Starting phenix.real_space_refine on Fri Sep 11 22:43:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d4a_27179/09_2026/8d4a_27179.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d4a_27179/09_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_27179/09_2026/8d4a_27179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d4a_27179/09_2026/8d4a_27179.map" model { file = "/net/cci-nas-00/data/ceres_data/8d4a_27179/09_2026/8d4a_27179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d4a_27179/09_2026/8d4a_27179.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8d4a_27179/09_2026/8d4a_27179.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d4a_27179/09_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-2.2.1-6174/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: {'RNAv2': 41} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 5, 'rna3p': 35} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 593 Classifications: {'RNAv2': 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: 2.33, per 1000 atoms: 0.20 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: 0.78 Conformation dependent library (CDL) restraints added in 556.1 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: 1.73 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: 3.32 Time building geometry restraints manager: 1.14 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: 16268 2.01 - 4.02: 531 4.02 - 6.03: 66 6.03 - 8.04: 7 8.04 - 10.04: 2 Bond angle restraints: 16874 Sorted by residual: angle pdb=" C3' G B 41 " pdb=" O3' G B 41 " pdb=" P G B 42 " ideal model delta sigma weight residual 119.70 124.93 -5.23 1.20e+00 6.94e-01 1.90e+01 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 ... (remaining 16869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 6909 35.27 - 70.54: 287 70.54 - 105.81: 18 105.81 - 141.08: 0 141.08 - 176.35: 2 Dihedral angle restraints: 7216 sinusoidal: 3648 harmonic: 3568 Sorted by residual: dihedral pdb=" C4' U B 5 " pdb=" C3' U B 5 " pdb=" C2' U B 5 " pdb=" C1' U B 5 " ideal model delta sinusoidal sigma weight residual 36.34 -38.67 75.02 1 3.10e+00 1.04e-01 7.41e+02 dihedral pdb=" C4' A C 23 " pdb=" C3' A C 23 " pdb=" C2' A C 23 " pdb=" C1' A C 23 " ideal model delta sinusoidal sigma weight residual 36.35 -37.79 74.14 1 3.10e+00 1.04e-01 7.26e+02 dihedral pdb=" C4' G C 21 " pdb=" C3' G C 21 " pdb=" C2' G C 21 " pdb=" C1' G C 21 " ideal model delta sinusoidal sigma weight residual 36.34 -37.30 73.64 1 3.10e+00 1.04e-01 7.18e+02 ... (remaining 7213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1598 0.070 - 0.141: 197 0.141 - 0.211: 40 0.211 - 0.282: 50 0.282 - 0.352: 9 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 -2.50 -2.15 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" C3' A C 23 " pdb=" C4' A C 23 " pdb=" O3' A C 23 " pdb=" C2' A C 23 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C2' A B 13 " pdb=" C3' A B 13 " pdb=" O2' A B 13 " pdb=" C1' A B 13 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.30e+00 ... (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: 0.000 Normalize map: mean=0, sd=1: 5.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.790 Find NCS groups from input model: 0.070 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:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.320 ------------------------------------------------------------------------------- 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= 0.289 Angle : 0.810 10.044 16880 Z= 0.470 Chirality : 0.067 0.352 1894 Planarity : 0.004 0.066 1841 Dihedral : 17.045 176.354 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 0.00591 / 0.29 (12213) covalent geometry : angle 0.80968 / 0.47 (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 : 0.354 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.9985 time to fit residues: 116.7931 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 : 0.331 ------------------------------------------------------------------------------- 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: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 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 = 0.3052 r_free = 0.3052 target = 0.078719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.059878 restraints weight = 21193.981| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 2.02 r_work: 0.2586 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2462 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12217 Z= 0.212 Angle : 0.906 23.249 16880 Z= 0.418 Chirality : 0.090 1.397 1894 Planarity : 0.004 0.043 1841 Dihedral : 15.831 163.706 2387 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.01 % Allowed : 6.23 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.40 (0.24), residues: 1201 helix: 0.85 (0.21), residues: 611 sheet: -0.48 (0.38), residues: 157 loop : -0.10 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 660 TYR 0.017 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 0.00455 / 0.21 (12213) covalent geometry : angle 0.90542 / 0.42 (16874) hydrogen bonds : bond 0.05450 / 3.59 ( 577) hydrogen bonds : angle 4.37032 / 3.02 ( 1598) metal coordination : bond 0.00536 / 0.27 ( 4) metal coordination : angle 1.15446 / 0.55 ( 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 : 0.362 Fit side-chains REVERT: A 840 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8407 (mmpt) REVERT: A 861 ASP cc_start: 0.8555 (t70) cc_final: 0.8193 (t0) outliers start: 11 outliers final: 2 residues processed: 52 average time/residue: 0.7751 time to fit residues: 43.3388 Evaluate side-chains 46 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 109 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 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: 2.9990 chunk 18 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3031 r_free = 0.3031 target = 0.077352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.058642 restraints weight = 21555.652| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 2.01 r_work: 0.2566 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2437 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 12217 Z= 0.266 Angle : 0.763 13.255 16880 Z= 0.370 Chirality : 0.071 0.952 1894 Planarity : 0.004 0.041 1841 Dihedral : 16.038 165.093 2387 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.92 % Allowed : 7.06 % Favored : 92.03 % 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: 0.83 (0.24), residues: 1201 helix: 1.31 (0.21), residues: 606 sheet: -0.53 (0.38), residues: 157 loop : 0.05 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 507 TYR 0.018 0.001 TYR A 544 PHE 0.018 0.002 PHE A 757 TRP 0.009 0.001 TRP A 480 HIS 0.003 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.27 (12213) covalent geometry : angle 0.76249 / 0.37 (16874) hydrogen bonds : bond 0.05248 / 3.48 ( 577) hydrogen bonds : angle 4.15301 / 2.86 ( 1598) metal coordination : bond 0.00724 / 0.36 ( 4) metal coordination : angle 1.05207 / 0.47 ( 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 58 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.445 Fit side-chains REVERT: A 366 ASN cc_start: 0.8864 (t0) cc_final: 0.8654 (t0) REVERT: A 368 GLU cc_start: 0.8200 (pm20) cc_final: 0.7879 (pm20) REVERT: A 442 ASN cc_start: 0.8321 (m110) cc_final: 0.7945 (m-40) REVERT: A 630 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8067 (mtpm) REVERT: A 674 ASP cc_start: 0.8893 (m-30) cc_final: 0.8657 (m-30) REVERT: A 861 ASP cc_start: 0.8669 (t70) cc_final: 0.8386 (t0) outliers start: 10 outliers final: 4 residues processed: 53 average time/residue: 0.7250 time to fit residues: 41.5515 Evaluate side-chains 47 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 31 optimal weight: 0.0770 chunk 125 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.3071 r_free = 0.3071 target = 0.079566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.060858 restraints weight = 21223.149| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.03 r_work: 0.2598 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12217 Z= 0.156 Angle : 0.662 9.333 16880 Z= 0.325 Chirality : 0.061 0.697 1894 Planarity : 0.003 0.038 1841 Dihedral : 16.146 156.685 2387 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.82 % Allowed : 8.43 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.24), residues: 1201 helix: 1.57 (0.21), residues: 605 sheet: -0.41 (0.38), residues: 157 loop : 0.10 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 307 TYR 0.016 0.001 TYR A 544 PHE 0.016 0.001 PHE A 180 TRP 0.010 0.001 TRP A 480 HIS 0.004 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (12213) covalent geometry : angle 0.66234 / 0.32 (16874) hydrogen bonds : bond 0.04373 / 2.87 ( 577) hydrogen bonds : angle 3.94726 / 2.71 ( 1598) metal coordination : bond 0.00521 / 0.26 ( 4) metal coordination : angle 0.87801 / 0.36 ( 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 66 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.494 Fit side-chains REVERT: A 103 ARG cc_start: 0.8783 (mtt-85) cc_final: 0.8225 (mtt-85) REVERT: A 442 ASN cc_start: 0.8231 (m110) cc_final: 0.7894 (m-40) REVERT: A 861 ASP cc_start: 0.8578 (t70) cc_final: 0.8346 (t0) REVERT: A 1211 ASN cc_start: 0.8401 (m110) cc_final: 0.8200 (m-40) outliers start: 9 outliers final: 3 residues processed: 64 average time/residue: 0.6609 time to fit residues: 45.8831 Evaluate side-chains 51 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 601 ASP 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: 1.9990 chunk 28 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 96 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3050 r_free = 0.3050 target = 0.078315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.059640 restraints weight = 21364.165| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 2.01 r_work: 0.2569 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2443 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 12217 Z= 0.215 Angle : 0.679 8.555 16880 Z= 0.333 Chirality : 0.062 0.649 1894 Planarity : 0.003 0.035 1841 Dihedral : 16.033 145.587 2387 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.92 % Allowed : 8.80 % 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: 1.20 (0.25), residues: 1201 helix: 1.69 (0.21), residues: 605 sheet: -0.44 (0.38), residues: 157 loop : 0.14 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 307 TYR 0.017 0.001 TYR A 544 PHE 0.016 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 0.00483 / 0.22 (12213) covalent geometry : angle 0.67917 / 0.33 (16874) hydrogen bonds : bond 0.04592 / 3.03 ( 577) hydrogen bonds : angle 3.90511 / 2.68 ( 1598) metal coordination : bond 0.00636 / 0.32 ( 4) metal coordination : angle 1.06326 / 0.47 ( 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 62 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.446 Fit side-chains REVERT: A 103 ARG cc_start: 0.8694 (mtt-85) cc_final: 0.7837 (mtt-85) REVERT: A 442 ASN cc_start: 0.8297 (m110) cc_final: 0.7945 (m-40) REVERT: A 630 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8123 (mtpm) REVERT: A 711 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8783 (mm-40) REVERT: A 840 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8522 (mmpt) REVERT: A 861 ASP cc_start: 0.8547 (t70) cc_final: 0.8311 (t0) REVERT: A 1200 LYS cc_start: 0.8212 (tttt) cc_final: 0.7839 (mppt) outliers start: 10 outliers final: 3 residues processed: 58 average time/residue: 0.6807 time to fit residues: 42.6809 Evaluate side-chains 52 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 711 GLN Chi-restraints excluded: chain A residue 840 LYS 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: 1.9990 chunk 22 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3061 r_free = 0.3061 target = 0.078858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.060148 restraints weight = 21305.002| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 2.02 r_work: 0.2585 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 12217 Z= 0.186 Angle : 0.650 9.084 16880 Z= 0.319 Chirality : 0.059 0.596 1894 Planarity : 0.003 0.036 1841 Dihedral : 16.011 145.018 2387 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.28 % Allowed : 8.80 % Favored : 89.92 % 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: 1.27 (0.25), residues: 1201 helix: 1.77 (0.21), residues: 605 sheet: -0.43 (0.38), residues: 157 loop : 0.15 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 307 TYR 0.017 0.001 TYR A 544 PHE 0.015 0.001 PHE A 180 TRP 0.010 0.001 TRP A 480 HIS 0.004 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (12213) covalent geometry : angle 0.65008 / 0.32 (16874) hydrogen bonds : bond 0.04374 / 2.88 ( 577) hydrogen bonds : angle 3.83292 / 2.62 ( 1598) metal coordination : bond 0.00567 / 0.28 ( 4) metal coordination : angle 0.88584 / 0.38 ( 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 67 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.294 Fit side-chains REVERT: A 103 ARG cc_start: 0.8677 (mtt-85) cc_final: 0.8042 (mtt-85) REVERT: A 225 GLN cc_start: 0.7943 (mp10) cc_final: 0.7658 (mp10) REVERT: A 442 ASN cc_start: 0.8339 (m110) cc_final: 0.7985 (m110) REVERT: A 630 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8117 (mtpm) REVERT: A 711 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8819 (mm-40) REVERT: A 840 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8537 (mmpt) REVERT: A 1200 LYS cc_start: 0.8267 (tttt) cc_final: 0.7912 (mppt) outliers start: 14 outliers final: 5 residues processed: 61 average time/residue: 0.6927 time to fit residues: 45.5322 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 : 0.359 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 53 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 109 optimal weight: 0.0980 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 57 optimal weight: 0.3980 chunk 119 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.080707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.062058 restraints weight = 21151.506| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 2.03 r_work: 0.2627 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12217 Z= 0.130 Angle : 0.617 9.268 16880 Z= 0.306 Chirality : 0.054 0.503 1894 Planarity : 0.003 0.031 1841 Dihedral : 15.948 142.630 2387 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.92 % Allowed : 9.35 % Favored : 89.73 % 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: 1.37 (0.25), residues: 1201 helix: 1.85 (0.21), residues: 606 sheet: -0.29 (0.39), residues: 157 loop : 0.15 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 307 TYR 0.015 0.001 TYR A 544 PHE 0.014 0.001 PHE A 180 TRP 0.011 0.001 TRP A 480 HIS 0.004 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (12213) covalent geometry : angle 0.61715 / 0.31 (16874) hydrogen bonds : bond 0.04001 / 2.63 ( 577) hydrogen bonds : angle 3.74806 / 2.57 ( 1598) metal coordination : bond 0.00421 / 0.21 ( 4) metal coordination : angle 0.61649 / 0.24 ( 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 61 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.469 Fit side-chains REVERT: A 103 ARG cc_start: 0.8662 (mtt-85) cc_final: 0.8044 (mtt-85) REVERT: A 225 GLN cc_start: 0.7965 (mp10) cc_final: 0.7659 (mp10) REVERT: A 442 ASN cc_start: 0.8277 (m110) cc_final: 0.7928 (m110) REVERT: A 711 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8804 (mm-40) REVERT: A 1147 GLU cc_start: 0.8456 (pm20) cc_final: 0.8221 (pm20) REVERT: A 1211 ASN cc_start: 0.8227 (m-40) cc_final: 0.7706 (p0) outliers start: 10 outliers final: 4 residues processed: 59 average time/residue: 0.7028 time to fit residues: 45.0456 Evaluate side-chains 51 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 742 GLU 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: 0.6980 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 0.0470 chunk 21 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.081142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.062352 restraints weight = 21022.447| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.08 r_work: 0.2670 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12217 Z= 0.141 Angle : 0.617 7.922 16880 Z= 0.305 Chirality : 0.054 0.494 1894 Planarity : 0.003 0.035 1841 Dihedral : 15.912 141.934 2387 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.73 % Allowed : 9.81 % 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: 1.46 (0.25), residues: 1201 helix: 1.92 (0.21), residues: 607 sheet: -0.25 (0.39), residues: 157 loop : 0.20 (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 0.014 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 0.00307 / 0.14 (12213) covalent geometry : angle 0.61716 / 0.31 (16874) hydrogen bonds : bond 0.04023 / 2.64 ( 577) hydrogen bonds : angle 3.71615 / 2.55 ( 1598) metal coordination : bond 0.00466 / 0.24 ( 4) metal coordination : angle 0.85375 / 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 59 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.444 Fit side-chains REVERT: A 103 ARG cc_start: 0.8667 (mtt-85) cc_final: 0.8056 (mtt-85) REVERT: A 225 GLN cc_start: 0.8031 (mp10) cc_final: 0.7687 (mp10) REVERT: A 442 ASN cc_start: 0.8313 (m110) cc_final: 0.7972 (m110) REVERT: A 630 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8055 (mtpm) REVERT: A 711 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8845 (mm-40) REVERT: A 1147 GLU cc_start: 0.8443 (pm20) cc_final: 0.8162 (pm20) REVERT: A 1211 ASN cc_start: 0.8245 (m-40) cc_final: 0.7750 (p0) outliers start: 8 outliers final: 4 residues processed: 56 average time/residue: 0.6906 time to fit residues: 41.7754 Evaluate side-chains 53 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 4 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.080393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.061600 restraints weight = 20828.889| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 2.06 r_work: 0.2655 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2388 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= 0.166 Angle : 0.629 7.214 16880 Z= 0.312 Chirality : 0.055 0.508 1894 Planarity : 0.003 0.038 1841 Dihedral : 15.934 141.964 2387 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.47 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: 1.48 (0.25), residues: 1201 helix: 1.95 (0.21), residues: 606 sheet: -0.29 (0.39), residues: 157 loop : 0.21 (0.32), 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 0.010 0.001 TRP A 480 HIS 0.003 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (12213) covalent geometry : angle 0.62928 / 0.31 (16874) hydrogen bonds : bond 0.04140 / 2.72 ( 577) hydrogen bonds : angle 3.73678 / 2.56 ( 1598) metal coordination : bond 0.00510 / 0.26 ( 4) metal coordination : angle 0.87297 / 0.39 ( 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 59 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.476 Fit side-chains REVERT: A 103 ARG cc_start: 0.8657 (mtt-85) cc_final: 0.8028 (mtt-85) REVERT: A 225 GLN cc_start: 0.8037 (mp10) cc_final: 0.7728 (mp10) REVERT: A 442 ASN cc_start: 0.8364 (m110) cc_final: 0.8025 (m110) REVERT: A 630 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8062 (mtpm) REVERT: A 840 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8601 (mmpt) REVERT: A 1147 GLU cc_start: 0.8491 (pm20) cc_final: 0.8160 (pm20) REVERT: A 1211 ASN cc_start: 0.8304 (m-40) cc_final: 0.7829 (p0) outliers start: 10 outliers final: 5 residues processed: 56 average time/residue: 0.6962 time to fit residues: 42.3944 Evaluate side-chains 52 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 59 optimal weight: 1.9990 chunk 112 optimal weight: 0.2980 chunk 110 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 12 optimal weight: 0.0060 chunk 6 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.081221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.062416 restraints weight = 21161.787| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.08 r_work: 0.2669 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12217 Z= 0.128 Angle : 0.612 7.305 16880 Z= 0.304 Chirality : 0.053 0.488 1894 Planarity : 0.003 0.041 1841 Dihedral : 15.956 142.259 2387 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: 1.52 (0.25), residues: 1201 helix: 1.98 (0.21), residues: 606 sheet: -0.26 (0.39), residues: 157 loop : 0.22 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 307 TYR 0.015 0.001 TYR A 544 PHE 0.014 0.001 PHE A 180 TRP 0.011 0.001 TRP A 480 HIS 0.004 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (12213) covalent geometry : angle 0.61212 / 0.30 (16874) hydrogen bonds : bond 0.04039 / 2.66 ( 577) hydrogen bonds : angle 3.70941 / 2.54 ( 1598) metal coordination : bond 0.00441 / 0.22 ( 4) metal coordination : angle 0.91797 / 0.39 ( 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 57 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.404 Fit side-chains REVERT: A 103 ARG cc_start: 0.8665 (mtt-85) cc_final: 0.8055 (mtt-85) REVERT: A 225 GLN cc_start: 0.8044 (mp10) cc_final: 0.7715 (mp10) REVERT: A 442 ASN cc_start: 0.8344 (m110) cc_final: 0.8008 (m110) REVERT: A 630 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8042 (mtpm) REVERT: A 840 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8596 (mmpt) REVERT: A 1147 GLU cc_start: 0.8471 (pm20) cc_final: 0.8155 (pm20) REVERT: A 1211 ASN cc_start: 0.8276 (m-40) cc_final: 0.7781 (p0) outliers start: 9 outliers final: 5 residues processed: 54 average time/residue: 0.6662 time to fit residues: 39.1702 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 : 0.413 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 60 optimal weight: 0.7980 chunk 88 optimal weight: 0.0070 chunk 38 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.081000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.062337 restraints weight = 20871.711| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.05 r_work: 0.2668 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12217 Z= 0.144 Angle : 0.610 7.220 16880 Z= 0.302 Chirality : 0.053 0.487 1894 Planarity : 0.003 0.039 1841 Dihedral : 15.947 142.093 2387 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.73 % Allowed : 10.17 % 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: 1.53 (0.25), residues: 1201 helix: 1.99 (0.21), residues: 607 sheet: -0.25 (0.39), residues: 157 loop : 0.22 (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 0.014 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 0.00314 / 0.14 (12213) covalent geometry : angle 0.60973 / 0.30 (16874) hydrogen bonds : bond 0.04039 / 2.66 ( 577) hydrogen bonds : angle 3.69707 / 2.53 ( 1598) metal coordination : bond 0.00437 / 0.22 ( 4) metal coordination : angle 0.83082 / 0.37 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3226.07 seconds wall clock time: 56 minutes 12.17 seconds (3372.17 seconds total)