Starting phenix.real_space_refine on Wed Aug 5 13:27:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ibw_35347/08_2026/8ibw_35347.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ibw_35347/08_2026/8ibw_35347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ibw_35347/08_2026/8ibw_35347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ibw_35347/08_2026/8ibw_35347.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ibw_35347/08_2026/8ibw_35347.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ibw_35347/08_2026/8ibw_35347.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ibw_35347/08_2026/8ibw_35347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ibw_35347/08_2026/8ibw_35347.map" } resolution = 3.6 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= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 24 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 125 5.49 5 S 38 5.16 5 C 5750 2.51 5 N 1874 2.21 5 O 2059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9848 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 891 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "B" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 872 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "C" Number of atoms: 7250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 922, 7250 Classifications: {'peptide': 922} Link IDs: {'PTRANS': 44, 'TRANS': 877} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 5, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 833 Classifications: {'RNAv2': 39} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 15} Link IDs: {'rna2p': 6, 'rna3p': 32} Chain breaks: 2 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1794 SG CYS C 114 13.182 85.010 80.553 1.00 94.26 S ATOM 1820 SG CYS C 117 12.830 83.352 84.085 1.00 94.75 S ATOM 7643 SG CYS C 934 46.425 52.273 131.118 1.00104.45 S ATOM 7669 SG CYS C 938 49.604 51.093 132.882 1.00108.40 S ATOM 7774 SG CYS C 951 49.287 50.685 129.072 1.00 96.27 S Time building chain proxies: 2.38, per 1000 atoms: 0.24 Number of scatterers: 9848 At special positions: 0 Unit cell: (99.9089, 118.573, 152.608, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 38 16.00 P 125 15.00 O 2059 8.00 N 1874 7.00 C 5750 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: 0.91 Conformation dependent library (CDL) restraints added in 288.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1201 " pdb="ZN ZN C1201 " - pdb=" NE2 HIS C 130 " pdb="ZN ZN C1201 " - pdb=" NE2 HIS C 135 " pdb="ZN ZN C1201 " - pdb=" SG CYS C 114 " pdb="ZN ZN C1201 " - pdb=" SG CYS C 117 " pdb=" ZN C1202 " pdb="ZN ZN C1202 " - pdb=" NE2 HIS C 946 " pdb="ZN ZN C1202 " - pdb=" SG CYS C 938 " pdb="ZN ZN C1202 " - pdb=" SG CYS C 934 " pdb="ZN ZN C1202 " - pdb=" SG CYS C 951 " Number of angles added : 5 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 60.2% alpha, 5.4% beta 46 base pairs and 77 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'C' and resid 135 through 143 removed outlier: 3.616A pdb=" N THR C 139 " --> pdb=" O HIS C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 172 Processing helix chain 'C' and resid 175 through 183 removed outlier: 4.023A pdb=" N GLY C 181 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 187 removed outlier: 4.470A pdb=" N GLY C 187 " --> pdb=" O PRO C 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 184 through 187' Processing helix chain 'C' and resid 189 through 198 removed outlier: 3.656A pdb=" N LYS C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 214 Processing helix chain 'C' and resid 261 through 283 Processing helix chain 'C' and resid 306 through 322 Processing helix chain 'C' and resid 324 through 334 removed outlier: 3.612A pdb=" N ALA C 328 " --> pdb=" O CYS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 357 removed outlier: 6.173A pdb=" N THR C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR C 350 " --> pdb=" O GLU C 346 " (cutoff:3.500A) Proline residue: C 353 - end of helix Processing helix chain 'C' and resid 365 through 373 Processing helix chain 'C' and resid 392 through 399 Processing helix chain 'C' and resid 413 through 420 removed outlier: 3.520A pdb=" N VAL C 420 " --> pdb=" O GLN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 436 Processing helix chain 'C' and resid 439 through 444 removed outlier: 3.609A pdb=" N GLN C 444 " --> pdb=" O ILE C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 469 through 487 removed outlier: 3.595A pdb=" N ILE C 478 " --> pdb=" O HIS C 474 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 479 " --> pdb=" O PHE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 520 Processing helix chain 'C' and resid 532 through 536 removed outlier: 3.513A pdb=" N ASP C 535 " --> pdb=" O LYS C 532 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR C 536 " --> pdb=" O ALA C 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 532 through 536' Processing helix chain 'C' and resid 538 through 549 removed outlier: 4.345A pdb=" N GLU C 544 " --> pdb=" O GLU C 540 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 565 Processing helix chain 'C' and resid 592 through 608 removed outlier: 3.603A pdb=" N ASN C 598 " --> pdb=" O PRO C 594 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 599 " --> pdb=" O ILE C 595 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL C 600 " --> pdb=" O LEU C 596 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 608 " --> pdb=" O ILE C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 655 Processing helix chain 'C' and resid 719 through 730 Processing helix chain 'C' and resid 733 through 744 Processing helix chain 'C' and resid 744 through 756 removed outlier: 4.234A pdb=" N GLY C 752 " --> pdb=" O ARG C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 779 Processing helix chain 'C' and resid 785 through 791 removed outlier: 4.210A pdb=" N TYR C 789 " --> pdb=" O PRO C 785 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS C 790 " --> pdb=" O LYS C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 817 Proline residue: C 808 - end of helix removed outlier: 4.478A pdb=" N GLY C 817 " --> pdb=" O ARG C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 821 Processing helix chain 'C' and resid 823 through 831 removed outlier: 3.714A pdb=" N LYS C 831 " --> pdb=" O ARG C 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 849 Processing helix chain 'C' and resid 861 through 870 Processing helix chain 'C' and resid 872 through 877 removed outlier: 4.599A pdb=" N GLU C 877 " --> pdb=" O VAL C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 885 through 889 removed outlier: 3.908A pdb=" N THR C 888 " --> pdb=" O PRO C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 911 Processing helix chain 'C' and resid 916 through 921 Processing helix chain 'C' and resid 943 through 950 Processing helix chain 'C' and resid 953 through 974 removed outlier: 4.421A pdb=" N GLY C 957 " --> pdb=" O ARG C 953 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA C 972 " --> pdb=" O PHE C 968 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1032 removed outlier: 3.614A pdb=" N LYS C1029 " --> pdb=" O GLU C1025 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR C1030 " --> pdb=" O LYS C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1034 through 1045 Processing helix chain 'C' and resid 1048 through 1052 removed outlier: 3.651A pdb=" N VAL C1052 " --> pdb=" O ALA C1049 " (cutoff:3.500A) Processing helix chain 'C' and resid 1066 through 1076 Processing helix chain 'C' and resid 1080 through 1105 removed outlier: 3.797A pdb=" N LEU C1084 " --> pdb=" O ARG C1080 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL C1087 " --> pdb=" O THR C1083 " (cutoff:3.500A) Proline residue: C1088 - end of helix Processing sheet with id=AA1, first strand: chain 'C' and resid 112 through 113 removed outlier: 3.763A pdb=" N TRP C 112 " --> pdb=" O PHE C 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 448 through 451 Processing sheet with id=AA3, first strand: chain 'C' and resid 629 through 634 Processing sheet with id=AA4, first strand: chain 'C' and resid 567 through 568 Processing sheet with id=AA5, first strand: chain 'C' and resid 571 through 572 Processing sheet with id=AA6, first strand: chain 'C' and resid 614 through 616 Processing sheet with id=AA7, first strand: chain 'C' and resid 701 through 702 Processing sheet with id=AA8, first strand: chain 'C' and resid 851 through 852 Processing sheet with id=AA9, first strand: chain 'C' and resid 981 through 982 Processing sheet with id=AB1, first strand: chain 'C' and resid 1007 through 1013 removed outlier: 5.932A pdb=" N ILE C1007 " --> pdb=" O THR C1055 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N CYS C1057 " --> pdb=" O ILE C1007 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP C1009 " --> pdb=" O CYS C1057 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE C1059 " --> pdb=" O ASP C1009 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLN C1011 " --> pdb=" O ILE C1059 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 371 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 121 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 77 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 1.21 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: 2673 1.33 - 1.45: 2366 1.45 - 1.57: 4964 1.57 - 1.70: 245 1.70 - 1.82: 54 Bond restraints: 10302 Sorted by residual: bond pdb=" C3' DC B 44 " pdb=" C2' DC B 44 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.10e+01 bond pdb=" CA LEU C 344 " pdb=" C LEU C 344 " ideal model delta sigma weight residual 1.524 1.484 0.040 1.27e-02 6.20e+03 9.77e+00 bond pdb=" C3' DC A 37 " pdb=" C2' DC A 37 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.51e+00 bond pdb=" C3' DG A 43 " pdb=" C2' DG A 43 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.30e+00 bond pdb=" C3' DG A 17 " pdb=" C2' DG A 17 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.94e+00 ... (remaining 10297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 13905 2.04 - 4.08: 508 4.08 - 6.12: 44 6.12 - 8.16: 10 8.16 - 10.19: 3 Bond angle restraints: 14470 Sorted by residual: angle pdb=" N LEU C 344 " pdb=" CA LEU C 344 " pdb=" C LEU C 344 " ideal model delta sigma weight residual 111.07 100.88 10.19 1.07e+00 8.73e-01 9.08e+01 angle pdb=" N3 DT B 58 " pdb=" C4 DT B 58 " pdb=" O4 DT B 58 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT A 11 " pdb=" C4 DT A 11 " pdb=" O4 DT A 11 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT B 36 " pdb=" C4 DT B 36 " pdb=" O4 DT B 36 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT A 38 " pdb=" C4 DT A 38 " pdb=" O4 DT A 38 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.83e+01 ... (remaining 14465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.59: 5218 32.59 - 65.18: 647 65.18 - 97.77: 30 97.77 - 130.36: 0 130.36 - 162.95: 3 Dihedral angle restraints: 5898 sinusoidal: 3266 harmonic: 2632 Sorted by residual: dihedral pdb=" C4' U D 129 " pdb=" C3' U D 129 " pdb=" C2' U D 129 " pdb=" C1' U D 129 " ideal model delta sinusoidal sigma weight residual 36.34 -37.48 73.82 1 3.10e+00 1.04e-01 7.21e+02 dihedral pdb=" C4' C D 126 " pdb=" C3' C D 126 " pdb=" C2' C D 126 " pdb=" C1' C D 126 " ideal model delta sinusoidal sigma weight residual 36.34 -36.02 72.36 1 3.10e+00 1.04e-01 6.96e+02 dihedral pdb=" C4' U D 31 " pdb=" C3' U D 31 " pdb=" C2' U D 31 " pdb=" C1' U D 31 " ideal model delta sinusoidal sigma weight residual 36.35 -35.86 72.21 1 3.10e+00 1.04e-01 6.94e+02 ... (remaining 5895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1325 0.063 - 0.127: 202 0.127 - 0.190: 57 0.190 - 0.254: 35 0.254 - 0.317: 14 Chirality restraints: 1633 Sorted by residual: chirality pdb=" C2' A D 245 " pdb=" C3' A D 245 " pdb=" O2' A D 245 " pdb=" C1' A D 245 " both_signs ideal model delta sigma weight residual False -2.79 -2.47 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA GLU C 200 " pdb=" N GLU C 200 " pdb=" C GLU C 200 " pdb=" CB GLU C 200 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C2' A D 247 " pdb=" C3' A D 247 " pdb=" O2' A D 247 " pdb=" C1' A D 247 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 1630 not shown) Planarity restraints: 1419 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 503 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C LEU C 503 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU C 503 " -0.022 2.00e-02 2.50e+03 pdb=" N GLU C 504 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 904 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.18e+00 pdb=" C VAL C 904 " -0.052 2.00e-02 2.50e+03 pdb=" O VAL C 904 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN C 905 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D 123 " -0.025 2.00e-02 2.50e+03 1.55e-02 6.59e+00 pdb=" N9 A D 123 " 0.042 2.00e-02 2.50e+03 pdb=" C8 A D 123 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A D 123 " -0.004 2.00e-02 2.50e+03 pdb=" C5 A D 123 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A D 123 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A D 123 " -0.004 2.00e-02 2.50e+03 pdb=" N1 A D 123 " -0.000 2.00e-02 2.50e+03 pdb=" C2 A D 123 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A D 123 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A D 123 " -0.015 2.00e-02 2.50e+03 ... (remaining 1416 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 119 2.59 - 3.17: 8555 3.17 - 3.75: 17113 3.75 - 4.32: 21764 4.32 - 4.90: 33206 Nonbonded interactions: 80757 Sorted by model distance: nonbonded pdb=" OG SER C 989 " pdb=" OE1 GLU C1035 " model vdw 2.018 3.040 nonbonded pdb=" OD1 ASP C 515 " pdb=" NZ LYS C 519 " model vdw 2.049 3.120 nonbonded pdb=" OP1 DT B 49 " pdb=" NH1 ARG C 188 " model vdw 2.151 3.120 nonbonded pdb=" NH2 ARG C 443 " pdb=" OG1 THR C 565 " model vdw 2.169 3.120 nonbonded pdb=" O ARG C 661 " pdb=" NH2 ARG C 693 " model vdw 2.172 3.120 ... (remaining 80752 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.110 Find NCS groups from input model: 0.050 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 : 0.005 0.040 10310 Z= 0.369 Angle : 0.835 10.194 14475 Z= 0.541 Chirality : 0.064 0.317 1633 Planarity : 0.006 0.055 1419 Dihedral : 23.086 162.948 4200 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.13 % Favored : 93.54 % Rotamer: Outliers : 0.39 % Allowed : 29.08 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.62 (0.28), residues: 914 helix: 0.33 (0.24), residues: 503 sheet: -0.60 (0.66), residues: 65 loop : -1.39 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 327 TYR 0.027 0.002 TYR C 626 PHE 0.013 0.001 PHE C 496 TRP 0.021 0.002 TRP C 351 HIS 0.010 0.001 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.37 (10302) covalent geometry : angle 0.83513 / 0.54 (14470) hydrogen bonds : bond 0.12320 / 13.85 ( 492) hydrogen bonds : angle 5.44297 / 7.27 ( 1310) metal coordination : bond 0.00678 / 0.68 ( 8) metal coordination : angle 0.54844 / 0.99 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.326 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 69 average time/residue: 0.0987 time to fit residues: 10.0478 Evaluate side-chains 60 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 6.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 751 HIS ** C1104 GLN ** 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 = 0.4092 r_free = 0.4092 target = 0.107756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.079448 restraints weight = 31993.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.081554 restraints weight = 17648.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.082862 restraints weight = 12569.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.083588 restraints weight = 10422.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.084041 restraints weight = 9418.895| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10310 Z= 0.168 Angle : 0.856 20.869 14475 Z= 0.409 Chirality : 0.065 1.007 1633 Planarity : 0.005 0.060 1419 Dihedral : 23.177 166.994 2431 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.81 % Favored : 94.86 % Rotamer: Outliers : 3.42 % Allowed : 27.24 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.08 (0.28), residues: 914 helix: 0.77 (0.23), residues: 507 sheet: -0.45 (0.69), residues: 59 loop : -1.15 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 151 TYR 0.009 0.001 TYR C 202 PHE 0.010 0.001 PHE C 449 TRP 0.016 0.001 TRP C 823 HIS 0.006 0.001 HIS C 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 (10302) covalent geometry : angle 0.85516 / 0.41 (14470) hydrogen bonds : bond 0.04996 / 5.72 ( 492) hydrogen bonds : angle 4.43061 / 6.04 ( 1310) metal coordination : bond 0.00422 / 0.44 ( 8) metal coordination : angle 1.57506 / 3.53 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: C 194 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.8874 (tttp) REVERT: C 267 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7616 (mm) REVERT: C 483 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8721 (tt) REVERT: C 516 SER cc_start: 0.8923 (OUTLIER) cc_final: 0.8652 (p) REVERT: C 948 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8808 (mp) REVERT: C 1097 MET cc_start: 0.8020 (tmm) cc_final: 0.7710 (tmm) outliers start: 26 outliers final: 11 residues processed: 93 average time/residue: 0.0911 time to fit residues: 12.5349 Evaluate side-chains 82 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1000 SER Chi-restraints excluded: chain C residue 1036 LEU Chi-restraints excluded: chain C residue 1051 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 16 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.106923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.078664 restraints weight = 32080.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.080742 restraints weight = 17688.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.082030 restraints weight = 12645.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.082752 restraints weight = 10509.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.083020 restraints weight = 9520.526| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10310 Z= 0.163 Angle : 0.734 15.856 14475 Z= 0.364 Chirality : 0.055 0.892 1633 Planarity : 0.004 0.055 1419 Dihedral : 23.178 168.815 2431 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.14 % Favored : 94.53 % Rotamer: Outliers : 3.42 % Allowed : 26.71 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.09 (0.28), residues: 914 helix: 0.99 (0.24), residues: 507 sheet: -0.50 (0.70), residues: 59 loop : -1.19 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 151 TYR 0.017 0.002 TYR C 626 PHE 0.010 0.001 PHE C 496 TRP 0.011 0.001 TRP C 351 HIS 0.007 0.001 HIS C 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (10302) covalent geometry : angle 0.73401 / 0.36 (14470) hydrogen bonds : bond 0.04565 / 5.24 ( 492) hydrogen bonds : angle 4.24137 / 5.77 ( 1310) metal coordination : bond 0.00422 / 0.38 ( 8) metal coordination : angle 1.34103 / 2.62 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: C 194 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8853 (ptmm) REVERT: C 765 MET cc_start: 0.8526 (mmp) cc_final: 0.8322 (mmt) REVERT: C 948 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8675 (mp) REVERT: C 982 LEU cc_start: 0.8972 (tt) cc_final: 0.8729 (pt) REVERT: C 1097 MET cc_start: 0.8072 (tmm) cc_final: 0.7572 (tmm) outliers start: 26 outliers final: 15 residues processed: 86 average time/residue: 0.0941 time to fit residues: 11.9133 Evaluate side-chains 85 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 686 ASN Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 899 THR Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1006 VAL Chi-restraints excluded: chain C residue 1036 LEU Chi-restraints excluded: chain C residue 1051 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 0 optimal weight: 40.0000 chunk 8 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 845 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.106571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.078463 restraints weight = 32328.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.080570 restraints weight = 17402.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.081906 restraints weight = 12282.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.082666 restraints weight = 10106.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.083117 restraints weight = 9090.756| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10310 Z= 0.153 Angle : 0.703 9.569 14475 Z= 0.351 Chirality : 0.049 0.522 1633 Planarity : 0.004 0.055 1419 Dihedral : 23.238 168.728 2431 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.92 % Favored : 94.75 % Rotamer: Outliers : 4.34 % Allowed : 26.58 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.27 (0.29), residues: 914 helix: 1.15 (0.24), residues: 513 sheet: -0.47 (0.68), residues: 59 loop : -1.17 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 151 TYR 0.012 0.001 TYR C 626 PHE 0.011 0.001 PHE C 968 TRP 0.011 0.001 TRP C 351 HIS 0.010 0.001 HIS C 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (10302) covalent geometry : angle 0.70278 / 0.35 (14470) hydrogen bonds : bond 0.04199 / 4.81 ( 492) hydrogen bonds : angle 4.12894 / 5.60 ( 1310) metal coordination : bond 0.00425 / 0.40 ( 8) metal coordination : angle 1.37475 / 2.75 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 67 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 178 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7921 (p0) REVERT: C 194 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8868 (ptmm) REVERT: C 410 ASP cc_start: 0.7217 (p0) cc_final: 0.6647 (p0) REVERT: C 483 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8760 (tt) REVERT: C 748 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8120 (mtp180) REVERT: C 948 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8810 (mp) REVERT: C 961 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7839 (ptm160) REVERT: C 982 LEU cc_start: 0.8957 (tt) cc_final: 0.8693 (pt) REVERT: C 1097 MET cc_start: 0.8176 (tmm) cc_final: 0.7656 (tmm) outliers start: 33 outliers final: 19 residues processed: 95 average time/residue: 0.0960 time to fit residues: 13.3670 Evaluate side-chains 86 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 686 ASN Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 748 ARG Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 899 THR Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 961 ARG Chi-restraints excluded: chain C residue 974 GLU Chi-restraints excluded: chain C residue 1000 SER Chi-restraints excluded: chain C residue 1006 VAL Chi-restraints excluded: chain C residue 1051 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 51 optimal weight: 0.0670 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.107426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.079311 restraints weight = 32418.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.081383 restraints weight = 17683.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.082686 restraints weight = 12605.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.083415 restraints weight = 10436.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.083762 restraints weight = 9445.472| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10310 Z= 0.128 Angle : 0.670 10.297 14475 Z= 0.336 Chirality : 0.048 0.357 1633 Planarity : 0.004 0.054 1419 Dihedral : 23.262 169.032 2431 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.49 % Favored : 95.19 % Rotamer: Outliers : 3.82 % Allowed : 26.84 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.42 (0.29), residues: 914 helix: 1.25 (0.24), residues: 513 sheet: -0.32 (0.67), residues: 59 loop : -1.08 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 151 TYR 0.006 0.001 TYR C 614 PHE 0.019 0.001 PHE C 213 TRP 0.011 0.001 TRP C 351 HIS 0.009 0.001 HIS C 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (10302) covalent geometry : angle 0.66957 / 0.34 (14470) hydrogen bonds : bond 0.03907 / 4.51 ( 492) hydrogen bonds : angle 4.01376 / 5.42 ( 1310) metal coordination : bond 0.00313 / 0.31 ( 8) metal coordination : angle 1.32523 / 2.53 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: C 164 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8552 (tt0) REVERT: C 178 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7978 (p0) REVERT: C 194 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8836 (ptmm) REVERT: C 410 ASP cc_start: 0.7050 (p0) cc_final: 0.6571 (p0) REVERT: C 483 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8737 (tt) REVERT: C 748 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.8037 (mtp180) REVERT: C 948 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8653 (mp) REVERT: C 964 LYS cc_start: 0.9119 (tptt) cc_final: 0.8901 (ttmm) REVERT: C 982 LEU cc_start: 0.8948 (tt) cc_final: 0.8669 (pt) REVERT: C 1097 MET cc_start: 0.8185 (tmm) cc_final: 0.7648 (tmm) outliers start: 29 outliers final: 17 residues processed: 91 average time/residue: 0.0954 time to fit residues: 12.5731 Evaluate side-chains 85 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 370 HIS Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 748 ARG Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1000 SER Chi-restraints excluded: chain C residue 1006 VAL Chi-restraints excluded: chain C residue 1051 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 79 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 60 optimal weight: 0.0570 chunk 99 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.107600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.079516 restraints weight = 32331.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.081624 restraints weight = 17608.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.082914 restraints weight = 12497.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.083648 restraints weight = 10361.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.083938 restraints weight = 9358.602| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10310 Z= 0.126 Angle : 0.665 10.671 14475 Z= 0.332 Chirality : 0.047 0.278 1633 Planarity : 0.004 0.054 1419 Dihedral : 23.286 168.865 2431 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.49 % Favored : 95.19 % Rotamer: Outliers : 4.74 % Allowed : 25.79 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.51 (0.29), residues: 914 helix: 1.30 (0.24), residues: 513 sheet: -0.25 (0.68), residues: 59 loop : -1.01 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 151 TYR 0.012 0.001 TYR C 626 PHE 0.010 0.001 PHE C 213 TRP 0.009 0.001 TRP C 351 HIS 0.009 0.001 HIS C 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 (10302) covalent geometry : angle 0.66505 / 0.33 (14470) hydrogen bonds : bond 0.03804 / 4.38 ( 492) hydrogen bonds : angle 3.96018 / 5.35 ( 1310) metal coordination : bond 0.00377 / 0.38 ( 8) metal coordination : angle 1.25268 / 2.30 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 67 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: C 164 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8538 (mt-10) REVERT: C 178 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7970 (p0) REVERT: C 194 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8827 (ptmm) REVERT: C 410 ASP cc_start: 0.7094 (p0) cc_final: 0.6648 (p0) REVERT: C 483 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8717 (tt) REVERT: C 748 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7980 (mtp180) REVERT: C 948 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8777 (mp) REVERT: C 969 VAL cc_start: 0.9000 (t) cc_final: 0.8752 (p) REVERT: C 973 MET cc_start: 0.8394 (mmp) cc_final: 0.7779 (tpp) REVERT: C 982 LEU cc_start: 0.8923 (tt) cc_final: 0.8626 (pt) outliers start: 36 outliers final: 23 residues processed: 96 average time/residue: 0.0905 time to fit residues: 12.8007 Evaluate side-chains 89 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 370 HIS Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 686 ASN Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 748 ARG Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 899 THR Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1000 SER Chi-restraints excluded: chain C residue 1006 VAL Chi-restraints excluded: chain C residue 1051 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 43 optimal weight: 0.8980 chunk 85 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 88 optimal weight: 0.3980 chunk 82 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 30.0000 chunk 11 optimal weight: 9.9990 chunk 52 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.108244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.080315 restraints weight = 32236.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.082435 restraints weight = 17546.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.083709 restraints weight = 12452.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.084491 restraints weight = 10331.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.084906 restraints weight = 9301.078| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10310 Z= 0.120 Angle : 0.656 10.118 14475 Z= 0.329 Chirality : 0.046 0.244 1633 Planarity : 0.004 0.055 1419 Dihedral : 23.283 169.192 2431 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.16 % Favored : 95.51 % Rotamer: Outliers : 3.82 % Allowed : 26.45 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.55 (0.29), residues: 914 helix: 1.33 (0.24), residues: 506 sheet: -0.19 (0.68), residues: 59 loop : -0.94 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 311 TYR 0.010 0.001 TYR C 626 PHE 0.008 0.001 PHE C 213 TRP 0.009 0.001 TRP C 351 HIS 0.009 0.001 HIS C 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 (10302) covalent geometry : angle 0.65574 / 0.33 (14470) hydrogen bonds : bond 0.03750 / 4.32 ( 492) hydrogen bonds : angle 3.94137 / 5.30 ( 1310) metal coordination : bond 0.00367 / 0.35 ( 8) metal coordination : angle 1.20759 / 2.20 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: C 164 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8584 (tt0) REVERT: C 194 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8816 (ptmm) REVERT: C 410 ASP cc_start: 0.6935 (p0) cc_final: 0.6580 (p0) REVERT: C 483 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8717 (tt) REVERT: C 948 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8581 (mp) REVERT: C 982 LEU cc_start: 0.8900 (tt) cc_final: 0.8602 (pt) REVERT: C 1095 SER cc_start: 0.8816 (t) cc_final: 0.8488 (p) REVERT: C 1097 MET cc_start: 0.8114 (tmm) cc_final: 0.7673 (tmm) outliers start: 29 outliers final: 20 residues processed: 90 average time/residue: 0.0833 time to fit residues: 11.2423 Evaluate side-chains 87 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 370 HIS Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1000 SER Chi-restraints excluded: chain C residue 1006 VAL Chi-restraints excluded: chain C residue 1051 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 84 optimal weight: 0.0470 chunk 65 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 0.0010 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.0088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.109235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.082103 restraints weight = 31995.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.084233 restraints weight = 17191.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.085553 restraints weight = 12135.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.086327 restraints weight = 10007.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.086764 restraints weight = 9003.343| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10310 Z= 0.124 Angle : 0.666 10.821 14475 Z= 0.335 Chirality : 0.046 0.244 1633 Planarity : 0.004 0.055 1419 Dihedral : 23.290 168.693 2431 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.16 % Favored : 95.51 % Rotamer: Outliers : 3.68 % Allowed : 26.84 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.57 (0.29), residues: 914 helix: 1.37 (0.24), residues: 508 sheet: -0.23 (0.68), residues: 59 loop : -0.99 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 517 TYR 0.015 0.001 TYR C 626 PHE 0.012 0.001 PHE C 749 TRP 0.009 0.001 TRP C 351 HIS 0.011 0.001 HIS C 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (10302) covalent geometry : angle 0.66543 / 0.33 (14470) hydrogen bonds : bond 0.03810 / 4.41 ( 492) hydrogen bonds : angle 3.90829 / 5.25 ( 1310) metal coordination : bond 0.00451 / 0.45 ( 8) metal coordination : angle 1.24160 / 2.26 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: C 164 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8499 (mt-10) REVERT: C 194 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8776 (ptmm) REVERT: C 410 ASP cc_start: 0.6888 (p0) cc_final: 0.6499 (p0) REVERT: C 483 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8706 (tt) REVERT: C 948 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8601 (mp) REVERT: C 982 LEU cc_start: 0.8836 (tt) cc_final: 0.8544 (pt) REVERT: C 1095 SER cc_start: 0.8877 (t) cc_final: 0.8570 (p) REVERT: C 1097 MET cc_start: 0.8104 (tmm) cc_final: 0.7654 (tmm) outliers start: 28 outliers final: 22 residues processed: 88 average time/residue: 0.0740 time to fit residues: 10.2491 Evaluate side-chains 88 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 370 HIS Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 686 ASN Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 899 THR Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1000 SER Chi-restraints excluded: chain C residue 1006 VAL Chi-restraints excluded: chain C residue 1051 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 58 optimal weight: 0.0970 chunk 30 optimal weight: 0.0070 chunk 62 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 84 optimal weight: 0.0870 chunk 63 optimal weight: 0.9980 overall best weight: 0.4374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 196 GLN C 598 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.109902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.082911 restraints weight = 31910.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.084946 restraints weight = 17340.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.086278 restraints weight = 12279.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.087051 restraints weight = 10133.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.087459 restraints weight = 9131.778| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10310 Z= 0.118 Angle : 0.665 14.296 14475 Z= 0.331 Chirality : 0.046 0.249 1633 Planarity : 0.004 0.056 1419 Dihedral : 23.275 169.308 2431 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.72 % Favored : 95.95 % Rotamer: Outliers : 3.55 % Allowed : 27.11 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.62 (0.29), residues: 914 helix: 1.42 (0.24), residues: 502 sheet: -0.21 (0.68), residues: 59 loop : -0.94 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 492 TYR 0.008 0.001 TYR C 626 PHE 0.009 0.001 PHE C 749 TRP 0.010 0.001 TRP C 152 HIS 0.010 0.001 HIS C 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 (10302) covalent geometry : angle 0.66521 / 0.33 (14470) hydrogen bonds : bond 0.03667 / 4.26 ( 492) hydrogen bonds : angle 3.85131 / 5.13 ( 1310) metal coordination : bond 0.00472 / 0.45 ( 8) metal coordination : angle 1.25203 / 2.29 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: C 164 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8543 (tt0) REVERT: C 167 LEU cc_start: 0.8999 (tp) cc_final: 0.8709 (tp) REVERT: C 194 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8792 (ptmm) REVERT: C 196 GLN cc_start: 0.8538 (tm130) cc_final: 0.8307 (tm-30) REVERT: C 410 ASP cc_start: 0.6990 (p0) cc_final: 0.6636 (p0) REVERT: C 483 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8701 (tt) REVERT: C 628 TYR cc_start: 0.5794 (m-80) cc_final: 0.5580 (m-80) REVERT: C 948 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8582 (mp) REVERT: C 973 MET cc_start: 0.8282 (mmp) cc_final: 0.7951 (tpp) REVERT: C 982 LEU cc_start: 0.8845 (tt) cc_final: 0.8543 (pt) REVERT: C 1095 SER cc_start: 0.8911 (t) cc_final: 0.8642 (p) REVERT: C 1097 MET cc_start: 0.8135 (tmm) cc_final: 0.7678 (tmm) outliers start: 27 outliers final: 20 residues processed: 89 average time/residue: 0.0634 time to fit residues: 8.8225 Evaluate side-chains 88 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 370 HIS Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 654 MET Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1000 SER Chi-restraints excluded: chain C residue 1006 VAL Chi-restraints excluded: chain C residue 1051 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 15 optimal weight: 0.0870 chunk 6 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 0.0170 chunk 90 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.109731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.082631 restraints weight = 31788.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.084791 restraints weight = 17189.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.086111 restraints weight = 12120.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.086852 restraints weight = 10018.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.087293 restraints weight = 9040.313| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10310 Z= 0.126 Angle : 0.675 13.857 14475 Z= 0.337 Chirality : 0.046 0.251 1633 Planarity : 0.004 0.056 1419 Dihedral : 23.272 168.731 2431 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.38 % Favored : 95.30 % Rotamer: Outliers : 3.42 % Allowed : 27.76 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.67 (0.29), residues: 914 helix: 1.48 (0.24), residues: 507 sheet: -0.23 (0.67), residues: 59 loop : -0.97 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 151 TYR 0.013 0.001 TYR C 626 PHE 0.020 0.001 PHE C 496 TRP 0.012 0.001 TRP C 701 HIS 0.010 0.001 HIS C 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 (10302) covalent geometry : angle 0.67493 / 0.34 (14470) hydrogen bonds : bond 0.03743 / 4.32 ( 492) hydrogen bonds : angle 3.85584 / 5.18 ( 1310) metal coordination : bond 0.00450 / 0.44 ( 8) metal coordination : angle 1.22007 / 2.25 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: C 164 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8555 (tt0) REVERT: C 167 LEU cc_start: 0.8978 (tp) cc_final: 0.8659 (tp) REVERT: C 194 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8817 (ptmm) REVERT: C 196 GLN cc_start: 0.8522 (tm130) cc_final: 0.8275 (tm-30) REVERT: C 410 ASP cc_start: 0.7006 (p0) cc_final: 0.6637 (p0) REVERT: C 483 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8717 (tt) REVERT: C 948 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8582 (mp) REVERT: C 973 MET cc_start: 0.8355 (mmp) cc_final: 0.8035 (tpp) REVERT: C 982 LEU cc_start: 0.8867 (tt) cc_final: 0.8563 (pt) REVERT: C 1095 SER cc_start: 0.8928 (t) cc_final: 0.8609 (p) REVERT: C 1097 MET cc_start: 0.8160 (tmm) cc_final: 0.7677 (tmm) outliers start: 26 outliers final: 19 residues processed: 88 average time/residue: 0.0626 time to fit residues: 8.3839 Evaluate side-chains 88 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 370 HIS Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1000 SER Chi-restraints excluded: chain C residue 1006 VAL Chi-restraints excluded: chain C residue 1051 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 43 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 96 optimal weight: 0.3980 chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.108976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.081772 restraints weight = 32227.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.083882 restraints weight = 17540.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.085193 restraints weight = 12434.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.085961 restraints weight = 10282.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.086380 restraints weight = 9259.870| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10310 Z= 0.135 Angle : 0.682 13.885 14475 Z= 0.340 Chirality : 0.047 0.247 1633 Planarity : 0.004 0.056 1419 Dihedral : 23.289 168.314 2431 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.60 % Favored : 95.08 % Rotamer: Outliers : 3.16 % Allowed : 27.50 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.70 (0.29), residues: 914 helix: 1.49 (0.24), residues: 509 sheet: -0.39 (0.66), residues: 59 loop : -0.90 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 492 TYR 0.024 0.001 TYR C 626 PHE 0.017 0.001 PHE C 597 TRP 0.014 0.001 TRP C 701 HIS 0.010 0.001 HIS C 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (10302) covalent geometry : angle 0.68140 / 0.34 (14470) hydrogen bonds : bond 0.03843 / 4.43 ( 492) hydrogen bonds : angle 3.85703 / 5.20 ( 1310) metal coordination : bond 0.00418 / 0.40 ( 8) metal coordination : angle 1.24992 / 2.36 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1681.77 seconds wall clock time: 29 minutes 43.11 seconds (1783.11 seconds total)