Starting phenix.real_space_refine on Sun Nov 17 02:17:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfo_40446/11_2024/8sfo_40446.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfo_40446/11_2024/8sfo_40446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfo_40446/11_2024/8sfo_40446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfo_40446/11_2024/8sfo_40446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfo_40446/11_2024/8sfo_40446.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfo_40446/11_2024/8sfo_40446.cif" } resolution = 3.3 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= -0.001 sd= 0.028 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: 6 Type Number sf(0) Gaussians P 118 5.49 5 Mg 2 5.21 5 S 23 5.16 5 C 7660 2.51 5 N 2157 2.21 5 O 2646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12606 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 10138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1240, 10138 Classifications: {'peptide': 1240} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 46, 'TRANS': 1193} Chain breaks: 2 Chain: "B" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 826 Classifications: {'RNA': 39} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 16} Link IDs: {'rna2p': 6, 'rna3p': 32} Chain: "C" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 815 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "D" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 825 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.92, per 1000 atoms: 0.63 Number of scatterers: 12606 At special positions: 0 Unit cell: (90.24, 104.34, 142.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 23 16.00 P 118 15.00 Mg 2 11.99 O 2646 8.00 N 2157 7.00 C 7660 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: 3.39 Conformation dependent library (CDL) restraints added in 1.4 seconds 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 9 sheets defined 55.8% alpha, 9.7% beta 40 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 5.03 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 removed outlier: 3.734A pdb=" N PHE A 7 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 34 removed outlier: 3.572A pdb=" N HIS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN A 34 " --> pdb=" O HIS A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 67 Proline residue: A 52 - end of helix removed outlier: 4.063A pdb=" N ILE A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR A 58 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 86 Processing helix chain 'A' and resid 88 through 112 removed outlier: 3.988A pdb=" N TYR A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 131 removed outlier: 3.961A pdb=" N GLY A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.686A pdb=" N LEU A 137 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 removed outlier: 3.768A pdb=" N LEU A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 161 Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 178 removed outlier: 3.663A pdb=" N ASN A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 196 through 215 removed outlier: 3.943A pdb=" N LYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 230 removed outlier: 4.043A pdb=" N GLU A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 241 removed outlier: 3.696A pdb=" N PHE A 241 " --> pdb=" O ILE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 289 through 298 removed outlier: 3.939A pdb=" N SER A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 344 Processing helix chain 'A' and resid 344 through 355 removed outlier: 3.986A pdb=" N THR A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 359 removed outlier: 3.873A pdb=" N ILE A 359 " --> pdb=" O LEU A 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 356 through 359' Processing helix chain 'A' and resid 360 through 363 removed outlier: 3.540A pdb=" N HIS A 363 " --> pdb=" O ASP A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 404 through 416 removed outlier: 3.765A pdb=" N HIS A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 428 through 452 removed outlier: 3.600A pdb=" N SER A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 482 removed outlier: 3.578A pdb=" N LYS A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 509 through 522 removed outlier: 3.505A pdb=" N ASN A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 600 through 610 Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 612 through 619 Processing helix chain 'A' and resid 639 through 647 removed outlier: 3.574A pdb=" N ASN A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 664 removed outlier: 3.693A pdb=" N ALA A 660 " --> pdb=" O GLN A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 687 Processing helix chain 'A' and resid 694 through 698 removed outlier: 4.295A pdb=" N SER A 697 " --> pdb=" O ASP A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 704 removed outlier: 3.909A pdb=" N TYR A 704 " --> pdb=" O SER A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 716 through 719 removed outlier: 3.786A pdb=" N TYR A 719 " --> pdb=" O PRO A 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 716 through 719' Processing helix chain 'A' and resid 728 through 737 Processing helix chain 'A' and resid 747 through 751 removed outlier: 3.519A pdb=" N PHE A 750 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.596A pdb=" N PHE A 769 " --> pdb=" O TRP A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 861 through 866 removed outlier: 3.643A pdb=" N PHE A 864 " --> pdb=" O ASP A 861 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER A 866 " --> pdb=" O ARG A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 899 removed outlier: 3.912A pdb=" N ARG A 891 " --> pdb=" O LYS A 887 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 892 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 955 Processing helix chain 'A' and resid 964 through 987 removed outlier: 3.558A pdb=" N GLN A 974 " --> pdb=" O GLY A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1007 Processing helix chain 'A' and resid 1015 through 1025 removed outlier: 3.933A pdb=" N CYS A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1088 removed outlier: 3.763A pdb=" N THR A1087 " --> pdb=" O VAL A1084 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE A1088 " --> pdb=" O TRP A1085 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1084 through 1088' Processing helix chain 'A' and resid 1090 through 1100 Processing helix chain 'A' and resid 1177 through 1190 Processing helix chain 'A' and resid 1199 through 1205 removed outlier: 3.508A pdb=" N GLU A1205 " --> pdb=" O PRO A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1223 removed outlier: 3.809A pdb=" N ILE A1212 " --> pdb=" O ASP A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1254 Processing helix chain 'A' and resid 1261 through 1282 removed outlier: 3.633A pdb=" N LEU A1277 " --> pdb=" O LYS A1273 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A1282 " --> pdb=" O LEU A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1307 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.815A pdb=" N LEU A 787 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 11.531A pdb=" N ALA A 554 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N TYR A 595 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LEU A 556 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.815A pdb=" N LEU A 787 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA4, first strand: chain 'A' and resid 626 through 628 Processing sheet with id=AA5, first strand: chain 'A' and resid 907 through 909 removed outlier: 7.278A pdb=" N ILE A 915 " --> pdb=" O SER A 931 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N SER A 931 " --> pdb=" O ILE A 915 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE A 917 " --> pdb=" O GLN A 929 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLN A 929 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL A 919 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 990 through 994 Processing sheet with id=AA7, first strand: chain 'A' and resid 1104 through 1106 Processing sheet with id=AA8, first strand: chain 'A' and resid 1145 through 1147 Processing sheet with id=AA9, first strand: chain 'A' and resid 1159 through 1162 504 hydrogen bonds defined for protein. 1425 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 99 hydrogen bonds 194 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 7.24 Time building geometry restraints manager: 3.87 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: 2362 1.33 - 1.45: 3783 1.45 - 1.57: 6712 1.57 - 1.69: 234 1.69 - 1.81: 38 Bond restraints: 13129 Sorted by residual: bond pdb=" C3' DG D 24 " pdb=" O3' DG D 24 " ideal model delta sigma weight residual 1.422 1.481 -0.059 3.00e-02 1.11e+03 3.88e+00 bond pdb=" C3' DA D 32 " pdb=" O3' DA D 32 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.73e+00 bond pdb=" CB GLU A 350 " pdb=" CG GLU A 350 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.08e+00 bond pdb=" CB ASN A 354 " pdb=" CG ASN A 354 " ideal model delta sigma weight residual 1.516 1.551 -0.035 2.50e-02 1.60e+03 1.97e+00 bond pdb=" CA ILE A 905 " pdb=" C ILE A 905 " ideal model delta sigma weight residual 1.523 1.540 -0.017 1.27e-02 6.20e+03 1.86e+00 ... (remaining 13124 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.02: 18193 5.02 - 10.04: 50 10.04 - 15.06: 22 15.06 - 20.09: 2 20.09 - 25.11: 1 Bond angle restraints: 18268 Sorted by residual: angle pdb=" O3' DG D 6 " pdb=" P DA D 7 " pdb=" OP1 DA D 7 " ideal model delta sigma weight residual 108.00 133.11 -25.11 3.00e+00 1.11e-01 7.00e+01 angle pdb=" O3' DC C 7 " pdb=" P DA C 8 " pdb=" OP1 DA C 8 " ideal model delta sigma weight residual 108.00 125.09 -17.09 3.00e+00 1.11e-01 3.24e+01 angle pdb=" OP1 DA D 7 " pdb=" P DA D 7 " pdb=" OP2 DA D 7 " ideal model delta sigma weight residual 120.00 103.52 16.48 3.00e+00 1.11e-01 3.02e+01 angle pdb=" OP1 DA C 8 " pdb=" P DA C 8 " pdb=" OP2 DA C 8 " ideal model delta sigma weight residual 120.00 106.10 13.90 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CG1 ILE A 905 " pdb=" CB ILE A 905 " pdb=" CG2 ILE A 905 " ideal model delta sigma weight residual 110.70 97.09 13.61 3.00e+00 1.11e-01 2.06e+01 ... (remaining 18263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.27: 7080 31.27 - 62.54: 609 62.54 - 93.81: 46 93.81 - 125.09: 3 125.09 - 156.36: 3 Dihedral angle restraints: 7741 sinusoidal: 4083 harmonic: 3658 Sorted by residual: dihedral pdb=" O4' C B 11 " pdb=" C1' C B 11 " pdb=" N1 C B 11 " pdb=" C2 C B 11 " ideal model delta sinusoidal sigma weight residual 200.00 49.49 150.51 1 1.50e+01 4.44e-03 7.98e+01 dihedral pdb=" O4' U B 12 " pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sinusoidal sigma weight residual 200.00 76.88 123.12 1 1.50e+01 4.44e-03 6.60e+01 dihedral pdb=" CA PHE A 598 " pdb=" C PHE A 598 " pdb=" N PRO A 599 " pdb=" CA PRO A 599 " ideal model delta harmonic sigma weight residual -180.00 -149.41 -30.59 0 5.00e+00 4.00e-02 3.74e+01 ... (remaining 7738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 2013 0.147 - 0.295: 7 0.295 - 0.442: 16 0.442 - 0.590: 0 0.590 - 0.737: 2 Chirality restraints: 2038 Sorted by residual: chirality pdb=" P DA D 7 " pdb=" OP1 DA D 7 " pdb=" OP2 DA D 7 " pdb=" O5' DA D 7 " both_signs ideal model delta sigma weight residual True 2.35 -3.08 -0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" P DA C 8 " pdb=" OP1 DA C 8 " pdb=" OP2 DA C 8 " pdb=" O5' DA C 8 " both_signs ideal model delta sigma weight residual True 2.35 -2.95 -0.61 2.00e-01 2.50e+01 9.26e+00 chirality pdb=" P DA C 28 " pdb=" OP1 DA C 28 " pdb=" OP2 DA C 28 " pdb=" O5' DA C 28 " both_signs ideal model delta sigma weight residual True 2.35 -2.77 -0.43 2.00e-01 2.50e+01 4.60e+00 ... (remaining 2035 not shown) Planarity restraints: 1922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 146 " -0.038 2.00e-02 2.50e+03 7.42e-02 5.50e+01 pdb=" C LEU A 146 " 0.128 2.00e-02 2.50e+03 pdb=" O LEU A 146 " -0.048 2.00e-02 2.50e+03 pdb=" N GLY A 147 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC C 12 " -0.018 2.00e-02 2.50e+03 2.36e-02 1.25e+01 pdb=" N1 DC C 12 " 0.056 2.00e-02 2.50e+03 pdb=" C2 DC C 12 " -0.037 2.00e-02 2.50e+03 pdb=" O2 DC C 12 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DC C 12 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DC C 12 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC C 12 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DC C 12 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DC C 12 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 103 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.96e+00 pdb=" C ARG A 103 " -0.046 2.00e-02 2.50e+03 pdb=" O ARG A 103 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN A 104 " 0.015 2.00e-02 2.50e+03 ... (remaining 1919 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 132 2.63 - 3.19: 10173 3.19 - 3.76: 20724 3.76 - 4.33: 27593 4.33 - 4.90: 44032 Nonbonded interactions: 102654 Sorted by model distance: nonbonded pdb=" OP1 DC D 31 " pdb="MG MG A1402 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASP A 908 " pdb="MG MG A1401 " model vdw 2.141 2.170 nonbonded pdb=" O ASN A1090 " pdb=" OG SER A1093 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR A 109 " pdb=" OD1 ASN A 116 " model vdw 2.281 3.040 nonbonded pdb=" O LYS A1158 " pdb=" OH TYR A1236 " model vdw 2.287 3.040 ... (remaining 102649 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: 1.370 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: 0.530 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 36.520 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 : 0.004 0.064 13129 Z= 0.240 Angle : 0.863 25.108 18268 Z= 0.409 Chirality : 0.059 0.737 2038 Planarity : 0.005 0.074 1922 Dihedral : 20.068 156.358 5373 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.18 % Allowed : 13.63 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: -0.41 (0.22), residues: 1234 helix: -0.09 (0.19), residues: 603 sheet: -0.51 (0.43), residues: 131 loop : -0.19 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 676 HIS 0.005 0.001 HIS A 300 PHE 0.012 0.001 PHE A1103 TYR 0.021 0.002 TYR A 595 ARG 0.006 0.001 ARG A 574 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 1.280 Fit side-chains revert: symmetry clash REVERT: A 475 LEU cc_start: 0.8628 (tp) cc_final: 0.8396 (tp) outliers start: 2 outliers final: 0 residues processed: 57 average time/residue: 0.2922 time to fit residues: 25.0229 Evaluate side-chains 35 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 363 HIS A 630 ASN A 941 GLN A1024 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13129 Z= 0.278 Angle : 0.586 10.676 18268 Z= 0.314 Chirality : 0.039 0.165 2038 Planarity : 0.004 0.041 1922 Dihedral : 21.206 173.722 2823 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.17 % Allowed : 12.64 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.17 (0.24), residues: 1234 helix: 1.50 (0.21), residues: 619 sheet: -0.30 (0.43), residues: 119 loop : 0.26 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1085 HIS 0.003 0.001 HIS A 300 PHE 0.013 0.001 PHE A 198 TYR 0.016 0.001 TYR A 595 ARG 0.004 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 47 average time/residue: 0.2368 time to fit residues: 18.0895 Evaluate side-chains 31 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1227 ASN ** A1290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13129 Z= 0.295 Angle : 0.573 10.235 18268 Z= 0.306 Chirality : 0.039 0.235 2038 Planarity : 0.003 0.039 1922 Dihedral : 21.223 173.140 2823 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.90 % Allowed : 13.18 % Favored : 85.92 % 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: 1.74 (0.25), residues: 1234 helix: 2.16 (0.22), residues: 614 sheet: -0.39 (0.45), residues: 117 loop : 0.38 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1085 HIS 0.004 0.001 HIS A 368 PHE 0.012 0.001 PHE A 198 TYR 0.016 0.001 TYR A 595 ARG 0.003 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 1.367 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 39 average time/residue: 0.2336 time to fit residues: 15.4169 Evaluate side-chains 32 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1216 VAL Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 HIS A1227 ASN ** A1280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 13129 Z= 0.417 Angle : 0.639 10.978 18268 Z= 0.340 Chirality : 0.041 0.271 2038 Planarity : 0.004 0.045 1922 Dihedral : 21.339 174.202 2823 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.81 % Allowed : 13.81 % Favored : 84.39 % 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: 1.83 (0.25), residues: 1234 helix: 2.24 (0.22), residues: 611 sheet: -0.61 (0.44), residues: 117 loop : 0.50 (0.30), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1085 HIS 0.010 0.001 HIS A 368 PHE 0.016 0.002 PHE A1249 TYR 0.016 0.002 TYR A 83 ARG 0.005 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 23 time to evaluate : 1.239 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 42 average time/residue: 0.2293 time to fit residues: 16.2313 Evaluate side-chains 29 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1216 VAL Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13129 Z= 0.176 Angle : 0.526 11.566 18268 Z= 0.282 Chirality : 0.038 0.220 2038 Planarity : 0.003 0.040 1922 Dihedral : 21.223 175.533 2823 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.99 % Allowed : 14.89 % Favored : 84.12 % 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: 2.09 (0.25), residues: 1234 helix: 2.52 (0.22), residues: 607 sheet: -0.47 (0.45), residues: 117 loop : 0.54 (0.30), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1085 HIS 0.006 0.001 HIS A 368 PHE 0.015 0.001 PHE A 172 TYR 0.017 0.001 TYR A 595 ARG 0.002 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: A 983 MET cc_start: 0.6189 (tpp) cc_final: 0.5922 (ttt) outliers start: 11 outliers final: 7 residues processed: 35 average time/residue: 0.2500 time to fit residues: 14.7762 Evaluate side-chains 29 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13129 Z= 0.342 Angle : 0.581 11.769 18268 Z= 0.310 Chirality : 0.040 0.197 2038 Planarity : 0.003 0.043 1922 Dihedral : 21.206 176.198 2823 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.62 % Allowed : 14.62 % Favored : 83.75 % 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: 2.07 (0.25), residues: 1234 helix: 2.48 (0.22), residues: 612 sheet: -0.56 (0.45), residues: 119 loop : 0.58 (0.30), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1085 HIS 0.008 0.001 HIS A 368 PHE 0.014 0.001 PHE A 198 TYR 0.015 0.001 TYR A 595 ARG 0.004 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 20 time to evaluate : 1.360 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 37 average time/residue: 0.2105 time to fit residues: 13.9743 Evaluate side-chains 31 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 19 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1299 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13129 Z= 0.340 Angle : 0.587 12.911 18268 Z= 0.313 Chirality : 0.040 0.176 2038 Planarity : 0.003 0.042 1922 Dihedral : 21.158 176.570 2823 Min Nonbonded Distance : 1.482 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.44 % Allowed : 15.25 % Favored : 83.30 % 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: 2.08 (0.25), residues: 1234 helix: 2.48 (0.22), residues: 610 sheet: -0.62 (0.45), residues: 119 loop : 0.62 (0.30), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1085 HIS 0.009 0.001 HIS A 368 PHE 0.012 0.001 PHE A 198 TYR 0.016 0.001 TYR A 595 ARG 0.003 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 19 time to evaluate : 1.331 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 34 average time/residue: 0.1990 time to fit residues: 12.5322 Evaluate side-chains 30 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 18 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1030 ASP Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13129 Z= 0.222 Angle : 0.538 13.077 18268 Z= 0.286 Chirality : 0.039 0.250 2038 Planarity : 0.003 0.041 1922 Dihedral : 21.097 177.672 2823 Min Nonbonded Distance : 1.378 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.44 % Allowed : 15.52 % Favored : 83.03 % 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: 2.17 (0.25), residues: 1234 helix: 2.58 (0.22), residues: 612 sheet: -0.59 (0.45), residues: 121 loop : 0.62 (0.30), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1085 HIS 0.008 0.001 HIS A 368 PHE 0.011 0.001 PHE A1117 TYR 0.018 0.001 TYR A 595 ARG 0.002 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 21 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 36 average time/residue: 0.2260 time to fit residues: 14.0592 Evaluate side-chains 31 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 19 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 109 optimal weight: 0.0470 chunk 114 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 HIS A1126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13129 Z= 0.242 Angle : 0.560 13.733 18268 Z= 0.294 Chirality : 0.039 0.243 2038 Planarity : 0.003 0.039 1922 Dihedral : 21.083 178.415 2823 Min Nonbonded Distance : 1.235 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.35 % Allowed : 15.43 % Favored : 83.21 % 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: 2.21 (0.25), residues: 1234 helix: 2.63 (0.22), residues: 611 sheet: -0.62 (0.44), residues: 121 loop : 0.66 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1085 HIS 0.008 0.001 HIS A 368 PHE 0.010 0.001 PHE A 198 TYR 0.017 0.001 TYR A 595 ARG 0.002 0.000 ARG A1121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 20 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 34 average time/residue: 0.2271 time to fit residues: 13.3080 Evaluate side-chains 33 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 19 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1030 ASP Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1299 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 134 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 11 optimal weight: 0.0870 chunk 82 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 890 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13129 Z= 0.150 Angle : 0.537 14.013 18268 Z= 0.278 Chirality : 0.038 0.261 2038 Planarity : 0.003 0.036 1922 Dihedral : 21.010 179.542 2823 Min Nonbonded Distance : 1.263 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.99 % Allowed : 16.16 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.28 (0.25), residues: 1234 helix: 2.65 (0.22), residues: 613 sheet: -0.59 (0.44), residues: 131 loop : 0.76 (0.31), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1085 HIS 0.006 0.001 HIS A 368 PHE 0.006 0.001 PHE A 619 TYR 0.017 0.001 TYR A 595 ARG 0.001 0.000 ARG A 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 34 average time/residue: 0.2199 time to fit residues: 13.0248 Evaluate side-chains 32 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1030 ASP Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3139 r_free = 0.3139 target = 0.044689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.030998 restraints weight = 69823.910| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 4.07 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13129 Z= 0.150 Angle : 0.538 13.873 18268 Z= 0.278 Chirality : 0.037 0.243 2038 Planarity : 0.003 0.034 1922 Dihedral : 20.930 177.970 2823 Min Nonbonded Distance : 1.225 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.08 % Allowed : 15.88 % Favored : 83.03 % 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: 2.38 (0.25), residues: 1234 helix: 2.71 (0.22), residues: 613 sheet: -0.32 (0.45), residues: 124 loop : 0.75 (0.31), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1085 HIS 0.006 0.001 HIS A 368 PHE 0.008 0.001 PHE A1117 TYR 0.016 0.001 TYR A 595 ARG 0.002 0.000 ARG A 790 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1916.62 seconds wall clock time: 36 minutes 29.12 seconds (2189.12 seconds total)