Starting phenix.real_space_refine on Wed Jul 30 06:03:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d4a_27179/07_2025/8d4a_27179.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d4a_27179/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d4a_27179/07_2025/8d4a_27179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d4a_27179/07_2025/8d4a_27179.map" model { file = "/net/cci-nas-00/data/ceres_data/8d4a_27179/07_2025/8d4a_27179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d4a_27179/07_2025/8d4a_27179.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.25, per 1000 atoms: 0.70 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: 2.92 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 4.79 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: 7.12 Time building geometry restraints manager: 3.50 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: 7.210 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 39.480 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.030 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (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 TRP 0.011 0.002 TRP A 480 HIS 0.005 0.001 HIS A 640 PHE 0.023 0.003 PHE A 757 TYR 0.019 0.002 TYR A1139 ARG 0.013 0.001 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.17279 ( 577) hydrogen bonds : angle 6.16489 ( 1598) metal coordination : bond 0.00623 ( 4) metal coordination : angle 1.69200 ( 6) covalent geometry : bond 0.00570 (12213) covalent geometry : angle 0.71264 (16874) *********************** 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 : 1.452 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 1.9672 time to fit residues: 230.8001 Evaluate side-chains 43 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 HIS A 887 HIS A1086 GLN A1210 HIS A1230 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.077873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.059054 restraints weight = 21223.576| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 2.02 r_work: 0.2575 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2448 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1640 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= 0.179 Angle : 0.538 7.567 16880 Z= 0.300 Chirality : 0.040 0.219 1894 Planarity : 0.004 0.042 1841 Dihedral : 18.475 174.121 2619 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.82 % Allowed : 6.14 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1201 helix: 0.93 (0.21), residues: 612 sheet: -0.38 (0.39), residues: 157 loop : -0.03 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 480 HIS 0.003 0.001 HIS A 640 PHE 0.017 0.001 PHE A 180 TYR 0.017 0.001 TYR A 544 ARG 0.009 0.001 ARG A 660 Details of bonding type rmsd hydrogen bonds : bond 0.04510 ( 577) hydrogen bonds : angle 4.16855 ( 1598) metal coordination : bond 0.00586 ( 4) metal coordination : angle 0.84030 ( 6) covalent geometry : bond 0.00398 (12213) covalent geometry : angle 0.53827 (16874) *********************** 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 63 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 1.319 Fit side-chains REVERT: A 442 ASN cc_start: 0.8152 (m110) cc_final: 0.7745 (m-40) REVERT: A 674 ASP cc_start: 0.8828 (m-30) cc_final: 0.8612 (m-30) REVERT: A 840 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8571 (mmpt) REVERT: A 861 ASP cc_start: 0.8598 (t70) cc_final: 0.8315 (t0) outliers start: 9 outliers final: 1 residues processed: 59 average time/residue: 1.4967 time to fit residues: 96.0060 Evaluate side-chains 47 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 124 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 31 optimal weight: 0.0770 chunk 35 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 114 optimal weight: 0.0870 chunk 92 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 143 GLN A1159 HIS A1211 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.080074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.061201 restraints weight = 21252.591| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 2.07 r_work: 0.2594 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 12217 Z= 0.112 Angle : 0.473 7.274 16880 Z= 0.263 Chirality : 0.037 0.215 1894 Planarity : 0.003 0.031 1841 Dihedral : 18.396 165.270 2619 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.82 % Allowed : 6.78 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.24), residues: 1201 helix: 1.51 (0.21), residues: 607 sheet: -0.26 (0.39), residues: 157 loop : 0.11 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 480 HIS 0.003 0.000 HIS A 640 PHE 0.014 0.001 PHE A 180 TYR 0.015 0.001 TYR A 544 ARG 0.006 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 577) hydrogen bonds : angle 3.79010 ( 1598) metal coordination : bond 0.00395 ( 4) metal coordination : angle 0.61744 ( 6) covalent geometry : bond 0.00241 (12213) covalent geometry : angle 0.47329 (16874) *********************** 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 72 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 1.195 Fit side-chains REVERT: A 368 GLU cc_start: 0.8016 (pm20) cc_final: 0.7782 (pm20) REVERT: A 442 ASN cc_start: 0.8094 (m110) cc_final: 0.7736 (m-40) REVERT: A 993 GLN cc_start: 0.8711 (tt0) cc_final: 0.8506 (tt0) outliers start: 9 outliers final: 4 residues processed: 69 average time/residue: 1.7440 time to fit residues: 131.2173 Evaluate side-chains 55 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 485 HIS Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 115 optimal weight: 0.0170 chunk 60 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 203 ASN A1086 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.076505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.057653 restraints weight = 21379.233| |-----------------------------------------------------------------------------| r_work (start): 0.2656 rms_B_bonded: 2.02 r_work: 0.2529 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2403 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12217 Z= 0.227 Angle : 0.529 7.276 16880 Z= 0.292 Chirality : 0.041 0.237 1894 Planarity : 0.003 0.031 1841 Dihedral : 18.422 149.933 2619 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.01 % Allowed : 8.16 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.24), residues: 1201 helix: 1.65 (0.21), residues: 605 sheet: -0.42 (0.39), residues: 157 loop : 0.17 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 480 HIS 0.003 0.001 HIS A 640 PHE 0.018 0.002 PHE A 757 TYR 0.018 0.001 TYR A 544 ARG 0.007 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.04477 ( 577) hydrogen bonds : angle 3.87519 ( 1598) metal coordination : bond 0.00662 ( 4) metal coordination : angle 1.10468 ( 6) covalent geometry : bond 0.00519 (12213) covalent geometry : angle 0.52902 (16874) *********************** 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 58 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 1.210 Fit side-chains REVERT: A 442 ASN cc_start: 0.8392 (m110) cc_final: 0.8041 (m110) REVERT: A 1211 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.7710 (p0) outliers start: 11 outliers final: 5 residues processed: 53 average time/residue: 1.4334 time to fit residues: 83.0651 Evaluate side-chains 49 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 1211 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 12 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3044 r_free = 0.3044 target = 0.077893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.059032 restraints weight = 21164.291| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 2.03 r_work: 0.2581 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2138 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= 0.147 Angle : 0.486 7.211 16880 Z= 0.269 Chirality : 0.038 0.222 1894 Planarity : 0.003 0.028 1841 Dihedral : 18.396 148.902 2619 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.73 % Allowed : 8.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.25), residues: 1201 helix: 1.78 (0.21), residues: 606 sheet: -0.36 (0.39), residues: 157 loop : 0.25 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 480 HIS 0.003 0.001 HIS A 640 PHE 0.015 0.001 PHE A 180 TYR 0.016 0.001 TYR A 544 ARG 0.007 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 577) hydrogen bonds : angle 3.75800 ( 1598) metal coordination : bond 0.00502 ( 4) metal coordination : angle 0.77167 ( 6) covalent geometry : bond 0.00329 (12213) covalent geometry : angle 0.48594 (16874) *********************** 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 59 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 1.561 Fit side-chains REVERT: A 225 GLN cc_start: 0.7914 (mp10) cc_final: 0.7636 (mp10) REVERT: A 442 ASN cc_start: 0.8361 (m110) cc_final: 0.8026 (m110) REVERT: A 1211 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7811 (p0) outliers start: 8 outliers final: 5 residues processed: 56 average time/residue: 1.9515 time to fit residues: 119.6926 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 : 2.095 ------------------------------------------------------------------------------- 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 1211 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 123 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3022 r_free = 0.3022 target = 0.075269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.056530 restraints weight = 21517.431| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 2.00 r_work: 0.2542 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2417 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 12217 Z= 0.311 Angle : 0.579 7.241 16880 Z= 0.317 Chirality : 0.043 0.258 1894 Planarity : 0.003 0.031 1841 Dihedral : 18.480 149.978 2619 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.56 % Allowed : 8.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.25), residues: 1201 helix: 1.73 (0.21), residues: 601 sheet: -0.52 (0.39), residues: 157 loop : 0.30 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 480 HIS 0.003 0.001 HIS A1219 PHE 0.021 0.002 PHE A 757 TYR 0.020 0.002 TYR A 544 ARG 0.007 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.04988 ( 577) hydrogen bonds : angle 3.96591 ( 1598) metal coordination : bond 0.00821 ( 4) metal coordination : angle 1.49869 ( 6) covalent geometry : bond 0.00713 (12213) covalent geometry : angle 0.57840 (16874) *********************** 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 64 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 1.295 Fit side-chains REVERT: A 442 ASN cc_start: 0.8565 (m110) cc_final: 0.8269 (m110) REVERT: A 630 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8079 (mtpm) REVERT: A 711 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8895 (mm-40) REVERT: A 1147 GLU cc_start: 0.8556 (pm20) cc_final: 0.8274 (pm20) REVERT: A 1200 LYS cc_start: 0.8343 (tttt) cc_final: 0.7992 (mppt) REVERT: A 1211 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.7905 (p0) outliers start: 17 outliers final: 9 residues processed: 58 average time/residue: 1.5231 time to fit residues: 96.3336 Evaluate side-chains 56 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 485 HIS Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 603 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 96 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3044 r_free = 0.3044 target = 0.076553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.057718 restraints weight = 21419.460| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 2.07 r_work: 0.2583 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12217 Z= 0.202 Angle : 0.519 7.220 16880 Z= 0.286 Chirality : 0.040 0.236 1894 Planarity : 0.003 0.030 1841 Dihedral : 18.469 149.143 2619 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.10 % Allowed : 9.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1201 helix: 1.86 (0.21), residues: 600 sheet: -0.49 (0.38), residues: 157 loop : 0.32 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 480 HIS 0.003 0.001 HIS A 640 PHE 0.015 0.001 PHE A 180 TYR 0.017 0.001 TYR A 544 ARG 0.007 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.04362 ( 577) hydrogen bonds : angle 3.84153 ( 1598) metal coordination : bond 0.00626 ( 4) metal coordination : angle 0.95658 ( 6) covalent geometry : bond 0.00460 (12213) covalent geometry : angle 0.51856 (16874) *********************** 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 59 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 1.225 Fit side-chains REVERT: A 1 MET cc_start: 0.4680 (ttm) cc_final: 0.4347 (mtm) REVERT: A 442 ASN cc_start: 0.8380 (m110) cc_final: 0.8067 (m110) REVERT: A 630 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8066 (mtpm) REVERT: A 711 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8857 (mm-40) REVERT: A 1147 GLU cc_start: 0.8579 (pm20) cc_final: 0.8267 (pm20) REVERT: A 1200 LYS cc_start: 0.8307 (tttt) cc_final: 0.7945 (mppt) REVERT: A 1211 ASN cc_start: 0.8373 (OUTLIER) cc_final: 0.7872 (p0) outliers start: 12 outliers final: 8 residues processed: 55 average time/residue: 1.5139 time to fit residues: 90.5281 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 : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 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 43 optimal weight: 3.9990 chunk 11 optimal weight: 0.0670 chunk 111 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 overall best weight: 1.1324 ------------------------------------------------------------------------------- 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 = 0.3048 r_free = 0.3048 target = 0.076737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.057899 restraints weight = 21193.905| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 2.06 r_work: 0.2586 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12217 Z= 0.196 Angle : 0.517 7.229 16880 Z= 0.285 Chirality : 0.039 0.235 1894 Planarity : 0.003 0.029 1841 Dihedral : 18.468 149.163 2619 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.28 % Allowed : 9.35 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.25), residues: 1201 helix: 1.88 (0.21), residues: 602 sheet: -0.51 (0.38), residues: 157 loop : 0.34 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 480 HIS 0.003 0.001 HIS A 640 PHE 0.015 0.001 PHE A 757 TYR 0.017 0.001 TYR A 544 ARG 0.007 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.04323 ( 577) hydrogen bonds : angle 3.80677 ( 1598) metal coordination : bond 0.00607 ( 4) metal coordination : angle 0.97063 ( 6) covalent geometry : bond 0.00445 (12213) covalent geometry : angle 0.51654 (16874) *********************** 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 62 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 1.358 Fit side-chains REVERT: A 442 ASN cc_start: 0.8410 (m110) cc_final: 0.8103 (m110) REVERT: A 630 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8049 (mtpm) REVERT: A 711 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8859 (mm-40) REVERT: A 1200 LYS cc_start: 0.8304 (tttt) cc_final: 0.7944 (mppt) REVERT: A 1211 ASN cc_start: 0.8365 (OUTLIER) cc_final: 0.7882 (p0) outliers start: 14 outliers final: 9 residues processed: 56 average time/residue: 1.3061 time to fit residues: 81.0533 Evaluate side-chains 56 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 485 HIS Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 43 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 = 0.3057 r_free = 0.3057 target = 0.077325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.058536 restraints weight = 21159.017| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 2.01 r_work: 0.2588 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2462 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12217 Z= 0.180 Angle : 0.506 7.187 16880 Z= 0.279 Chirality : 0.039 0.230 1894 Planarity : 0.003 0.030 1841 Dihedral : 18.458 148.998 2619 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.19 % Allowed : 9.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.25), residues: 1201 helix: 1.94 (0.21), residues: 602 sheet: -0.47 (0.38), residues: 157 loop : 0.37 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 480 HIS 0.003 0.001 HIS A 640 PHE 0.015 0.001 PHE A 180 TYR 0.017 0.001 TYR A 544 ARG 0.007 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 577) hydrogen bonds : angle 3.78170 ( 1598) metal coordination : bond 0.00572 ( 4) metal coordination : angle 0.86896 ( 6) covalent geometry : bond 0.00409 (12213) covalent geometry : angle 0.50583 (16874) *********************** 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: 13 poor density : 47 time to evaluate : 2.953 Fit side-chains REVERT: A 225 GLN cc_start: 0.7814 (mp10) cc_final: 0.7591 (mm110) REVERT: A 442 ASN cc_start: 0.8451 (m110) cc_final: 0.8173 (m110) REVERT: A 630 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8024 (mtpm) REVERT: A 1200 LYS cc_start: 0.8350 (tttt) cc_final: 0.8008 (mppt) REVERT: A 1211 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.8001 (p0) outliers start: 13 outliers final: 8 residues processed: 55 average time/residue: 1.7696 time to fit residues: 108.1644 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 : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 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 1211 ASN Chi-restraints excluded: chain A residue 1231 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 107 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 111 optimal weight: 0.0060 chunk 9 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- 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 = 0.3066 r_free = 0.3066 target = 0.077775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.058960 restraints weight = 21126.207| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.01 r_work: 0.2595 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12217 Z= 0.162 Angle : 0.504 8.773 16880 Z= 0.276 Chirality : 0.038 0.227 1894 Planarity : 0.003 0.029 1841 Dihedral : 18.434 148.896 2619 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.01 % Allowed : 9.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1201 helix: 1.92 (0.21), residues: 608 sheet: -0.45 (0.38), residues: 157 loop : 0.29 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 480 HIS 0.003 0.001 HIS A 640 PHE 0.015 0.001 PHE A 180 TYR 0.016 0.001 TYR A 544 ARG 0.008 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 577) hydrogen bonds : angle 3.74495 ( 1598) metal coordination : bond 0.00531 ( 4) metal coordination : angle 0.81707 ( 6) covalent geometry : bond 0.00367 (12213) covalent geometry : angle 0.50404 (16874) ********************** 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 61 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 1.429 Fit side-chains REVERT: A 225 GLN cc_start: 0.7889 (mp10) cc_final: 0.7633 (mm110) REVERT: A 442 ASN cc_start: 0.8472 (m110) cc_final: 0.8186 (m110) REVERT: A 630 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8034 (mtpm) REVERT: A 783 GLN cc_start: 0.8428 (tm-30) cc_final: 0.8119 (tm-30) REVERT: A 1200 LYS cc_start: 0.8339 (tttt) cc_final: 0.8001 (mppt) REVERT: A 1211 ASN cc_start: 0.8373 (OUTLIER) cc_final: 0.8058 (p0) outliers start: 11 outliers final: 9 residues processed: 56 average time/residue: 1.5865 time to fit residues: 98.4220 Evaluate side-chains 56 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 485 HIS Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1211 ASN Chi-restraints excluded: chain A residue 1231 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 109 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 114 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3086 r_free = 0.3086 target = 0.078912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.060108 restraints weight = 21046.247| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 2.05 r_work: 0.2626 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12217 Z= 0.123 Angle : 0.481 7.736 16880 Z= 0.263 Chirality : 0.037 0.216 1894 Planarity : 0.003 0.031 1841 Dihedral : 18.381 148.345 2619 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.82 % Allowed : 10.27 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.25), residues: 1201 helix: 2.01 (0.21), residues: 610 sheet: -0.36 (0.39), residues: 157 loop : 0.38 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 480 HIS 0.003 0.001 HIS A 640 PHE 0.014 0.001 PHE A 180 TYR 0.015 0.001 TYR A 544 ARG 0.008 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 577) hydrogen bonds : angle 3.67033 ( 1598) metal coordination : bond 0.00422 ( 4) metal coordination : angle 0.69184 ( 6) covalent geometry : bond 0.00273 (12213) covalent geometry : angle 0.48070 (16874) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7829.82 seconds wall clock time: 140 minutes 19.85 seconds (8419.85 seconds total)