Starting phenix.real_space_refine on Fri Feb 14 09:20:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ibw_35347/02_2025/8ibw_35347.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ibw_35347/02_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_35347/02_2025/8ibw_35347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ibw_35347/02_2025/8ibw_35347.map" model { file = "/net/cci-nas-00/data/ceres_data/8ibw_35347/02_2025/8ibw_35347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ibw_35347/02_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-5592/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: 5.78, per 1000 atoms: 0.59 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: 2.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.73 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: 5.04 Time building geometry restraints manager: 2.91 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 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: 0.080 Process input model: 30.380 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.850 ------------------------------------------------------------------------------- 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 10302 Z= 0.274 Angle : 0.729 10.194 14470 Z= 0.415 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 *********************** 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 : 0.858 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 69 average time/residue: 0.2215 time to fit residues: 22.3154 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 : 0.913 ------------------------------------------------------------------------------- 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 10302 Z= 0.245 Angle : 0.642 8.991 14470 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 *********************** 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 : 0.952 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: 0.2193 time to fit residues: 29.5238 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 : 1.129 ------------------------------------------------------------------------------- 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: 7.9990 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 10302 Z= 0.207 Angle : 0.589 9.028 14470 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 *********************** 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 : 1.009 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: 0.2338 time to fit residues: 33.1005 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 : 0.975 ------------------------------------------------------------------------------- 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 10302 Z= 0.175 Angle : 0.561 9.611 14470 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 *********************** 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 : 0.925 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: 0.2185 time to fit residues: 29.9688 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 : 0.937 ------------------------------------------------------------------------------- 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: 9.9990 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 10302 Z= 0.262 Angle : 0.598 7.419 14470 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 *********************** 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 : 0.926 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: 0.2226 time to fit residues: 29.5219 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 : 0.979 ------------------------------------------------------------------------------- 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: 9.9990 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: 1.6986 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.106560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.079459 restraints weight = 31870.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.081516 restraints weight = 17539.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.082772 restraints weight = 12484.329| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10302 Z= 0.200 Angle : 0.566 9.578 14470 Z= 0.303 Chirality : 0.036 0.177 1633 Planarity : 0.004 0.053 1419 Dihedral : 23.692 169.187 2569 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.60 % Favored : 95.08 % Rotamer: Outliers : 3.82 % Allowed : 28.42 % 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: 0.46 (0.29), residues: 914 helix: 1.25 (0.24), residues: 514 sheet: -0.27 (0.70), residues: 59 loop : -1.03 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 701 HIS 0.008 0.001 HIS C 751 PHE 0.014 0.001 PHE C 496 TYR 0.019 0.001 TYR C 626 ARG 0.006 0.000 ARG C 150 *********************** 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 94 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: C 167 LEU cc_start: 0.9073 (tp) cc_final: 0.8825 (tp) REVERT: C 194 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8712 (tttp) REVERT: C 948 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8821 (mp) REVERT: C 1097 MET cc_start: 0.8296 (tmm) cc_final: 0.7682 (tmm) outliers start: 29 outliers final: 24 residues processed: 91 average time/residue: 0.1896 time to fit residues: 26.0788 Evaluate side-chains 87 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 79 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 83 optimal weight: 0.0980 chunk 51 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 750 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 = 0.4092 r_free = 0.4092 target = 0.106903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.079907 restraints weight = 32229.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.081996 restraints weight = 17648.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.083284 restraints weight = 12488.510| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10302 Z= 0.190 Angle : 0.575 14.107 14470 Z= 0.303 Chirality : 0.036 0.177 1633 Planarity : 0.004 0.055 1419 Dihedral : 23.688 169.877 2569 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.49 % Favored : 95.19 % Rotamer: Outliers : 4.08 % Allowed : 27.76 % Favored : 68.16 % 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: 0.51 (0.29), residues: 914 helix: 1.31 (0.24), residues: 513 sheet: -0.26 (0.70), residues: 59 loop : -1.01 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 701 HIS 0.011 0.001 HIS C 751 PHE 0.007 0.001 PHE C 597 TYR 0.022 0.001 TYR C 626 ARG 0.006 0.000 ARG C 150 *********************** 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 98 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: C 167 LEU cc_start: 0.9021 (tp) cc_final: 0.8763 (tp) REVERT: C 194 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8700 (tttp) REVERT: C 196 GLN cc_start: 0.8475 (tm-30) cc_final: 0.8121 (tm-30) REVERT: C 640 MET cc_start: 0.8679 (tpp) cc_final: 0.8433 (tpp) REVERT: C 948 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8740 (mp) REVERT: C 1097 MET cc_start: 0.8255 (tmm) cc_final: 0.7655 (tmm) outliers start: 31 outliers final: 24 residues processed: 95 average time/residue: 0.2007 time to fit residues: 27.9722 Evaluate side-chains 87 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 97 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 60 optimal weight: 0.0970 chunk 19 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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 ** 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 = 0.4054 r_free = 0.4054 target = 0.104747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.077521 restraints weight = 32124.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.079554 restraints weight = 17784.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.080809 restraints weight = 12698.813| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10302 Z= 0.272 Angle : 0.615 12.922 14470 Z= 0.327 Chirality : 0.038 0.167 1633 Planarity : 0.004 0.054 1419 Dihedral : 23.792 169.569 2569 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.88 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: 0.28 (0.28), residues: 914 helix: 1.13 (0.24), residues: 516 sheet: -0.41 (0.69), residues: 59 loop : -1.14 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 701 HIS 0.009 0.001 HIS C 751 PHE 0.022 0.001 PHE C 597 TYR 0.010 0.002 TYR C 350 ARG 0.004 0.000 ARG C 150 *********************** 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 93 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 61 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: C 167 LEU cc_start: 0.9064 (tp) cc_final: 0.8806 (tp) REVERT: C 194 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8785 (tttp) REVERT: C 948 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8923 (mp) REVERT: C 1084 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8432 (mt) REVERT: C 1097 MET cc_start: 0.8255 (tmm) cc_final: 0.7627 (tmm) outliers start: 32 outliers final: 27 residues processed: 89 average time/residue: 0.1987 time to fit residues: 26.6138 Evaluate side-chains 89 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 59 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 510 ASP 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 939 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 0.0470 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 0.0270 chunk 10 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.7938 ------------------------------------------------------------------------------- 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 ** C 750 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 = 0.4104 r_free = 0.4104 target = 0.107529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.080717 restraints weight = 32060.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.082824 restraints weight = 17458.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.084132 restraints weight = 12305.013| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10302 Z= 0.163 Angle : 0.580 13.433 14470 Z= 0.306 Chirality : 0.036 0.180 1633 Planarity : 0.004 0.053 1419 Dihedral : 23.707 173.058 2569 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.27 % Favored : 95.40 % Rotamer: Outliers : 3.29 % Allowed : 29.08 % Favored : 67.63 % 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: 0.53 (0.29), residues: 914 helix: 1.31 (0.24), residues: 515 sheet: -0.17 (0.70), residues: 59 loop : -1.02 (0.33), residues: 340 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 0.016 0.001 PHE C 597 TYR 0.017 0.001 TYR C 626 ARG 0.004 0.000 ARG C 151 *********************** 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 94 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: C 194 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8686 (tttp) REVERT: C 196 GLN cc_start: 0.8361 (tm130) cc_final: 0.7998 (tm-30) REVERT: C 438 ILE cc_start: 0.6679 (OUTLIER) cc_final: 0.6442 (mp) REVERT: C 948 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8679 (mp) REVERT: C 1097 MET cc_start: 0.8223 (tmm) cc_final: 0.7616 (tmm) outliers start: 25 outliers final: 19 residues processed: 93 average time/residue: 0.1830 time to fit residues: 26.2037 Evaluate side-chains 84 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 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 948 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 960 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 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 85 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 57 optimal weight: 0.0170 chunk 51 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 750 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 = 0.4112 r_free = 0.4112 target = 0.107992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.081297 restraints weight = 31961.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.083381 restraints weight = 17379.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.084665 restraints weight = 12286.539| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10302 Z= 0.161 Angle : 0.600 13.844 14470 Z= 0.309 Chirality : 0.036 0.185 1633 Planarity : 0.004 0.054 1419 Dihedral : 23.671 173.517 2569 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.70 % Favored : 94.97 % Rotamer: Outliers : 2.89 % Allowed : 28.82 % 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: 0.60 (0.29), residues: 914 helix: 1.36 (0.24), residues: 515 sheet: -0.11 (0.69), residues: 59 loop : -0.97 (0.34), residues: 340 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 0.022 0.001 PHE C 180 TYR 0.016 0.001 TYR C 626 ARG 0.003 0.000 ARG C 150 ********************** 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 85 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: C 194 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8653 (tttp) REVERT: C 196 GLN cc_start: 0.8318 (tm130) cc_final: 0.8019 (tm-30) REVERT: C 438 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.6453 (mp) REVERT: C 948 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8777 (mp) REVERT: C 1097 MET cc_start: 0.8258 (tmm) cc_final: 0.7755 (tmm) outliers start: 22 outliers final: 17 residues processed: 82 average time/residue: 0.1848 time to fit residues: 23.1520 Evaluate side-chains 80 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ASP 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 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 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: 5.9990 chunk 75 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 83 optimal weight: 0.1980 chunk 64 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.105102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.077922 restraints weight = 31971.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.079921 restraints weight = 17757.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.081188 restraints weight = 12719.176| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10302 Z= 0.277 Angle : 0.649 12.677 14470 Z= 0.338 Chirality : 0.038 0.169 1633 Planarity : 0.004 0.054 1419 Dihedral : 23.767 173.554 2569 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.69 % Favored : 93.98 % Rotamer: Outliers : 3.16 % Allowed : 28.68 % Favored : 68.16 % 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: 0.37 (0.29), residues: 914 helix: 1.15 (0.24), residues: 519 sheet: -0.23 (0.70), residues: 59 loop : -1.07 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 701 HIS 0.010 0.001 HIS C 751 PHE 0.020 0.002 PHE C 597 TYR 0.019 0.002 TYR C 626 ARG 0.003 0.000 ARG C 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2958.73 seconds wall clock time: 53 minutes 52.21 seconds (3232.21 seconds total)