Starting phenix.real_space_refine on Tue May 13 11:10:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ibw_35347/05_2025/8ibw_35347.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ibw_35347/05_2025/8ibw_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ibw_35347/05_2025/8ibw_35347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ibw_35347/05_2025/8ibw_35347.map" model { file = "/net/cci-nas-00/data/ceres_data/8ibw_35347/05_2025/8ibw_35347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ibw_35347/05_2025/8ibw_35347.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.058 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 833 Classifications: {'RNA': 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: 5.88, per 1000 atoms: 0.60 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: 2.47 Conformation dependent library (CDL) restraints added in 938.5 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: 3.77 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: 4.59 Time building geometry restraints manager: 2.88 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=" 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=" N GLY C 111 " pdb=" CA GLY C 111 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.16e+00 bond pdb=" CA VAL C 340 " pdb=" C VAL C 340 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.27e-02 6.20e+03 4.10e+00 bond pdb=" CA GLY C 341 " pdb=" C GLY C 341 " ideal model delta sigma weight residual 1.514 1.486 0.028 1.41e-02 5.03e+03 4.01e+00 bond pdb=" C4' G D 244 " pdb=" O4' G D 244 " ideal model delta sigma weight residual 1.454 1.429 0.025 1.50e-02 4.44e+03 2.73e+00 ... (remaining 10297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 14121 2.04 - 4.08: 302 4.08 - 6.12: 36 6.12 - 8.16: 8 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=" CA GLU C 200 " pdb=" CB GLU C 200 " pdb=" CG GLU C 200 " ideal model delta sigma weight residual 114.10 121.60 -7.50 2.00e+00 2.50e-01 1.41e+01 angle pdb=" O4' G D 244 " pdb=" C4' G D 244 " pdb=" C3' G D 244 " ideal model delta sigma weight residual 106.10 102.40 3.70 1.00e+00 1.00e+00 1.37e+01 angle pdb=" C4' G D 244 " pdb=" O4' G D 244 " pdb=" C1' G D 244 " ideal model delta sigma weight residual 109.70 106.00 3.70 1.00e+00 1.00e+00 1.37e+01 angle pdb=" CB MET C1097 " pdb=" CG MET C1097 " pdb=" SD MET C1097 " ideal model delta sigma weight residual 112.70 122.73 -10.03 3.00e+00 1.11e-01 1.12e+01 ... (remaining 14465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.59: 5324 32.59 - 65.18: 666 65.18 - 97.77: 42 97.77 - 130.36: 1 130.36 - 162.95: 3 Dihedral angle restraints: 6036 sinusoidal: 3404 harmonic: 2632 Sorted by residual: dihedral pdb=" O4' G D 244 " pdb=" C4' G D 244 " pdb=" C3' G D 244 " pdb=" C2' G D 244 " ideal model delta sinusoidal sigma weight residual 24.00 -40.21 64.21 1 8.00e+00 1.56e-02 8.47e+01 dihedral pdb=" C5' G D 244 " pdb=" C4' G D 244 " pdb=" C3' G D 244 " pdb=" O3' G D 244 " ideal model delta sinusoidal sigma weight residual 147.00 85.24 61.76 1 8.00e+00 1.56e-02 7.90e+01 dihedral pdb=" C4' G D 244 " pdb=" C3' G D 244 " pdb=" C2' G D 244 " pdb=" C1' G D 244 " ideal model delta sinusoidal sigma weight residual -35.00 20.94 -55.94 1 8.00e+00 1.56e-02 6.60e+01 ... (remaining 6033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1403 0.058 - 0.115: 211 0.115 - 0.173: 18 0.173 - 0.231: 0 0.231 - 0.289: 1 Chirality restraints: 1633 Sorted by residual: 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=" CB ILE C 746 " pdb=" CA ILE C 746 " pdb=" CG1 ILE C 746 " pdb=" CG2 ILE C 746 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CA SER C 343 " pdb=" N SER C 343 " pdb=" C SER C 343 " pdb=" CB SER C 343 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.46e-01 ... (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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 29.460 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 : 0.004 0.040 10310 Z= 0.220 Angle : 0.729 10.194 14475 Z= 0.414 Chirality : 0.040 0.289 1633 Planarity : 0.006 0.055 1419 Dihedral : 23.494 162.948 4338 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (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 TRP 0.021 0.002 TRP C 351 HIS 0.010 0.001 HIS C 673 PHE 0.013 0.001 PHE C 496 TYR 0.027 0.002 TYR C 626 ARG 0.015 0.001 ARG C 327 Details of bonding type rmsd hydrogen bonds : bond 0.12320 ( 492) hydrogen bonds : angle 5.44297 ( 1310) metal coordination : bond 0.00678 ( 8) metal coordination : angle 0.54844 ( 5) covalent geometry : bond 0.00446 (10302) covalent geometry : angle 0.72949 (14470) *********************** 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 : 0.876 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 69 average time/residue: 0.2068 time to fit residues: 20.8309 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 : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4064 r_free = 0.4064 target = 0.106260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.077695 restraints weight = 31591.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.079834 restraints weight = 17057.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.081167 restraints weight = 12075.367| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10310 Z= 0.175 Angle : 0.643 8.991 14475 Z= 0.343 Chirality : 0.039 0.194 1633 Planarity : 0.004 0.060 1419 Dihedral : 23.903 171.810 2569 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.47 % Favored : 94.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.28), residues: 914 helix: 0.79 (0.23), residues: 516 sheet: -0.52 (0.70), residues: 59 loop : -1.31 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 823 HIS 0.006 0.001 HIS C 744 PHE 0.010 0.001 PHE C 496 TYR 0.011 0.002 TYR C 626 ARG 0.010 0.001 ARG C 166 Details of bonding type rmsd hydrogen bonds : bond 0.04401 ( 492) hydrogen bonds : angle 4.30447 ( 1310) metal coordination : bond 0.00465 ( 8) metal coordination : angle 1.92630 ( 5) covalent geometry : bond 0.00390 (10302) covalent geometry : angle 0.64228 (14470) *********************** 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 98 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 194 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8843 (tttp) REVERT: C 948 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8820 (mp) REVERT: C 1097 MET cc_start: 0.8082 (tmm) cc_final: 0.7507 (tmm) outliers start: 26 outliers final: 11 residues processed: 93 average time/residue: 0.2141 time to fit residues: 28.6418 Evaluate side-chains 81 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 503 LEU 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 698 VAL Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 899 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 974 GLU Chi-restraints excluded: chain C residue 980 VAL 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 2 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.106272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.078135 restraints weight = 31974.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.080302 restraints weight = 17019.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.081624 restraints weight = 11910.388| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1510 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= 0.152 Angle : 0.589 9.028 14475 Z= 0.316 Chirality : 0.037 0.187 1633 Planarity : 0.004 0.057 1419 Dihedral : 23.698 170.415 2569 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.49 % Favored : 95.19 % Rotamer: Outliers : 4.47 % Allowed : 26.58 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.29), residues: 914 helix: 1.08 (0.24), residues: 517 sheet: -0.41 (0.70), residues: 59 loop : -1.19 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 351 HIS 0.007 0.001 HIS C 751 PHE 0.009 0.001 PHE C 496 TYR 0.010 0.001 TYR C 626 ARG 0.005 0.000 ARG C1101 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 492) hydrogen bonds : angle 4.13961 ( 1310) metal coordination : bond 0.00376 ( 8) metal coordination : angle 1.55486 ( 5) covalent geometry : bond 0.00334 (10302) covalent geometry : angle 0.58887 (14470) *********************** 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 105 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 71 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 178 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7906 (p0) REVERT: C 194 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.8766 (tttp) REVERT: C 270 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7351 (pp) REVERT: C 410 ASP cc_start: 0.7222 (p0) cc_final: 0.6615 (p0) REVERT: C 948 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8743 (mp) REVERT: C 1097 MET cc_start: 0.8293 (tmm) cc_final: 0.7692 (tmm) outliers start: 34 outliers final: 20 residues processed: 100 average time/residue: 0.2381 time to fit residues: 33.7389 Evaluate side-chains 90 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 189 THR Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 370 HIS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 424 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 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 868 HIS Chi-restraints excluded: chain C residue 948 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 58 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1104 GLN ** 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 = 0.4115 r_free = 0.4115 target = 0.108027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.080824 restraints weight = 31749.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.082893 restraints weight = 17346.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.084200 restraints weight = 12304.154| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1830 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= 0.131 Angle : 0.562 9.611 14475 Z= 0.300 Chirality : 0.036 0.182 1633 Planarity : 0.004 0.056 1419 Dihedral : 23.648 170.119 2569 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.27 % Favored : 95.40 % Rotamer: Outliers : 4.08 % Allowed : 26.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.29), residues: 914 helix: 1.23 (0.24), residues: 514 sheet: -0.18 (0.70), residues: 59 loop : -1.09 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 351 HIS 0.008 0.001 HIS C 751 PHE 0.009 0.001 PHE C 213 TYR 0.010 0.001 TYR C 626 ARG 0.007 0.000 ARG C1101 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 492) hydrogen bonds : angle 3.97793 ( 1310) metal coordination : bond 0.00476 ( 8) metal coordination : angle 1.59644 ( 5) covalent geometry : bond 0.00285 (10302) covalent geometry : angle 0.56082 (14470) *********************** 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 99 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 68 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 194 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8805 (tttt) REVERT: C 196 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8138 (tm-30) REVERT: C 948 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8784 (mp) REVERT: C 1097 MET cc_start: 0.8289 (tmm) cc_final: 0.7840 (tmm) outliers start: 31 outliers final: 22 residues processed: 94 average time/residue: 0.2096 time to fit residues: 28.7454 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 : 0.886 ------------------------------------------------------------------------------- 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 370 HIS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 438 ILE 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 686 ASN 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 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 974 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 6 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 ASN C 845 GLN ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.105894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.078401 restraints weight = 31822.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.080444 restraints weight = 17697.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.081709 restraints weight = 12658.821| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10310 Z= 0.188 Angle : 0.599 7.419 14475 Z= 0.321 Chirality : 0.038 0.179 1633 Planarity : 0.004 0.055 1419 Dihedral : 23.720 168.117 2569 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.47 % Favored : 94.20 % Rotamer: Outliers : 4.34 % Allowed : 27.37 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.29), residues: 914 helix: 1.16 (0.24), residues: 514 sheet: -0.24 (0.70), residues: 59 loop : -1.09 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 701 HIS 0.009 0.001 HIS C 751 PHE 0.006 0.001 PHE C 530 TYR 0.028 0.002 TYR C 626 ARG 0.004 0.000 ARG C 151 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 492) hydrogen bonds : angle 4.08835 ( 1310) metal coordination : bond 0.00601 ( 8) metal coordination : angle 1.68070 ( 5) covalent geometry : bond 0.00417 (10302) covalent geometry : angle 0.59800 (14470) *********************** 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: 33 poor density : 64 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: C 194 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8824 (tttt) REVERT: C 196 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8296 (tm-30) REVERT: C 626 TYR cc_start: 0.5608 (t80) cc_final: 0.5401 (t80) REVERT: C 948 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8802 (mp) REVERT: C 1097 MET cc_start: 0.8240 (tmm) cc_final: 0.7600 (tmm) outliers start: 33 outliers final: 24 residues processed: 92 average time/residue: 0.1928 time to fit residues: 25.8489 Evaluate side-chains 85 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 189 THR 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 503 LEU 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 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 1000 SER Chi-restraints excluded: chain C residue 1006 VAL Chi-restraints excluded: chain C residue 1051 CYS Chi-restraints excluded: chain C residue 1059 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 8 optimal weight: 0.2980 chunk 51 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** 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 = 0.4100 r_free = 0.4100 target = 0.107380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.080376 restraints weight = 31658.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.082397 restraints weight = 17387.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.083671 restraints weight = 12361.363| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2257 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= 0.126 Angle : 0.555 10.016 14475 Z= 0.296 Chirality : 0.036 0.179 1633 Planarity : 0.004 0.054 1419 Dihedral : 23.659 169.848 2569 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.83 % Favored : 95.84 % Rotamer: Outliers : 3.55 % Allowed : 28.68 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.29), residues: 914 helix: 1.32 (0.24), residues: 514 sheet: -0.22 (0.70), residues: 59 loop : -1.00 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 351 HIS 0.008 0.001 HIS C 751 PHE 0.015 0.001 PHE C 496 TYR 0.018 0.001 TYR C 626 ARG 0.006 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 492) hydrogen bonds : angle 3.93710 ( 1310) metal coordination : bond 0.00408 ( 8) metal coordination : angle 1.46788 ( 5) covalent geometry : bond 0.00275 (10302) covalent geometry : angle 0.55406 (14470) *********************** 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 93 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: C 167 LEU cc_start: 0.9058 (tp) cc_final: 0.8803 (tp) REVERT: C 194 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8690 (tttp) REVERT: C 640 MET cc_start: 0.8659 (tpp) cc_final: 0.8410 (tpp) REVERT: C 948 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8823 (mp) REVERT: C 1097 MET cc_start: 0.8308 (tmm) cc_final: 0.7719 (tmm) outliers start: 27 outliers final: 22 residues processed: 91 average time/residue: 0.1783 time to fit residues: 24.6446 Evaluate side-chains 83 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 189 THR 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 438 ILE 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 593 SER 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 758 ILE Chi-restraints excluded: chain C residue 868 HIS 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 Chi-restraints excluded: chain C residue 1059 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.107164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.080053 restraints weight = 32047.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.082140 restraints weight = 17527.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.083391 restraints weight = 12410.455| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2381 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= 0.131 Angle : 0.561 8.742 14475 Z= 0.299 Chirality : 0.036 0.177 1633 Planarity : 0.004 0.054 1419 Dihedral : 23.662 169.828 2569 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.03 % Favored : 94.64 % Rotamer: Outliers : 3.42 % Allowed : 29.08 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.29), residues: 914 helix: 1.34 (0.24), residues: 513 sheet: -0.21 (0.69), residues: 59 loop : -1.00 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 701 HIS 0.010 0.001 HIS C 751 PHE 0.007 0.001 PHE C 597 TYR 0.022 0.001 TYR C 626 ARG 0.005 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 492) hydrogen bonds : angle 3.89197 ( 1310) metal coordination : bond 0.00453 ( 8) metal coordination : angle 1.32718 ( 5) covalent geometry : bond 0.00289 (10302) covalent geometry : angle 0.56074 (14470) *********************** 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 92 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 167 LEU cc_start: 0.8995 (tp) cc_final: 0.8732 (tp) REVERT: C 194 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8813 (tttt) REVERT: C 196 GLN cc_start: 0.8509 (tm130) cc_final: 0.7849 (tm-30) REVERT: C 948 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8731 (mp) REVERT: C 1095 SER cc_start: 0.8889 (t) cc_final: 0.8650 (p) REVERT: C 1097 MET cc_start: 0.8257 (tmm) cc_final: 0.7651 (tmm) outliers start: 26 outliers final: 23 residues processed: 89 average time/residue: 0.1974 time to fit residues: 26.7639 Evaluate side-chains 87 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 189 THR 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 438 ILE 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 593 SER Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 686 ASN 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 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 Chi-restraints excluded: chain C residue 1059 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 97 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 694 GLN ** 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 = 0.4040 r_free = 0.4040 target = 0.103935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.076792 restraints weight = 31916.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.078750 restraints weight = 17814.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.079957 restraints weight = 12798.407| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10310 Z= 0.222 Angle : 0.638 8.967 14475 Z= 0.339 Chirality : 0.039 0.169 1633 Planarity : 0.005 0.054 1419 Dihedral : 23.811 168.761 2569 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.13 % Favored : 93.54 % Rotamer: Outliers : 4.21 % Allowed : 27.76 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.28), residues: 914 helix: 1.07 (0.24), residues: 516 sheet: -0.41 (0.69), residues: 59 loop : -1.16 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 701 HIS 0.011 0.001 HIS C 751 PHE 0.020 0.002 PHE C 597 TYR 0.030 0.002 TYR C 626 ARG 0.004 0.000 ARG C 492 Details of bonding type rmsd hydrogen bonds : bond 0.04394 ( 492) hydrogen bonds : angle 4.18443 ( 1310) metal coordination : bond 0.00735 ( 8) metal coordination : angle 1.93496 ( 5) covalent geometry : bond 0.00494 (10302) covalent geometry : angle 0.63740 (14470) *********************** 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 91 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 59 time to evaluate : 0.891 Fit side-chains REVERT: C 167 LEU cc_start: 0.9078 (tp) cc_final: 0.8825 (tp) REVERT: C 194 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8788 (tttp) REVERT: C 694 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: C 948 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8810 (mp) REVERT: C 1095 SER cc_start: 0.8812 (t) cc_final: 0.8599 (p) REVERT: C 1097 MET cc_start: 0.8255 (tmm) cc_final: 0.7617 (tmm) outliers start: 32 outliers final: 25 residues processed: 88 average time/residue: 0.1913 time to fit residues: 24.9456 Evaluate side-chains 85 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 57 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 189 THR 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 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 593 SER 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 694 GLN 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 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 Chi-restraints excluded: chain C residue 1059 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 84 optimal weight: 0.0970 chunk 15 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 39 optimal weight: 0.0570 chunk 69 optimal weight: 3.9990 overall best weight: 1.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.105606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.078463 restraints weight = 31914.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.080593 restraints weight = 16811.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.081914 restraints weight = 11717.734| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2699 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= 0.150 Angle : 0.605 17.434 14475 Z= 0.315 Chirality : 0.037 0.173 1633 Planarity : 0.004 0.055 1419 Dihedral : 23.795 171.137 2569 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.92 % Favored : 94.75 % Rotamer: Outliers : 3.82 % Allowed : 27.63 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.28), residues: 914 helix: 1.15 (0.24), residues: 515 sheet: -0.38 (0.69), residues: 59 loop : -1.08 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 701 HIS 0.010 0.001 HIS C 751 PHE 0.019 0.001 PHE C 597 TYR 0.022 0.001 TYR C 626 ARG 0.006 0.000 ARG C 693 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 492) hydrogen bonds : angle 4.04143 ( 1310) metal coordination : bond 0.00430 ( 8) metal coordination : angle 1.47287 ( 5) covalent geometry : bond 0.00332 (10302) covalent geometry : angle 0.60470 (14470) *********************** 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 89 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 167 LEU cc_start: 0.9045 (tp) cc_final: 0.8789 (tp) REVERT: C 194 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8779 (tttp) REVERT: C 196 GLN cc_start: 0.8429 (tm130) cc_final: 0.8069 (tm-30) REVERT: C 948 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8806 (mp) REVERT: C 1084 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8360 (mt) REVERT: C 1097 MET cc_start: 0.8239 (tmm) cc_final: 0.7612 (tmm) outliers start: 29 outliers final: 25 residues processed: 86 average time/residue: 0.1756 time to fit residues: 23.3883 Evaluate side-chains 87 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 59 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 189 THR 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 438 ILE Chi-restraints excluded: chain C residue 452 LYS 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 593 SER 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 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 Chi-restraints excluded: chain C residue 1059 ILE Chi-restraints excluded: chain C residue 1084 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 85 optimal weight: 6.9990 chunk 74 optimal weight: 0.0470 chunk 64 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 57 optimal weight: 0.1980 chunk 51 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.108118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.081390 restraints weight = 31898.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.083508 restraints weight = 17336.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.084782 restraints weight = 12235.073| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2828 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= 0.117 Angle : 0.572 10.895 14475 Z= 0.300 Chirality : 0.036 0.177 1633 Planarity : 0.004 0.055 1419 Dihedral : 23.705 173.622 2569 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.49 % Favored : 95.19 % Rotamer: Outliers : 3.55 % Allowed : 28.03 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.29), residues: 914 helix: 1.36 (0.24), residues: 514 sheet: -0.17 (0.70), residues: 59 loop : -1.01 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 701 HIS 0.010 0.001 HIS C 751 PHE 0.019 0.001 PHE C 180 TYR 0.010 0.001 TYR C 626 ARG 0.003 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.03491 ( 492) hydrogen bonds : angle 3.94407 ( 1310) metal coordination : bond 0.00479 ( 8) metal coordination : angle 1.37207 ( 5) covalent geometry : bond 0.00252 (10302) covalent geometry : angle 0.57185 (14470) ********************** 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: 27 poor density : 67 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 194 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8705 (tttp) REVERT: C 196 GLN cc_start: 0.8350 (tm130) cc_final: 0.7988 (tm-30) REVERT: C 438 ILE cc_start: 0.6667 (OUTLIER) cc_final: 0.6449 (mp) REVERT: C 948 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8782 (mp) REVERT: C 1097 MET cc_start: 0.8249 (tmm) cc_final: 0.7728 (tmm) outliers start: 27 outliers final: 21 residues processed: 91 average time/residue: 0.1814 time to fit residues: 25.1939 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 : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 452 LYS 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 593 SER Chi-restraints excluded: chain C residue 621 VAL 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 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 Chi-restraints excluded: chain C residue 1059 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** 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 = 0.4034 r_free = 0.4034 target = 0.103595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.076386 restraints weight = 32016.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.078355 restraints weight = 17946.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.079589 restraints weight = 12931.107| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10310 Z= 0.257 Angle : 0.684 10.951 14475 Z= 0.359 Chirality : 0.040 0.165 1633 Planarity : 0.005 0.055 1419 Dihedral : 23.922 173.144 2569 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.13 % Favored : 93.54 % Rotamer: Outliers : 3.42 % Allowed : 28.29 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.28), residues: 914 helix: 0.96 (0.23), residues: 520 sheet: -0.80 (0.64), residues: 68 loop : -1.22 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 701 HIS 0.011 0.001 HIS C 751 PHE 0.023 0.002 PHE C 597 TYR 0.041 0.003 TYR C 626 ARG 0.003 0.000 ARG C 858 Details of bonding type rmsd hydrogen bonds : bond 0.04613 ( 492) hydrogen bonds : angle 4.27666 ( 1310) metal coordination : bond 0.00844 ( 8) metal coordination : angle 2.30033 ( 5) covalent geometry : bond 0.00571 (10302) covalent geometry : angle 0.68293 (14470) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3062.75 seconds wall clock time: 54 minutes 41.99 seconds (3281.99 seconds total)