Starting phenix.real_space_refine on Wed Sep 17 23:07:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d4a_27179/09_2025/8d4a_27179.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d4a_27179/09_2025/8d4a_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 { model { file = "/net/cci-nas-00/data/ceres_data/8d4a_27179/09_2025/8d4a_27179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d4a_27179/09_2025/8d4a_27179.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d4a_27179/09_2025/8d4a_27179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d4a_27179/09_2025/8d4a_27179.map" } 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-2.0-5805/lib/python3.9/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: 2.67, per 1000 atoms: 0.23 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: 1.01 Conformation dependent library (CDL) restraints added in 482.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 3.37 Time building geometry restraints manager: 1.35 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' DT D 5 " pdb=" O3' DT D 5 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 3.01e+00 bond pdb=" CG1 ILE A 81 " pdb=" CD1 ILE A 81 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.87e+00 bond pdb=" CG1 ILE A1161 " pdb=" CD1 ILE A1161 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.86e+00 bond pdb=" CG LEU A 119 " pdb=" CD1 LEU A 119 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.85e+00 bond pdb=" C HIS A 374 " pdb=" N TYR A 375 " ideal model delta sigma weight residual 1.327 1.304 0.023 1.71e-02 3.42e+03 1.81e+00 ... (remaining 12208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 16485 2.01 - 4.02: 341 4.02 - 6.03: 39 6.03 - 8.04: 7 8.04 - 10.04: 2 Bond angle restraints: 16874 Sorted by residual: angle pdb=" C SER A1122 " pdb=" N ASP A1123 " pdb=" CA ASP A1123 " ideal model delta sigma weight residual 121.54 129.23 -7.69 1.91e+00 2.74e-01 1.62e+01 angle pdb=" O3' G B 41 " pdb=" C3' G B 41 " pdb=" C2' G B 41 " ideal model delta sigma weight residual 113.70 118.98 -5.28 1.50e+00 4.44e-01 1.24e+01 angle pdb=" N ASP A 869 " pdb=" CA ASP A 869 " pdb=" C ASP A 869 " ideal model delta sigma weight residual 110.44 106.45 3.99 1.20e+00 6.94e-01 1.11e+01 angle pdb=" C4' G B 41 " pdb=" C3' G B 41 " pdb=" O3' G B 41 " ideal model delta sigma weight residual 113.00 117.79 -4.79 1.50e+00 4.44e-01 1.02e+01 angle pdb=" C ILE A 81 " pdb=" CA ILE A 81 " pdb=" CB ILE A 81 " ideal model delta sigma weight residual 110.63 113.60 -2.97 9.40e-01 1.13e+00 1.00e+01 ... (remaining 16869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 7110 35.27 - 70.54: 314 70.54 - 105.81: 21 105.81 - 141.08: 0 141.08 - 176.35: 3 Dihedral angle restraints: 7448 sinusoidal: 3880 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 7445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1660 0.066 - 0.132: 218 0.132 - 0.199: 14 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: 0.000 Normalize map: mean=0, sd=1: 3.830 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.440 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: 0.010 Load rotamer database and sin/cos tables:7.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 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= 0.247 Angle : 0.713 10.044 16880 Z= 0.407 Chirality : 0.045 0.331 1894 Planarity : 0.004 0.066 1841 Dihedral : 17.649 176.354 5142 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 aren 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 covalent geometry : bond 0.00570 (12213) covalent geometry : angle 0.71264 (16874) hydrogen bonds : bond 0.17279 ( 577) hydrogen bonds : angle 6.16489 ( 1598) metal coordination : bond 0.00623 ( 4) metal coordination : angle 1.69200 ( 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 : 0.439 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 1.0320 time to fit residues: 120.4015 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 : 0.449 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 366 ASN A 587 HIS A 887 HIS A1086 GLN A1210 HIS A1230 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.077791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.058996 restraints weight = 21257.472| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 2.01 r_work: 0.2574 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2446 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12217 Z= 0.178 Angle : 0.538 7.613 16880 Z= 0.300 Chirality : 0.040 0.220 1894 Planarity : 0.004 0.040 1841 Dihedral : 18.477 174.313 2619 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.82 % Allowed : 6.32 % Favored : 92.85 % 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 aren not related in a simple way. whole: 0.50 (0.24), residues: 1201 helix: 0.92 (0.21), residues: 612 sheet: -0.38 (0.39), residues: 157 loop : -0.04 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 660 TYR 0.017 0.001 TYR A 544 PHE 0.017 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 covalent geometry : bond 0.00399 (12213) covalent geometry : angle 0.53757 (16874) hydrogen bonds : bond 0.04624 ( 577) hydrogen bonds : angle 4.18467 ( 1598) metal coordination : bond 0.00596 ( 4) metal coordination : angle 0.86366 ( 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 62 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.454 Fit side-chains REVERT: A 442 ASN cc_start: 0.8143 (m110) cc_final: 0.7734 (m-40) REVERT: A 674 ASP cc_start: 0.8838 (m-30) cc_final: 0.8624 (m-30) REVERT: A 840 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8580 (mmpt) REVERT: A 861 ASP cc_start: 0.8597 (t70) cc_final: 0.8310 (t0) outliers start: 9 outliers final: 1 residues processed: 58 average time/residue: 0.7495 time to fit residues: 46.9372 Evaluate side-chains 46 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU 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: 8.9990 chunk 33 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A1086 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.074974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.056134 restraints weight = 21654.595| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 2.02 r_work: 0.2497 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: 0.8687 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 12217 Z= 0.312 Angle : 0.586 7.346 16880 Z= 0.322 Chirality : 0.044 0.258 1894 Planarity : 0.003 0.032 1841 Dihedral : 18.479 160.856 2619 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.01 % Allowed : 6.97 % 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 aren not related in a simple way. whole: 0.81 (0.24), residues: 1201 helix: 1.27 (0.21), residues: 607 sheet: -0.51 (0.39), residues: 157 loop : 0.08 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 307 TYR 0.019 0.002 TYR A 544 PHE 0.021 0.002 PHE A 757 TRP 0.010 0.002 TRP A 78 HIS 0.003 0.001 HIS A 640 Details of bonding type rmsd covalent geometry : bond 0.00714 (12213) covalent geometry : angle 0.58529 (16874) hydrogen bonds : bond 0.05155 ( 577) hydrogen bonds : angle 4.11270 ( 1598) metal coordination : bond 0.00851 ( 4) metal coordination : angle 1.17445 ( 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 61 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.467 Fit side-chains REVERT: A 442 ASN cc_start: 0.8392 (m110) cc_final: 0.8051 (m-40) REVERT: A 630 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8140 (mtpm) REVERT: A 674 ASP cc_start: 0.8872 (m-30) cc_final: 0.8656 (m-30) REVERT: A 861 ASP cc_start: 0.8623 (t70) cc_final: 0.8350 (t0) REVERT: A 1200 LYS cc_start: 0.8282 (tttt) cc_final: 0.7911 (mppt) outliers start: 11 outliers final: 8 residues processed: 57 average time/residue: 0.8352 time to fit residues: 51.2689 Evaluate side-chains 51 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 485 HIS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 1145 LEU 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: 0.7980 chunk 125 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.077481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.058591 restraints weight = 21289.555| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 2.04 r_work: 0.2551 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2427 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12217 Z= 0.156 Angle : 0.494 7.288 16880 Z= 0.274 Chirality : 0.038 0.224 1894 Planarity : 0.003 0.028 1841 Dihedral : 18.439 149.075 2619 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.92 % Allowed : 8.16 % Favored : 90.93 % 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 aren not related in a simple way. whole: 1.14 (0.24), residues: 1201 helix: 1.61 (0.21), residues: 605 sheet: -0.46 (0.39), residues: 157 loop : 0.16 (0.31), 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 covalent geometry : bond 0.00350 (12213) covalent geometry : angle 0.49356 (16874) hydrogen bonds : bond 0.04103 ( 577) hydrogen bonds : angle 3.86004 ( 1598) metal coordination : bond 0.00561 ( 4) metal coordination : angle 0.69793 ( 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 62 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.476 Fit side-chains REVERT: A 225 GLN cc_start: 0.7937 (mp10) cc_final: 0.7627 (mp10) REVERT: A 442 ASN cc_start: 0.8372 (m110) cc_final: 0.8029 (m110) REVERT: A 1211 ASN cc_start: 0.8346 (m110) cc_final: 0.7828 (p0) outliers start: 10 outliers final: 6 residues processed: 59 average time/residue: 0.7566 time to fit residues: 48.3181 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 : 0.532 ------------------------------------------------------------------------------- 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 485 HIS Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1231 MET 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: 1.9990 chunk 100 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.076228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.057302 restraints weight = 21351.196| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 2.06 r_work: 0.2560 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2434 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 12217 Z= 0.249 Angle : 0.542 7.281 16880 Z= 0.299 Chirality : 0.041 0.247 1894 Planarity : 0.003 0.029 1841 Dihedral : 18.457 149.666 2619 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.28 % Allowed : 8.52 % Favored : 90.19 % 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 aren not related in a simple way. whole: 1.26 (0.25), residues: 1201 helix: 1.72 (0.21), residues: 601 sheet: -0.53 (0.38), residues: 157 loop : 0.27 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 covalent geometry : bond 0.00569 (12213) covalent geometry : angle 0.54145 (16874) hydrogen bonds : bond 0.04659 ( 577) hydrogen bonds : angle 3.92368 ( 1598) metal coordination : bond 0.00743 ( 4) metal coordination : angle 1.14719 ( 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 63 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 442 ASN cc_start: 0.8512 (m110) cc_final: 0.8207 (m110) REVERT: A 630 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8121 (mtpm) REVERT: A 840 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8672 (mmpt) REVERT: A 1200 LYS cc_start: 0.8312 (tttt) cc_final: 0.7955 (mppt) outliers start: 14 outliers final: 7 residues processed: 57 average time/residue: 0.8378 time to fit residues: 51.3144 Evaluate side-chains 53 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 485 HIS 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 Chi-restraints excluded: chain A residue 1231 MET 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: 1.9990 chunk 120 optimal weight: 2.9990 chunk 117 optimal weight: 0.3980 chunk 86 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 41 optimal weight: 0.6980 chunk 94 optimal weight: 0.0000 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 956 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.078610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.059685 restraints weight = 21201.241| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.07 r_work: 0.2601 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2474 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12217 Z= 0.137 Angle : 0.487 7.244 16880 Z= 0.269 Chirality : 0.038 0.220 1894 Planarity : 0.003 0.028 1841 Dihedral : 18.451 148.588 2619 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.19 % Allowed : 9.17 % Favored : 89.64 % 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 aren not related in a simple way. whole: 1.39 (0.25), residues: 1201 helix: 1.85 (0.21), residues: 606 sheet: -0.41 (0.39), residues: 157 loop : 0.26 (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 0.003 0.001 HIS A 640 Details of bonding type rmsd covalent geometry : bond 0.00308 (12213) covalent geometry : angle 0.48713 (16874) hydrogen bonds : bond 0.03921 ( 577) hydrogen bonds : angle 3.74571 ( 1598) metal coordination : bond 0.00476 ( 4) metal coordination : angle 0.65170 ( 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 66 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.461 Fit side-chains REVERT: A 225 GLN cc_start: 0.8006 (mp10) cc_final: 0.7768 (mp10) REVERT: A 442 ASN cc_start: 0.8389 (m110) cc_final: 0.8096 (m110) REVERT: A 630 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8118 (mtpm) REVERT: A 1147 GLU cc_start: 0.8485 (pm20) cc_final: 0.8254 (pm20) REVERT: A 1200 LYS cc_start: 0.8270 (tttt) cc_final: 0.7939 (mppt) REVERT: A 1211 ASN cc_start: 0.8326 (m110) cc_final: 0.7931 (p0) outliers start: 13 outliers final: 6 residues processed: 59 average time/residue: 0.7814 time to fit residues: 49.8665 Evaluate side-chains 59 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 485 HIS Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 1145 LEU 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: 0.0980 chunk 82 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.076473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.057680 restraints weight = 21253.065| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 2.00 r_work: 0.2566 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2440 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 12217 Z= 0.230 Angle : 0.534 7.238 16880 Z= 0.294 Chirality : 0.041 0.241 1894 Planarity : 0.003 0.029 1841 Dihedral : 18.468 149.447 2619 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.47 % Allowed : 9.53 % Favored : 89.00 % 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 aren not related in a simple way. whole: 1.43 (0.25), residues: 1201 helix: 1.88 (0.21), residues: 601 sheet: -0.50 (0.38), residues: 157 loop : 0.34 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 307 TYR 0.018 0.001 TYR A 544 PHE 0.017 0.001 PHE A 757 TRP 0.010 0.001 TRP A 480 HIS 0.003 0.001 HIS A1219 Details of bonding type rmsd covalent geometry : bond 0.00526 (12213) covalent geometry : angle 0.53398 (16874) hydrogen bonds : bond 0.04505 ( 577) hydrogen bonds : angle 3.85736 ( 1598) metal coordination : bond 0.00674 ( 4) metal coordination : angle 1.16843 ( 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 63 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.463 Fit side-chains REVERT: A 1 MET cc_start: 0.4677 (OUTLIER) cc_final: 0.4250 (mtm) REVERT: A 225 GLN cc_start: 0.8086 (mp10) cc_final: 0.7817 (mp10) REVERT: A 442 ASN cc_start: 0.8492 (m110) cc_final: 0.8214 (m110) REVERT: A 630 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8116 (mtpm) REVERT: A 711 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8884 (mm-40) REVERT: A 1147 GLU cc_start: 0.8472 (pm20) cc_final: 0.8249 (pm20) REVERT: A 1200 LYS cc_start: 0.8346 (tttt) cc_final: 0.8007 (mppt) REVERT: A 1211 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.8003 (p0) outliers start: 16 outliers final: 8 residues processed: 57 average time/residue: 0.7953 time to fit residues: 49.0444 Evaluate side-chains 58 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 485 HIS 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 Chi-restraints excluded: chain A residue 1211 ASN Chi-restraints excluded: chain A residue 1231 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 88 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.077633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.058836 restraints weight = 21205.672| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 2.01 r_work: 0.2595 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12217 Z= 0.166 Angle : 0.504 7.223 16880 Z= 0.277 Chirality : 0.039 0.226 1894 Planarity : 0.003 0.028 1841 Dihedral : 18.425 148.891 2619 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.19 % Allowed : 9.99 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.25), residues: 1201 helix: 1.94 (0.21), residues: 602 sheet: -0.43 (0.38), residues: 157 loop : 0.39 (0.32), residues: 442 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 covalent geometry : bond 0.00377 (12213) covalent geometry : angle 0.50355 (16874) hydrogen bonds : bond 0.04107 ( 577) hydrogen bonds : angle 3.76830 ( 1598) metal coordination : bond 0.00536 ( 4) metal coordination : angle 0.81014 ( 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 64 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.456 Fit side-chains REVERT: A 1 MET cc_start: 0.4764 (OUTLIER) cc_final: 0.4386 (mtm) REVERT: A 225 GLN cc_start: 0.8090 (mp10) cc_final: 0.7812 (mp10) REVERT: A 442 ASN cc_start: 0.8456 (m110) cc_final: 0.8192 (m110) REVERT: A 630 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8117 (mtpm) REVERT: A 1200 LYS cc_start: 0.8333 (tttt) cc_final: 0.7994 (mppt) REVERT: A 1211 ASN cc_start: 0.8423 (m110) cc_final: 0.8028 (p0) outliers start: 13 outliers final: 8 residues processed: 59 average time/residue: 0.7556 time to fit residues: 48.3647 Evaluate side-chains 56 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 485 HIS Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1231 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 4 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 111 optimal weight: 0.0670 chunk 97 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.078787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.059996 restraints weight = 20946.119| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.01 r_work: 0.2623 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 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= 0.133 Angle : 0.490 7.169 16880 Z= 0.269 Chirality : 0.037 0.220 1894 Planarity : 0.003 0.029 1841 Dihedral : 18.381 148.429 2619 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.01 % Allowed : 10.27 % Favored : 88.73 % 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 aren not related in a simple way. whole: 1.54 (0.25), residues: 1201 helix: 1.95 (0.21), residues: 609 sheet: -0.36 (0.39), residues: 157 loop : 0.35 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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 covalent geometry : bond 0.00300 (12213) covalent geometry : angle 0.48936 (16874) hydrogen bonds : bond 0.03819 ( 577) hydrogen bonds : angle 3.68508 ( 1598) metal coordination : bond 0.00477 ( 4) metal coordination : angle 0.80272 ( 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: 11 poor density : 49 time to evaluate : 0.479 Fit side-chains REVERT: A 225 GLN cc_start: 0.8098 (mp10) cc_final: 0.7877 (mp10) REVERT: A 442 ASN cc_start: 0.8433 (m110) cc_final: 0.8162 (m110) REVERT: A 630 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8085 (mtpm) REVERT: A 1200 LYS cc_start: 0.8285 (tttt) cc_final: 0.7953 (mppt) REVERT: A 1211 ASN cc_start: 0.8313 (m110) cc_final: 0.8017 (p0) outliers start: 11 outliers final: 5 residues processed: 56 average time/residue: 0.7829 time to fit residues: 47.4795 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 : 0.463 ------------------------------------------------------------------------------- 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 485 HIS Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 630 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: 2.9990 chunk 112 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.078021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.059159 restraints weight = 21303.463| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.02 r_work: 0.2601 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2476 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12217 Z= 0.159 Angle : 0.502 7.157 16880 Z= 0.275 Chirality : 0.038 0.225 1894 Planarity : 0.003 0.032 1841 Dihedral : 18.389 148.757 2619 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.01 % Allowed : 10.45 % Favored : 88.54 % 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 aren not related in a simple way. whole: 1.56 (0.25), residues: 1201 helix: 1.97 (0.21), residues: 609 sheet: -0.36 (0.39), residues: 157 loop : 0.38 (0.32), residues: 435 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 covalent geometry : bond 0.00361 (12213) covalent geometry : angle 0.50146 (16874) hydrogen bonds : bond 0.04017 ( 577) hydrogen bonds : angle 3.72003 ( 1598) metal coordination : bond 0.00527 ( 4) metal coordination : angle 0.90862 ( 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: 11 poor density : 48 time to evaluate : 0.512 Fit side-chains REVERT: A 225 GLN cc_start: 0.8120 (mp10) cc_final: 0.7900 (mp10) REVERT: A 442 ASN cc_start: 0.8474 (m110) cc_final: 0.8207 (m110) REVERT: A 630 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8084 (mtpm) REVERT: A 1200 LYS cc_start: 0.8321 (tttt) cc_final: 0.7967 (mppt) REVERT: A 1211 ASN cc_start: 0.8381 (m110) cc_final: 0.8037 (p0) outliers start: 11 outliers final: 6 residues processed: 56 average time/residue: 0.7394 time to fit residues: 44.9455 Evaluate side-chains 51 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 485 HIS Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 630 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: 0.0020 chunk 88 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.078060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.059229 restraints weight = 21127.136| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.01 r_work: 0.2603 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12217 Z= 0.163 Angle : 0.505 8.218 16880 Z= 0.275 Chirality : 0.038 0.226 1894 Planarity : 0.003 0.031 1841 Dihedral : 18.391 148.852 2619 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.82 % Allowed : 10.45 % Favored : 88.73 % 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 aren not related in a simple way. whole: 1.56 (0.25), residues: 1201 helix: 1.97 (0.21), residues: 608 sheet: -0.36 (0.39), residues: 157 loop : 0.36 (0.32), residues: 436 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 covalent geometry : bond 0.00369 (12213) covalent geometry : angle 0.50489 (16874) hydrogen bonds : bond 0.04054 ( 577) hydrogen bonds : angle 3.72489 ( 1598) metal coordination : bond 0.00545 ( 4) metal coordination : angle 0.95506 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3790.38 seconds wall clock time: 65 minutes 48.84 seconds (3948.84 seconds total)