Starting phenix.real_space_refine on Fri Jul 3 04:21:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d4a_27179/07_2026/8d4a_27179.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d4a_27179/07_2026/8d4a_27179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d4a_27179/07_2026/8d4a_27179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d4a_27179/07_2026/8d4a_27179.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8d4a_27179/07_2026/8d4a_27179.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d4a_27179/07_2026/8d4a_27179.cif" model { file = "/net/cci-nas-00/data/ceres_data/8d4a_27179/07_2026/8d4a_27179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d4a_27179/07_2026/8d4a_27179.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 90 5.49 5 Mg 2 5.21 5 S 30 5.16 5 C 7151 2.51 5 N 2026 2.21 5 O 2498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11798 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1207, 9880 Classifications: {'peptide': 1207} Link IDs: {'PTRANS': 29, 'TRANS': 1177} Chain breaks: 2 Chain: "B" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 870 Classifications: {'RNA': 41} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 5, 'rna3p': 35} Chain: "C" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 593 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 5, 'rna3p_pur': 8, 'rna3p_pyr': 15} Link IDs: {'rna2p': 4, 'rna3p': 23} Chain: "D" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 220 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "G" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 231 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9380 SG CYS A1170 55.459 39.309 111.834 1.00 28.74 S ATOM 9400 SG CYS A1173 56.581 41.503 114.636 1.00 30.25 S ATOM 9522 SG CYS A1188 58.987 38.971 113.049 1.00 36.82 S ATOM 9546 SG CYS A1191 56.134 37.742 115.244 1.00 40.43 S Time building chain proxies: 2.29, per 1000 atoms: 0.19 Number of scatterers: 11798 At special positions: 0 Unit cell: (115.62, 99.64, 125.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 30 16.00 P 90 15.00 Mg 2 11.99 O 2498 8.00 N 2026 7.00 C 7151 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 460.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1170 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1188 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1173 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1191 " Number of angles added : 6 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2306 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 10 sheets defined 55.5% alpha, 13.4% beta 28 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.648A pdb=" N THR A 6 " --> pdb=" O HIS A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 48 removed outlier: 3.797A pdb=" N SER A 48 " --> pdb=" O ASN A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 79 Processing helix chain 'A' and resid 92 through 102 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 128 through 163 removed outlier: 3.644A pdb=" N ILE A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 153 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 163 " --> pdb=" O ARG A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 170 removed outlier: 3.991A pdb=" N ALA A 167 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N HIS A 168 " --> pdb=" O ASP A 165 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS A 170 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 196 removed outlier: 4.101A pdb=" N ILE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.865A pdb=" N ILE A 204 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER A 205 " --> pdb=" O PRO A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 201 through 205' Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 222 through 239 removed outlier: 4.302A pdb=" N LEU A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 263 through 275 Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 299 through 305 Processing helix chain 'A' and resid 310 through 317 Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.599A pdb=" N LYS A 333 " --> pdb=" O HIS A 329 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU A 337 " --> pdb=" O LYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 352 Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 371 through 375 removed outlier: 3.514A pdb=" N TYR A 375 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 391 Processing helix chain 'A' and resid 399 through 412 Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'A' and resid 418 through 438 Processing helix chain 'A' and resid 446 through 460 removed outlier: 4.455A pdb=" N PHE A 450 " --> pdb=" O ASN A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 483 Processing helix chain 'A' and resid 486 through 503 removed outlier: 3.510A pdb=" N GLY A 503 " --> pdb=" O PHE A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 557 removed outlier: 3.769A pdb=" N GLN A 539 " --> pdb=" O ASN A 535 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 557 " --> pdb=" O ASP A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 560 No H-bonds generated for 'chain 'A' and resid 558 through 560' Processing helix chain 'A' and resid 591 through 598 Processing helix chain 'A' and resid 615 through 625 removed outlier: 3.629A pdb=" N LYS A 621 " --> pdb=" O LYS A 617 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A 625 " --> pdb=" O LYS A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 653 Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 661 through 675 removed outlier: 3.728A pdb=" N SER A 675 " --> pdb=" O CYS A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 681 Processing helix chain 'A' and resid 682 through 687 Processing helix chain 'A' and resid 695 through 707 Processing helix chain 'A' and resid 716 through 726 Processing helix chain 'A' and resid 747 through 757 removed outlier: 3.747A pdb=" N PHE A 757 " --> pdb=" O TRP A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'A' and resid 808 through 818 removed outlier: 3.736A pdb=" N ASP A 818 " --> pdb=" O GLU A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 838 Processing helix chain 'A' and resid 882 through 886 removed outlier: 3.504A pdb=" N SER A 886 " --> pdb=" O ARG A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 922 No H-bonds generated for 'chain 'A' and resid 920 through 922' Processing helix chain 'A' and resid 940 through 961 removed outlier: 4.010A pdb=" N LYS A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 945 " --> pdb=" O GLN A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 967 Processing helix chain 'A' and resid 968 through 970 No H-bonds generated for 'chain 'A' and resid 968 through 970' Processing helix chain 'A' and resid 974 through 983 Processing helix chain 'A' and resid 999 through 1016 Processing helix chain 'A' and resid 1019 through 1028 removed outlier: 3.693A pdb=" N ILE A1026 " --> pdb=" O GLU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1054 removed outlier: 3.681A pdb=" N ASN A1042 " --> pdb=" O GLY A1038 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET A1043 " --> pdb=" O ILE A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1100 Processing helix chain 'A' and resid 1105 through 1117 Processing helix chain 'A' and resid 1202 through 1209 removed outlier: 5.928A pdb=" N HIS A1207 " --> pdb=" O ASN A1204 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1232 removed outlier: 3.708A pdb=" N SER A1224 " --> pdb=" O ILE A1220 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A1230 " --> pdb=" O GLU A1226 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 18 removed outlier: 3.925A pdb=" N ALA A 770 " --> pdb=" O ALA A 794 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASN A 796 " --> pdb=" O GLU A 768 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU A 768 " --> pdb=" O ASN A 796 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE A 769 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LYS A 248 " --> pdb=" O PHE A 769 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A 771 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N HIS A 566 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LYS A 248 " --> pdb=" O HIS A 566 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLY A 568 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N THR A 250 " --> pdb=" O GLY A 568 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE A 570 " --> pdb=" O THR A 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 708 through 715 removed outlier: 6.651A pdb=" N VAL A 611 " --> pdb=" O GLY A 568 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N GLY A 568 " --> pdb=" O VAL A 611 " (cutoff:3.500A) removed outlier: 14.983A pdb=" N SER A 613 " --> pdb=" O HIS A 566 " (cutoff:3.500A) removed outlier: 17.816A pdb=" N HIS A 566 " --> pdb=" O SER A 613 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N HIS A 566 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LYS A 248 " --> pdb=" O HIS A 566 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLY A 568 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N THR A 250 " --> pdb=" O GLY A 568 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE A 570 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A 771 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LYS A 248 " --> pdb=" O PHE A 769 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE A 769 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU A 768 " --> pdb=" O ASN A 796 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASN A 796 " --> pdb=" O GLU A 768 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA A 770 " --> pdb=" O ALA A 794 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 115 Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 123 Processing sheet with id=AA5, first strand: chain 'A' and resid 866 through 867 removed outlier: 4.372A pdb=" N VAL A 859 " --> pdb=" O LEU A 867 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 866 through 867 removed outlier: 4.372A pdb=" N VAL A 859 " --> pdb=" O LEU A 867 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLU A1063 " --> pdb=" O ILE A 847 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ARG A 849 " --> pdb=" O GLU A1063 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 887 through 896 removed outlier: 6.782A pdb=" N ILE A 872 " --> pdb=" O ALA A 893 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR A 895 " --> pdb=" O PHE A 870 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE A 870 " --> pdb=" O THR A 895 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N GLU A 871 " --> pdb=" O LYS A 914 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU A 916 " --> pdb=" O GLU A 871 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LYS A 875 " --> pdb=" O ASP A 918 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1072 through 1073 Processing sheet with id=AA9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB1, first strand: chain 'A' and resid 1178 through 1180 520 hydrogen bonds defined for protein. 1470 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 1.12 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: 2645 1.33 - 1.45: 2991 1.45 - 1.57: 6357 1.57 - 1.69: 177 1.69 - 1.81: 43 Bond restraints: 12213 Sorted by residual: bond pdb=" C3' DA G 3 " pdb=" C2' DA G 3 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.19e+00 bond pdb=" C3' DT D 5 " pdb=" O3' DT D 5 " ideal model delta sigma weight residual 1.435 1.474 -0.039 1.30e-02 5.92e+03 9.01e+00 bond pdb=" C3' DA G 4 " pdb=" C2' DA G 4 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.54e+00 bond pdb=" C1' DT D 7 " pdb=" N1 DT D 7 " ideal model delta sigma weight residual 1.468 1.498 -0.030 1.40e-02 5.10e+03 4.63e+00 bond pdb=" C3' DA G 9 " pdb=" O3' DA G 9 " ideal model delta sigma weight residual 1.435 1.407 0.028 1.30e-02 5.92e+03 4.49e+00 ... (remaining 12208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 16447 2.01 - 4.02: 379 4.02 - 6.03: 39 6.03 - 8.04: 7 8.04 - 10.04: 2 Bond angle restraints: 16874 Sorted by residual: angle pdb=" N3 DT D 10 " pdb=" C4 DT D 10 " pdb=" O4 DT D 10 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT D 11 " pdb=" C4 DT D 11 " pdb=" O4 DT D 11 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT D 6 " pdb=" C4 DT D 6 " pdb=" O4 DT D 6 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT D 5 " pdb=" C4 DT D 5 " pdb=" O4 DT D 5 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT D 1 " pdb=" C4 DT D 1 " pdb=" O4 DT D 1 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 16869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 6995 35.27 - 70.54: 209 70.54 - 105.81: 9 105.81 - 141.08: 0 141.08 - 176.35: 3 Dihedral angle restraints: 7216 sinusoidal: 3648 harmonic: 3568 Sorted by residual: dihedral pdb=" O4' U B 14 " pdb=" C1' U B 14 " pdb=" N1 U B 14 " pdb=" C2 U B 14 " ideal model delta sinusoidal sigma weight residual 200.00 48.75 151.25 1 1.50e+01 4.44e-03 8.01e+01 dihedral pdb=" CA ILE A 734 " pdb=" C ILE A 734 " pdb=" N ASN A 735 " pdb=" CA ASN A 735 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA TYR A1139 " pdb=" C TYR A1139 " pdb=" N ARG A1140 " pdb=" CA ARG A1140 " ideal model delta harmonic sigma weight residual 180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 7213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1645 0.066 - 0.132: 232 0.132 - 0.199: 15 0.199 - 0.265: 1 0.265 - 0.331: 1 Chirality restraints: 1894 Sorted by residual: chirality pdb=" C3' G B 41 " pdb=" C4' G B 41 " pdb=" O3' G B 41 " pdb=" C2' G B 41 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA ASN A1227 " pdb=" N ASN A1227 " pdb=" C ASN A1227 " pdb=" CB ASN A1227 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C1' U B 14 " pdb=" O4' U B 14 " pdb=" C2' U B 14 " pdb=" N1 U B 14 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 8.08e-01 ... (remaining 1891 not shown) Planarity restraints: 1841 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 337 " -0.044 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO A 338 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 338 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 338 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 255 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C THR A 255 " -0.037 2.00e-02 2.50e+03 pdb=" O THR A 255 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA A 256 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 170 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO A 171 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 171 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 171 " 0.027 5.00e-02 4.00e+02 ... (remaining 1838 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 219 2.66 - 3.22: 10073 3.22 - 3.78: 19328 3.78 - 4.34: 28550 4.34 - 4.90: 43674 Nonbonded interactions: 101844 Sorted by model distance: nonbonded pdb=" OE2 GLU A1063 " pdb="MG MG A1302 " model vdw 2.098 2.170 nonbonded pdb=" OE1 GLU A1063 " pdb="MG MG A1302 " model vdw 2.106 2.170 nonbonded pdb=" OD1 ASP A 848 " pdb="MG MG A1302 " model vdw 2.130 2.170 nonbonded pdb=" O PHE A 218 " pdb=" OH TYR A 223 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR A 393 " pdb=" OD1 ASP A 426 " model vdw 2.260 3.040 ... (remaining 101839 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.800 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 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 : 0.006 0.053 12217 Z= 0.287 Angle : 0.728 10.044 16880 Z= 0.453 Chirality : 0.045 0.331 1894 Planarity : 0.004 0.066 1841 Dihedral : 15.537 176.354 4910 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.09 % Allowed : 0.00 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.22), residues: 1201 helix: -0.14 (0.19), residues: 603 sheet: -0.25 (0.40), residues: 155 loop : -0.35 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 357 TYR 0.019 0.002 TYR A1139 PHE 0.023 0.003 PHE A 757 TRP 0.011 0.002 TRP A 480 HIS 0.005 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.29 (12213) covalent geometry : angle 0.72791 / 0.45 (16874) hydrogen bonds : bond 0.17279 / 11.43 ( 577) hydrogen bonds : angle 6.16489 / 4.26 ( 1598) metal coordination : bond 0.00623 / 0.31 ( 4) metal coordination : angle 1.69200 / 0.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.448 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.9517 time to fit residues: 111.1453 Evaluate side-chains 42 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0270 chunk 66 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 587 HIS A1086 GLN A1210 HIS A1230 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.077791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.058782 restraints weight = 21215.188| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 2.03 r_work: 0.2574 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2451 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12217 Z= 0.184 Angle : 0.570 7.809 16880 Z= 0.316 Chirality : 0.041 0.215 1894 Planarity : 0.004 0.039 1841 Dihedral : 14.320 161.679 2387 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.01 % Allowed : 5.96 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.24), residues: 1201 helix: 0.87 (0.21), residues: 611 sheet: -0.49 (0.38), residues: 157 loop : -0.08 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 660 TYR 0.016 0.001 TYR A 544 PHE 0.018 0.001 PHE A 180 TRP 0.009 0.001 TRP A 78 HIS 0.003 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (12213) covalent geometry : angle 0.57014 / 0.32 (16874) hydrogen bonds : bond 0.05283 / 3.56 ( 577) hydrogen bonds : angle 4.35719 / 3.01 ( 1598) metal coordination : bond 0.00568 / 0.29 ( 4) metal coordination : angle 1.12153 / 0.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.422 Fit side-chains REVERT: A 840 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8368 (mmpt) REVERT: A 861 ASP cc_start: 0.8538 (t70) cc_final: 0.8170 (t0) outliers start: 11 outliers final: 3 residues processed: 53 average time/residue: 0.7350 time to fit residues: 42.0614 Evaluate side-chains 47 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 840 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 127 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 18 optimal weight: 0.4980 chunk 98 optimal weight: 0.6980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 HIS A 887 HIS A1159 HIS A1230 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.076803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.057936 restraints weight = 21542.748| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 2.01 r_work: 0.2531 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2405 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 12217 Z= 0.215 Angle : 0.539 7.432 16880 Z= 0.301 Chirality : 0.042 0.258 1894 Planarity : 0.003 0.039 1841 Dihedral : 14.359 162.999 2387 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.82 % Allowed : 6.60 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.24), residues: 1201 helix: 1.37 (0.21), residues: 606 sheet: -0.50 (0.39), residues: 157 loop : 0.10 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 660 TYR 0.017 0.001 TYR A 544 PHE 0.017 0.002 PHE A 180 TRP 0.010 0.001 TRP A 480 HIS 0.003 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (12213) covalent geometry : angle 0.53912 / 0.30 (16874) hydrogen bonds : bond 0.04842 / 3.27 ( 577) hydrogen bonds : angle 4.09136 / 2.81 ( 1598) metal coordination : bond 0.00645 / 0.32 ( 4) metal coordination : angle 0.93133 / 0.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.436 Fit side-chains REVERT: A 442 ASN cc_start: 0.8138 (m110) cc_final: 0.7730 (m-40) REVERT: A 630 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8051 (mtpm) REVERT: A 674 ASP cc_start: 0.8846 (m-30) cc_final: 0.8630 (m-30) REVERT: A 861 ASP cc_start: 0.8589 (t70) cc_final: 0.8297 (t0) REVERT: A 993 GLN cc_start: 0.8757 (tt0) cc_final: 0.8551 (tt0) outliers start: 9 outliers final: 5 residues processed: 55 average time/residue: 0.7117 time to fit residues: 42.1819 Evaluate side-chains 48 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 1231 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 110 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1086 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.075976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.057083 restraints weight = 21393.976| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 2.01 r_work: 0.2514 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2389 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 12217 Z= 0.246 Angle : 0.548 7.445 16880 Z= 0.305 Chirality : 0.043 0.356 1894 Planarity : 0.003 0.036 1841 Dihedral : 14.339 150.169 2387 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.01 % Allowed : 7.97 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.25), residues: 1201 helix: 1.54 (0.21), residues: 605 sheet: -0.54 (0.38), residues: 157 loop : 0.09 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 307 TYR 0.018 0.001 TYR A 544 PHE 0.018 0.002 PHE A 757 TRP 0.010 0.001 TRP A 480 HIS 0.003 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.25 (12213) covalent geometry : angle 0.54715 / 0.30 (16874) hydrogen bonds : bond 0.04739 / 3.18 ( 577) hydrogen bonds : angle 4.03607 / 2.77 ( 1598) metal coordination : bond 0.00725 / 0.37 ( 4) metal coordination : angle 1.18717 / 0.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.420 Fit side-chains REVERT: A 442 ASN cc_start: 0.8300 (m110) cc_final: 0.7973 (m-40) REVERT: A 630 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8104 (mtpm) REVERT: A 674 ASP cc_start: 0.8834 (m-30) cc_final: 0.8630 (m-30) REVERT: A 840 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8444 (mmpt) REVERT: A 861 ASP cc_start: 0.8586 (t70) cc_final: 0.8326 (t0) REVERT: A 1200 LYS cc_start: 0.8244 (tttt) cc_final: 0.7867 (mppt) outliers start: 11 outliers final: 4 residues processed: 55 average time/residue: 0.6761 time to fit residues: 40.1661 Evaluate side-chains 48 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 96 optimal weight: 0.1980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.077991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.059110 restraints weight = 21334.421| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 2.04 r_work: 0.2562 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2436 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12217 Z= 0.131 Angle : 0.491 7.354 16880 Z= 0.273 Chirality : 0.039 0.221 1894 Planarity : 0.003 0.032 1841 Dihedral : 14.290 148.896 2387 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.01 % Allowed : 8.71 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.25), residues: 1201 helix: 1.68 (0.21), residues: 606 sheet: -0.47 (0.39), residues: 157 loop : 0.15 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 307 TYR 0.016 0.001 TYR A 544 PHE 0.015 0.001 PHE A 180 TRP 0.011 0.001 TRP A 480 HIS 0.003 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (12213) covalent geometry : angle 0.49039 / 0.27 (16874) hydrogen bonds : bond 0.04054 / 2.74 ( 577) hydrogen bonds : angle 3.83140 / 2.62 ( 1598) metal coordination : bond 0.00501 / 0.25 ( 4) metal coordination : angle 0.75581 / 0.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.406 Fit side-chains REVERT: A 225 GLN cc_start: 0.7895 (mp10) cc_final: 0.7586 (mp10) REVERT: A 442 ASN cc_start: 0.8287 (m110) cc_final: 0.7931 (m110) REVERT: A 630 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8059 (mtpm) REVERT: A 711 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8822 (mm-40) REVERT: A 861 ASP cc_start: 0.8545 (t70) cc_final: 0.8340 (t0) REVERT: A 1147 GLU cc_start: 0.8457 (pm20) cc_final: 0.8104 (pm20) REVERT: A 1200 LYS cc_start: 0.8229 (tttt) cc_final: 0.7897 (mppt) outliers start: 11 outliers final: 4 residues processed: 61 average time/residue: 0.6754 time to fit residues: 44.5371 Evaluate side-chains 54 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 689 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.075279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.056416 restraints weight = 21479.570| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 2.02 r_work: 0.2498 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2372 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 12217 Z= 0.301 Angle : 0.562 7.284 16880 Z= 0.310 Chirality : 0.043 0.255 1894 Planarity : 0.003 0.033 1841 Dihedral : 14.269 149.883 2387 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.19 % Allowed : 9.35 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.25), residues: 1201 helix: 1.69 (0.21), residues: 605 sheet: -0.57 (0.38), residues: 157 loop : 0.14 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 307 TYR 0.019 0.001 TYR A 544 PHE 0.019 0.002 PHE A 757 TRP 0.008 0.001 TRP A 480 HIS 0.004 0.001 HIS A1219 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.30 (12213) covalent geometry : angle 0.56204 / 0.31 (16874) hydrogen bonds : bond 0.04822 / 3.23 ( 577) hydrogen bonds : angle 3.94217 / 2.70 ( 1598) metal coordination : bond 0.00805 / 0.41 ( 4) metal coordination : angle 1.31630 / 0.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.424 Fit side-chains REVERT: A 442 ASN cc_start: 0.8436 (m110) cc_final: 0.8106 (m110) REVERT: A 630 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8135 (mtpm) REVERT: A 711 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8836 (mm-40) REVERT: A 840 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8588 (mmpt) REVERT: A 861 ASP cc_start: 0.8644 (t70) cc_final: 0.8432 (t0) REVERT: A 1200 LYS cc_start: 0.8300 (tttt) cc_final: 0.7934 (mppt) outliers start: 13 outliers final: 7 residues processed: 55 average time/residue: 0.6661 time to fit residues: 39.7099 Evaluate side-chains 53 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1231 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 109 optimal weight: 0.2980 chunk 68 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 119 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.077779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.058979 restraints weight = 21257.694| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 2.02 r_work: 0.2557 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2432 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12217 Z= 0.129 Angle : 0.497 7.738 16880 Z= 0.276 Chirality : 0.038 0.222 1894 Planarity : 0.003 0.031 1841 Dihedral : 14.245 148.701 2387 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.92 % Allowed : 9.72 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.25), residues: 1201 helix: 1.84 (0.21), residues: 605 sheet: -0.47 (0.39), residues: 157 loop : 0.21 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 307 TYR 0.016 0.001 TYR A 544 PHE 0.015 0.001 PHE A 180 TRP 0.011 0.001 TRP A 480 HIS 0.003 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (12213) covalent geometry : angle 0.49643 / 0.28 (16874) hydrogen bonds : bond 0.04032 / 2.73 ( 577) hydrogen bonds : angle 3.79126 / 2.59 ( 1598) metal coordination : bond 0.00462 / 0.23 ( 4) metal coordination : angle 0.73030 / 0.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.282 Fit side-chains REVERT: A 442 ASN cc_start: 0.8284 (m110) cc_final: 0.7949 (m110) REVERT: A 711 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8785 (mm-40) REVERT: A 1200 LYS cc_start: 0.8203 (tttt) cc_final: 0.7852 (mppt) outliers start: 10 outliers final: 5 residues processed: 55 average time/residue: 0.6264 time to fit residues: 37.4220 Evaluate side-chains 49 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 88 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 7 optimal weight: 0.0010 chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 956 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.078949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.059907 restraints weight = 21122.914| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 2.09 r_work: 0.2612 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2485 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12217 Z= 0.129 Angle : 0.497 10.669 16880 Z= 0.275 Chirality : 0.038 0.222 1894 Planarity : 0.003 0.037 1841 Dihedral : 14.171 148.385 2387 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.01 % Allowed : 9.62 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.25), residues: 1201 helix: 1.91 (0.21), residues: 607 sheet: -0.32 (0.39), residues: 157 loop : 0.24 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 307 TYR 0.015 0.001 TYR A 544 PHE 0.015 0.001 PHE A 180 TRP 0.010 0.001 TRP A 480 HIS 0.003 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (12213) covalent geometry : angle 0.49691 / 0.27 (16874) hydrogen bonds : bond 0.03862 / 2.62 ( 577) hydrogen bonds : angle 3.72141 / 2.55 ( 1598) metal coordination : bond 0.00472 / 0.24 ( 4) metal coordination : angle 0.88679 / 0.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.408 Fit side-chains REVERT: A 122 MET cc_start: 0.8973 (mmt) cc_final: 0.8732 (mmm) REVERT: A 442 ASN cc_start: 0.8315 (m110) cc_final: 0.7985 (m110) REVERT: A 630 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8092 (mtpm) REVERT: A 711 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8856 (mm-40) REVERT: A 840 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8601 (mmpt) REVERT: A 1200 LYS cc_start: 0.8255 (tttt) cc_final: 0.7919 (mppt) REVERT: A 1211 ASN cc_start: 0.8278 (m-40) cc_final: 0.7865 (p0) outliers start: 11 outliers final: 5 residues processed: 57 average time/residue: 0.5796 time to fit residues: 35.9483 Evaluate side-chains 56 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 4 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.078379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.059527 restraints weight = 20904.721| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 2.01 r_work: 0.2606 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12217 Z= 0.154 Angle : 0.508 10.005 16880 Z= 0.279 Chirality : 0.039 0.227 1894 Planarity : 0.003 0.036 1841 Dihedral : 14.171 148.615 2387 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.10 % Allowed : 9.81 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.25), residues: 1201 helix: 1.95 (0.21), residues: 607 sheet: -0.38 (0.39), residues: 157 loop : 0.26 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 307 TYR 0.016 0.001 TYR A 544 PHE 0.014 0.001 PHE A 180 TRP 0.011 0.001 TRP A 480 HIS 0.003 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (12213) covalent geometry : angle 0.50739 / 0.28 (16874) hydrogen bonds : bond 0.03965 / 2.68 ( 577) hydrogen bonds : angle 3.73048 / 2.55 ( 1598) metal coordination : bond 0.00527 / 0.27 ( 4) metal coordination : angle 0.87569 / 0.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.457 Fit side-chains REVERT: A 122 MET cc_start: 0.8946 (mmt) cc_final: 0.8698 (mmm) REVERT: A 442 ASN cc_start: 0.8406 (m110) cc_final: 0.8098 (m110) REVERT: A 630 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8077 (mtpm) REVERT: A 840 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8673 (mmpt) REVERT: A 1200 LYS cc_start: 0.8271 (tttt) cc_final: 0.7954 (mppt) REVERT: A 1211 ASN cc_start: 0.8357 (m-40) cc_final: 0.7965 (p0) outliers start: 12 outliers final: 6 residues processed: 56 average time/residue: 0.5925 time to fit residues: 35.9778 Evaluate side-chains 53 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 13 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.078654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.059780 restraints weight = 21251.607| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 2.02 r_work: 0.2611 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12217 Z= 0.143 Angle : 0.504 9.409 16880 Z= 0.277 Chirality : 0.038 0.223 1894 Planarity : 0.003 0.039 1841 Dihedral : 14.176 148.471 2387 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.82 % Allowed : 10.08 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.25), residues: 1201 helix: 1.95 (0.21), residues: 608 sheet: -0.34 (0.39), residues: 157 loop : 0.27 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 307 TYR 0.016 0.001 TYR A 544 PHE 0.014 0.001 PHE A 180 TRP 0.011 0.001 TRP A 480 HIS 0.003 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (12213) covalent geometry : angle 0.50382 / 0.28 (16874) hydrogen bonds : bond 0.03907 / 2.65 ( 577) hydrogen bonds : angle 3.71473 / 2.54 ( 1598) metal coordination : bond 0.00483 / 0.24 ( 4) metal coordination : angle 0.80702 / 0.34 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.418 Fit side-chains REVERT: A 122 MET cc_start: 0.8901 (mmt) cc_final: 0.8644 (mmm) REVERT: A 442 ASN cc_start: 0.8428 (m110) cc_final: 0.8117 (m110) REVERT: A 630 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8081 (mtpm) REVERT: A 840 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8640 (mmpt) REVERT: A 1200 LYS cc_start: 0.8264 (tttt) cc_final: 0.7946 (mppt) REVERT: A 1211 ASN cc_start: 0.8331 (m-40) cc_final: 0.7961 (p0) outliers start: 9 outliers final: 5 residues processed: 57 average time/residue: 0.6064 time to fit residues: 37.7139 Evaluate side-chains 53 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.078627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.059620 restraints weight = 21045.037| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 2.06 r_work: 0.2603 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2476 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12217 Z= 0.148 Angle : 0.501 9.222 16880 Z= 0.276 Chirality : 0.038 0.225 1894 Planarity : 0.003 0.063 1841 Dihedral : 14.175 148.511 2387 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.92 % Allowed : 9.99 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.25), residues: 1201 helix: 1.96 (0.21), residues: 609 sheet: -0.34 (0.39), residues: 157 loop : 0.27 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 307 TYR 0.016 0.001 TYR A 544 PHE 0.014 0.001 PHE A 180 TRP 0.011 0.001 TRP A 480 HIS 0.003 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (12213) covalent geometry : angle 0.50128 / 0.28 (16874) hydrogen bonds : bond 0.03934 / 2.67 ( 577) hydrogen bonds : angle 3.71669 / 2.54 ( 1598) metal coordination : bond 0.00502 / 0.25 ( 4) metal coordination : angle 0.84017 / 0.37 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3075.05 seconds wall clock time: 53 minutes 28.03 seconds (3208.03 seconds total)