 (13404) *********************** 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: 11 poor density : 87 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLN cc_start: 0.9078 (pt0) cc_final: 0.8711 (pt0) REVERT: A 638 MET cc_start: 0.8230 (mtt) cc_final: 0.7998 (mtt) REVERT: C 599 MET cc_start: 0.7698 (tpp) cc_final: 0.7458 (mtp) REVERT: C 1005 MET cc_start: 0.7393 (tmm) cc_final: 0.7117 (tmm) REVERT: C 1008 VAL cc_start: 0.6629 (t) cc_final: 0.6276 (t) REVERT: E 338 ARG cc_start: 0.8659 (ttp-110) cc_final: 0.8366 (ptp-110) outliers start: 11 outliers final: 4 residues processed: 95 average time/residue: 0.2539 time to fit residues: 33.6462 Evaluate side-chains 79 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 596 CYS Chi-restraints excluded: chain C residue 797 PHE Chi-restraints excluded: chain C residue 848 ASP 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 48 optimal weight: 1.9990 chunk 106 optimal weight: 0.0470 chunk 1 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 116 optimal weight: 40.0000 chunk 112 optimal weight: 5.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- 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 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.093938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.078554 restraints weight = 48782.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.080347 restraints weight = 31469.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.081330 restraints weight = 22670.934| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9864 Z= 0.212 Angle : 0.665 7.128 13404 Z= 0.353 Chirality : 0.044 0.185 1542 Planarity : 0.004 0.052 1742 Dihedral : 5.373 30.872 1359 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.78 % Allowed : 11.64 % Favored : 86.58 % 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: 0.91 (0.24), residues: 1267 helix: 2.00 (0.20), residues: 631 sheet: -0.96 (0.32), residues: 231 loop : -0.60 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 273 HIS 0.012 0.002 HIS A 184 PHE 0.018 0.002 PHE C 876 TYR 0.022 0.002 TYR A 761 ARG 0.004 0.001 ARG A 338 Details of bonding type rmsd hydrogen bonds : bond 0.04628 ( 628) hydrogen bonds : angle 4.90287 ( 1845) covalent geometry : bond 0.00451 ( 9864) covalent geometry : angle 0.66538 (13404) *********************** 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 93 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 MET cc_start: 0.8465 (pmm) cc_final: 0.8079 (pmm) REVERT: A 638 MET cc_start: 0.8416 (mtt) cc_final: 0.7995 (mtt) REVERT: C 924 ILE cc_start: 0.7278 (pt) cc_final: 0.7057 (pt) REVERT: C 1008 VAL cc_start: 0.7140 (t) cc_final: 0.6712 (t) outliers start: 17 outliers final: 10 residues processed: 86 average time/residue: 0.2519 time to fit residues: 30.2783 Evaluate side-chains 82 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 840 HIS 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 109 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 61 optimal weight: 0.0030 chunk 52 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 overall best weight: 3.3998 ------------------------------------------------------------------------------- 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** C 633 ASN ** 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 = 0.4131 r_free = 0.4131 target = 0.092741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.077294 restraints weight = 50671.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.078995 restraints weight = 35582.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.080211 restraints weight = 25104.792| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9864 Z= 0.226 Angle : 0.683 8.509 13404 Z= 0.361 Chirality : 0.044 0.177 1542 Planarity : 0.004 0.042 1742 Dihedral : 5.559 32.195 1359 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % 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: 0.34 (0.24), residues: 1267 helix: 1.64 (0.20), residues: 631 sheet: -1.52 (0.31), residues: 229 loop : -0.86 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 273 HIS 0.010 0.002 HIS A 184 PHE 0.020 0.002 PHE C 876 TYR 0.017 0.002 TYR A 761 ARG 0.006 0.001 ARG E 338 Details of bonding type rmsd hydrogen bonds : bond 0.04706 ( 628) hydrogen bonds : angle 5.08212 ( 1845) covalent geometry : bond 0.00480 ( 9864) covalent geometry : angle 0.68334 (13404) *********************** 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 87 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 MET cc_start: 0.6711 (tpt) cc_final: 0.6475 (mtp) REVERT: A 649 ILE cc_start: 0.7446 (mt) cc_final: 0.7217 (mt) REVERT: C 924 ILE cc_start: 0.7428 (pt) cc_final: 0.7185 (pt) REVERT: C 1005 MET cc_start: 0.7827 (ppp) cc_final: 0.7268 (tmm) REVERT: C 1008 VAL cc_start: 0.7120 (OUTLIER) cc_final: 0.6695 (t) REVERT: E 325 MET cc_start: 0.8629 (ttp) cc_final: 0.8273 (ttp) outliers start: 13 outliers final: 7 residues processed: 81 average time/residue: 0.2449 time to fit residues: 28.1794 Evaluate side-chains 77 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 LEU 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 960 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 37 optimal weight: 0.0000 chunk 78 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 123 optimal weight: 30.0000 chunk 49 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 ASN ** C 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 = 0.4209 r_free = 0.4209 target = 0.095841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.080369 restraints weight = 50098.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.082149 restraints weight = 31983.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.083355 restraints weight = 23731.294| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9864 Z= 0.128 Angle : 0.582 7.880 13404 Z= 0.304 Chirality : 0.042 0.180 1542 Planarity : 0.004 0.039 1742 Dihedral : 4.992 28.634 1359 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.26 % Allowed : 13.21 % Favored : 85.53 % 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: 0.69 (0.24), residues: 1267 helix: 1.93 (0.20), residues: 637 sheet: -1.18 (0.34), residues: 214 loop : -0.90 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 273 HIS 0.009 0.001 HIS C 840 PHE 0.018 0.002 PHE C 876 TYR 0.016 0.001 TYR A 761 ARG 0.007 0.000 ARG E 338 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 628) hydrogen bonds : angle 4.71800 ( 1845) covalent geometry : bond 0.00271 ( 9864) covalent geometry : angle 0.58225 (13404) *********************** 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 96 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 884 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.6923 (mt) REVERT: C 1005 MET cc_start: 0.7489 (ppp) cc_final: 0.7224 (ppp) REVERT: C 1008 VAL cc_start: 0.6799 (t) cc_final: 0.6497 (t) outliers start: 12 outliers final: 9 residues processed: 91 average time/residue: 0.2439 time to fit residues: 31.1934 Evaluate side-chains 85 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 857 PHE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 981 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 112 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.093468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.077934 restraints weight = 49922.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.079664 restraints weight = 32557.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.080850 restraints weight = 24312.768| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.5626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9864 Z= 0.194 Angle : 0.650 8.201 13404 Z= 0.341 Chirality : 0.044 0.196 1542 Planarity : 0.004 0.047 1742 Dihedral : 5.277 30.295 1359 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.94 % Allowed : 14.26 % Favored : 84.80 % 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: 0.51 (0.24), residues: 1267 helix: 1.82 (0.20), residues: 637 sheet: -1.45 (0.33), residues: 217 loop : -0.93 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 273 HIS 0.011 0.002 HIS A 622 PHE 0.041 0.002 PHE A 347 TYR 0.018 0.002 TYR A 761 ARG 0.006 0.001 ARG A 462 Details of bonding type rmsd hydrogen bonds : bond 0.04464 ( 628) hydrogen bonds : angle 4.95160 ( 1845) covalent geometry : bond 0.00418 ( 9864) covalent geometry : angle 0.64952 (13404) *********************** 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 81 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TYR cc_start: 0.7376 (m-10) cc_final: 0.6445 (m-80) REVERT: C 924 ILE cc_start: 0.7168 (pt) cc_final: 0.6952 (pt) REVERT: C 1008 VAL cc_start: 0.7034 (t) cc_final: 0.6577 (t) outliers start: 9 outliers final: 8 residues processed: 77 average time/residue: 0.2374 time to fit residues: 26.3280 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 : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 LEU 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 960 LEU Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 981 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.094234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.078833 restraints weight = 49986.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.080566 restraints weight = 32294.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.081754 restraints weight = 24070.865| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9864 Z= 0.161 Angle : 0.611 8.074 13404 Z= 0.320 Chirality : 0.043 0.193 1542 Planarity : 0.004 0.041 1742 Dihedral : 5.130 29.053 1359 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.26 % Allowed : 13.94 % 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: 0.49 (0.24), residues: 1267 helix: 1.82 (0.20), residues: 640 sheet: -1.47 (0.33), residues: 216 loop : -1.01 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 273 HIS 0.011 0.002 HIS A 184 PHE 0.037 0.002 PHE A 347 TYR 0.016 0.001 TYR A 761 ARG 0.005 0.000 ARG E 338 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 628) hydrogen bonds : angle 4.84945 ( 1845) covalent geometry : bond 0.00348 ( 9864) covalent geometry : angle 0.61089 (13404) ********************** 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 83 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TYR cc_start: 0.7342 (m-10) cc_final: 0.6421 (m-80) REVERT: C 1005 MET cc_start: 0.7661 (ppp) cc_final: 0.7454 (ppp) outliers start: 12 outliers final: 10 residues processed: 79 average time/residue: 0.2554 time to fit residues: 28.5637 Evaluate side-chains 81 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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 857 PHE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain C residue 1008 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 88 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 HIS ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.096979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.081776 restraints weight = 49779.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.083570 restraints weight = 31964.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.084820 restraints weight = 23715.069| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.5941 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= 0.114 Angle : 0.567 7.673 13404 Z= 0.293 Chirality : 0.042 0.166 1542 Planarity : 0.004 0.041 1742 Dihedral : 4.725 27.235 1359 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.73 % Allowed : 14.26 % Favored : 85.01 % 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: 0.84 (0.24), residues: 1267 helix: 2.16 (0.20), residues: 636 sheet: -1.25 (0.34), residues: 208 loop : -0.96 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 273 HIS 0.010 0.001 HIS A 184 PHE 0.036 0.002 PHE A 347 TYR 0.013 0.001 TYR A 761 ARG 0.005 0.000 ARG E 338 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 628) hydrogen bonds : angle 4.57619 ( 1845) covalent geometry : bond 0.00243 ( 9864) covalent geometry : angle 0.56676 (13404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3080.62 seconds wall clock time: 54 minutes 7.65 seconds (3247.65 seconds total)