Starting phenix.real_space_refine on Sat Nov 16 21:36:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4a_27179/11_2024/8d4a_27179.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4a_27179/11_2024/8d4a_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4a_27179/11_2024/8d4a_27179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4a_27179/11_2024/8d4a_27179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4a_27179/11_2024/8d4a_27179.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4a_27179/11_2024/8d4a_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-5513/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: 7.91, per 1000 atoms: 0.67 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: 3.21 Conformation dependent library (CDL) restraints added in 1.4 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: 4.67 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: 6.62 Time building geometry restraints manager: 3.68 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: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 38.970 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:13.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.030 ------------------------------------------------------------------------------- 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 12213 Z= 0.356 Angle : 0.713 10.044 16874 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 *********************** 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 : 1.316 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 2.1368 time to fit residues: 250.3040 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 : 1.332 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 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 12213 Z= 0.248 Angle : 0.538 7.567 16874 Z= 0.300 Chirality : 0.040 0.219 1894 Planarity : 0.004 0.042 1841 Dihedral : 18.475 174.123 2619 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.69 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 *********************** 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 : 1.308 Fit side-chains outliers start: 9 outliers final: 1 residues processed: 59 average time/residue: 1.5820 time to fit residues: 101.4657 Evaluate side-chains 44 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 79 optimal weight: 0.0270 chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 115 optimal weight: 0.0670 chunk 39 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1159 HIS A1211 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12213 Z= 0.173 Angle : 0.486 7.306 16874 Z= 0.271 Chirality : 0.038 0.220 1894 Planarity : 0.003 0.030 1841 Dihedral : 18.413 165.445 2619 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.82 % Allowed : 6.87 % Favored : 92.30 % 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: 1.05 (0.24), residues: 1201 helix: 1.50 (0.21), residues: 605 sheet: -0.30 (0.39), residues: 157 loop : 0.09 (0.30), residues: 439 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 0.015 0.001 TYR A 544 ARG 0.006 0.000 ARG A 307 *********************** 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 70 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 1.217 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 67 average time/residue: 1.5063 time to fit residues: 109.7783 Evaluate side-chains 51 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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 115 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1086 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12213 Z= 0.360 Angle : 0.546 7.291 16874 Z= 0.300 Chirality : 0.042 0.241 1894 Planarity : 0.003 0.029 1841 Dihedral : 18.432 149.990 2619 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.28 % Allowed : 8.25 % Favored : 90.47 % 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: 1.14 (0.24), residues: 1201 helix: 1.61 (0.21), residues: 605 sheet: -0.45 (0.39), residues: 157 loop : 0.16 (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 0.006 0.000 ARG A 307 *********************** 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: 14 poor density : 44 time to evaluate : 1.205 Fit side-chains REVERT: A 630 LYS cc_start: 0.7205 (OUTLIER) cc_final: 0.6935 (mtpm) outliers start: 14 outliers final: 7 residues processed: 53 average time/residue: 1.5152 time to fit residues: 87.4348 Evaluate side-chains 48 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 105 optimal weight: 0.0980 chunk 85 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12213 Z= 0.211 Angle : 0.490 7.216 16874 Z= 0.271 Chirality : 0.038 0.224 1894 Planarity : 0.003 0.028 1841 Dihedral : 18.411 148.908 2619 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.82 % Allowed : 8.62 % Favored : 90.56 % 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: 1.31 (0.25), residues: 1201 helix: 1.75 (0.21), residues: 607 sheet: -0.41 (0.39), residues: 157 loop : 0.26 (0.32), residues: 437 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 0.006 0.000 ARG A 307 *********************** 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 60 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 1.270 Fit side-chains revert: symmetry clash REVERT: A 630 LYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6876 (mtpm) outliers start: 9 outliers final: 5 residues processed: 56 average time/residue: 1.4955 time to fit residues: 91.2892 Evaluate side-chains 47 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 630 LYS Chi-restraints excluded: chain A residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.8980 chunk 111 optimal weight: 0.0030 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 57 optimal weight: 0.0770 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 65 optimal weight: 0.1980 overall best weight: 0.3148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12213 Z= 0.135 Angle : 0.465 7.216 16874 Z= 0.256 Chirality : 0.036 0.210 1894 Planarity : 0.003 0.030 1841 Dihedral : 18.358 147.789 2619 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.28 % Allowed : 9.17 % Favored : 89.55 % 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: 1.92 (0.21), residues: 608 sheet: -0.26 (0.39), residues: 157 loop : 0.28 (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 0.012 0.001 PHE A 180 TYR 0.014 0.001 TYR A 544 ARG 0.007 0.000 ARG A 307 *********************** 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 71 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 1.320 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 67 average time/residue: 1.3964 time to fit residues: 102.5047 Evaluate side-chains 54 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 601 ASP Chi-restraints excluded: chain A residue 742 GLU 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 119 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 chunk 69 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 75 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 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 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12213 Z= 0.240 Angle : 0.503 8.004 16874 Z= 0.276 Chirality : 0.039 0.228 1894 Planarity : 0.003 0.031 1841 Dihedral : 18.372 148.910 2619 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.73 % Allowed : 10.54 % 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 (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: 1.52 (0.25), residues: 1201 helix: 1.94 (0.21), residues: 608 sheet: -0.32 (0.39), residues: 157 loop : 0.33 (0.32), residues: 436 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 0.008 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 1.273 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 1.4485 time to fit residues: 86.9152 Evaluate side-chains 51 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 1.445 ------------------------------------------------------------------------------- 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 601 ASP Chi-restraints excluded: chain A residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 60 optimal weight: 0.0020 chunk 11 optimal weight: 0.0770 chunk 96 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.7748 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12213 Z= 0.209 Angle : 0.503 9.836 16874 Z= 0.276 Chirality : 0.038 0.220 1894 Planarity : 0.003 0.033 1841 Dihedral : 18.362 148.673 2619 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.01 % Allowed : 10.54 % Favored : 88.45 % 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: 1.55 (0.25), residues: 1201 helix: 1.97 (0.21), residues: 608 sheet: -0.33 (0.39), residues: 157 loop : 0.32 (0.32), residues: 436 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 0.014 0.001 PHE A 180 TYR 0.016 0.001 TYR A 544 ARG 0.007 0.000 ARG A 307 *********************** 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 56 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 1.219 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 54 average time/residue: 1.4270 time to fit residues: 84.3419 Evaluate side-chains 50 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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 742 GLU Chi-restraints excluded: chain A residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 0.0070 chunk 69 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 75 optimal weight: 0.4980 chunk 121 optimal weight: 2.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12213 Z= 0.174 Angle : 0.499 8.504 16874 Z= 0.271 Chirality : 0.037 0.216 1894 Planarity : 0.003 0.028 1841 Dihedral : 18.333 148.241 2619 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.82 % Allowed : 10.72 % Favored : 88.45 % 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: -0.26 (0.39), residues: 157 loop : 0.33 (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 *********************** 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 56 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 1.496 Fit side-chains REVERT: A 1 MET cc_start: 0.4572 (ttp) cc_final: 0.4037 (mtm) outliers start: 9 outliers final: 7 residues processed: 55 average time/residue: 1.5348 time to fit residues: 92.5630 Evaluate side-chains 48 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 742 GLU 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 74 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12213 Z= 0.237 Angle : 0.514 8.125 16874 Z= 0.280 Chirality : 0.039 0.227 1894 Planarity : 0.003 0.030 1841 Dihedral : 18.344 148.852 2619 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.73 % Allowed : 11.09 % Favored : 88.18 % 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: 1.54 (0.25), residues: 1201 helix: 1.93 (0.21), residues: 615 sheet: -0.33 (0.39), residues: 157 loop : 0.34 (0.32), residues: 429 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 0.016 0.001 TYR A 544 ARG 0.006 0.000 ARG A 307 ********************** 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 53 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 1.352 Fit side-chains REVERT: A 1 MET cc_start: 0.4647 (ttp) cc_final: 0.4206 (mtm) outliers start: 8 outliers final: 7 residues processed: 51 average time/residue: 1.4666 time to fit residues: 81.8964 Evaluate side-chains 48 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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 742 GLU 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 31 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.078669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.059786 restraints weight = 20930.447| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 2.07 r_work: 0.2618 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12213 Z= 0.208 Angle : 0.506 7.851 16874 Z= 0.276 Chirality : 0.038 0.221 1894 Planarity : 0.003 0.032 1841 Dihedral : 18.334 148.600 2619 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.82 % Allowed : 10.91 % Favored : 88.27 % 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: 1.58 (0.25), residues: 1201 helix: 1.95 (0.21), residues: 615 sheet: -0.28 (0.39), residues: 157 loop : 0.37 (0.32), residues: 429 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 0.016 0.001 TYR A 544 ARG 0.008 0.000 ARG A 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3229.77 seconds wall clock time: 59 minutes 51.51 seconds (3591.51 seconds total)