Starting phenix.real_space_refine on Sun Nov 17 04:02:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfn_40445/11_2024/8sfn_40445.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfn_40445/11_2024/8sfn_40445.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/8sfn_40445/11_2024/8sfn_40445.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfn_40445/11_2024/8sfn_40445.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfn_40445/11_2024/8sfn_40445.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfn_40445/11_2024/8sfn_40445.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= 0.000 sd= 0.025 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: 5 Type Number sf(0) Gaussians P 103 5.49 5 S 26 5.16 5 C 7836 2.51 5 N 2195 2.21 5 O 2647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 12807 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1302, 10652 Classifications: {'peptide': 1302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 49, 'TRANS': 1252} Chain breaks: 1 Chain: "B" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 761 Classifications: {'RNA': 36} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 15, 'rna3p_pyr': 14} Link IDs: {'rna2p': 6, 'rna3p': 29} Chain: "C" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 693 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "D" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 701 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Time building chain proxies: 8.40, per 1000 atoms: 0.66 Number of scatterers: 12807 At special positions: 0 Unit cell: (102.484, 94.9848, 135.812, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 P 103 15.00 O 2647 8.00 N 2195 7.00 C 7836 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: 3.35 Conformation dependent library (CDL) restraints added in 1.5 seconds 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2490 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 54.3% alpha, 13.0% beta 37 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 5.22 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 removed outlier: 3.544A pdb=" N PHE A 7 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 35 through 67 Proline residue: A 52 - end of helix Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.657A pdb=" N SER A 77 " --> pdb=" O TRP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 112 removed outlier: 3.934A pdb=" N TYR A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 133 removed outlier: 4.031A pdb=" N PHE A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.917A pdb=" N LEU A 137 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 138 " --> pdb=" O ALA A 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 134 through 138' Processing helix chain 'A' and resid 140 through 147 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 Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 197 through 215 Processing helix chain 'A' and resid 217 through 230 removed outlier: 3.875A pdb=" N HIS A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 241 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 288 removed outlier: 3.594A pdb=" N VAL A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 297 Processing helix chain 'A' and resid 325 through 344 removed outlier: 3.935A pdb=" N VAL A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 359 removed outlier: 4.001A pdb=" N THR A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASN A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 364 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 379 removed outlier: 3.906A pdb=" N ILE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 404 through 413 removed outlier: 4.036A pdb=" N VAL A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.523A pdb=" N ILE A 423 " --> pdb=" O ASN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 452 removed outlier: 3.997A pdb=" N GLU A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 484 removed outlier: 3.811A pdb=" N LYS A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 Processing helix chain 'A' and resid 507 through 522 removed outlier: 4.322A pdb=" N LEU A 511 " --> pdb=" O MET A 507 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER A 512 " --> pdb=" O GLU A 508 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 570 through 574 removed outlier: 3.671A pdb=" N GLY A 573 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 612 through 620 Processing helix chain 'A' and resid 639 through 647 removed outlier: 4.798A pdb=" N LEU A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 663 removed outlier: 3.770A 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 700 through 704 removed outlier: 3.505A 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 728 through 737 Processing helix chain 'A' and resid 747 through 751 Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.878A 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 819 through 831 removed outlier: 3.741A pdb=" N GLU A 825 " --> pdb=" O THR A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 846 Processing helix chain 'A' and resid 887 through 899 Processing helix chain 'A' and resid 939 through 957 removed outlier: 4.221A pdb=" N LYS A 943 " --> pdb=" O ASP A 939 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN A 946 " --> pdb=" O LYS A 942 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 987 removed outlier: 4.391A 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 1010 through 1024 removed outlier: 3.628A pdb=" N PHE A1015 " --> pdb=" O VAL A1011 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLU A1016 " --> pdb=" O TYR A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1100 Processing helix chain 'A' and resid 1177 through 1190 removed outlier: 3.566A pdb=" N GLU A1181 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1206 removed outlier: 3.979A pdb=" N ASN A1206 " --> pdb=" O LYS A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1224 removed outlier: 3.882A pdb=" N ILE A1212 " --> pdb=" O ASP A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1254 No H-bonds generated for 'chain 'A' and resid 1252 through 1254' Processing helix chain 'A' and resid 1261 through 1283 Processing helix chain 'A' and resid 1294 through 1307 Processing sheet with id=AA1, first strand: chain 'A' and resid 719 through 727 removed outlier: 5.658A pdb=" N LEU A 556 " --> pdb=" O MET A 593 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N TYR A 595 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ALA A 554 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 719 through 727 removed outlier: 5.658A pdb=" N LEU A 556 " --> pdb=" O MET A 593 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N TYR A 595 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ALA A 554 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 266 removed outlier: 3.737A pdb=" N ILE A 265 " --> pdb=" O ILE A 274 " (cutoff:3.500A) 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 805 through 811 removed outlier: 3.766A pdb=" N ASN A 808 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A 850 " --> pdb=" O ASN A 808 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 926 through 930 removed outlier: 6.729A pdb=" N VAL A 919 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN A 929 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE A 917 " --> pdb=" O GLN A 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 918 " --> pdb=" O GLY A 906 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU A 993 " --> pdb=" O ILE A 907 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1101 through 1106 removed outlier: 6.701A pdb=" N HIS A1116 " --> pdb=" O ASP A1102 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A1104 " --> pdb=" O ILE A1114 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE A1114 " --> pdb=" O LEU A1104 " (cutoff:3.500A) 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 1161 through 1162 removed outlier: 3.590A pdb=" N VAL A1161 " --> pdb=" O ARG A1174 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1226 through 1227 removed outlier: 4.290A pdb=" N PHE A1249 " --> pdb=" O SER A1239 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1572 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 7.48 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3357 1.34 - 1.46: 3240 1.46 - 1.58: 6456 1.58 - 1.70: 207 1.70 - 1.82: 44 Bond restraints: 13304 Sorted by residual: bond pdb=" CB PRO A1178 " pdb=" CG PRO A1178 " ideal model delta sigma weight residual 1.492 1.625 -0.133 5.00e-02 4.00e+02 7.07e+00 bond pdb=" CB GLU A 857 " pdb=" CG GLU A 857 " ideal model delta sigma weight residual 1.520 1.587 -0.067 3.00e-02 1.11e+03 5.02e+00 bond pdb=" CG1 ILE A 979 " pdb=" CD1 ILE A 979 " ideal model delta sigma weight residual 1.513 1.427 0.086 3.90e-02 6.57e+02 4.91e+00 bond pdb=" CB PHE A1249 " pdb=" CG PHE A1249 " ideal model delta sigma weight residual 1.502 1.552 -0.050 2.30e-02 1.89e+03 4.64e+00 bond pdb=" CB PRO A1042 " pdb=" CG PRO A1042 " ideal model delta sigma weight residual 1.492 1.598 -0.106 5.00e-02 4.00e+02 4.49e+00 ... (remaining 13299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.65: 18270 5.65 - 11.29: 142 11.29 - 16.94: 16 16.94 - 22.59: 5 22.59 - 28.23: 1 Bond angle restraints: 18434 Sorted by residual: angle pdb=" CA PRO A1178 " pdb=" N PRO A1178 " pdb=" CD PRO A1178 " ideal model delta sigma weight residual 112.00 96.92 15.08 1.40e+00 5.10e-01 1.16e+02 angle pdb=" O3' DG D 6 " pdb=" P DA D 7 " pdb=" OP1 DA D 7 " ideal model delta sigma weight residual 108.00 136.23 -28.23 3.00e+00 1.11e-01 8.86e+01 angle pdb=" O3' DA D 20 " pdb=" P DA D 21 " pdb=" OP1 DA D 21 " ideal model delta sigma weight residual 108.00 129.72 -21.72 3.00e+00 1.11e-01 5.24e+01 angle pdb=" O3' DA D 21 " pdb=" P DG D 22 " pdb=" OP1 DG D 22 " ideal model delta sigma weight residual 108.00 126.71 -18.71 3.00e+00 1.11e-01 3.89e+01 angle pdb=" CA ARG A 386 " pdb=" CB ARG A 386 " pdb=" CG ARG A 386 " ideal model delta sigma weight residual 114.10 126.42 -12.32 2.00e+00 2.50e-01 3.79e+01 ... (remaining 18429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.13: 7289 35.13 - 70.27: 570 70.27 - 105.40: 33 105.40 - 140.53: 2 140.53 - 175.66: 5 Dihedral angle restraints: 7899 sinusoidal: 4053 harmonic: 3846 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 47.25 152.75 1 1.50e+01 4.44e-03 8.06e+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 67.59 132.41 1 1.50e+01 4.44e-03 7.14e+01 dihedral pdb=" CA TYR A 746 " pdb=" C TYR A 746 " pdb=" N ASN A 747 " pdb=" CA ASN A 747 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 7896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 2002 0.152 - 0.305: 25 0.305 - 0.457: 20 0.457 - 0.610: 3 0.610 - 0.762: 3 Chirality restraints: 2053 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 -3.11 -0.76 2.00e-01 2.50e+01 1.45e+01 chirality pdb=" P DA D 21 " pdb=" OP1 DA D 21 " pdb=" OP2 DA D 21 " pdb=" O5' DA D 21 " both_signs ideal model delta sigma weight residual True 2.35 -3.02 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" P DG D 22 " pdb=" OP1 DG D 22 " pdb=" OP2 DG D 22 " pdb=" O5' DG D 22 " both_signs ideal model delta sigma weight residual True 2.35 -2.96 -0.61 2.00e-01 2.50e+01 9.35e+00 ... (remaining 2050 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A1177 " -0.134 5.00e-02 4.00e+02 1.89e-01 5.69e+01 pdb=" N PRO A1178 " 0.325 5.00e-02 4.00e+02 pdb=" CA PRO A1178 " -0.101 5.00e-02 4.00e+02 pdb=" CD PRO A1178 " -0.091 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1041 " 0.068 5.00e-02 4.00e+02 9.79e-02 1.53e+01 pdb=" N PRO A1042 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO A1042 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A1042 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 184 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ASP A 184 " 0.064 2.00e-02 2.50e+03 pdb=" O ASP A 184 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE A 185 " -0.021 2.00e-02 2.50e+03 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 811 2.73 - 3.27: 12732 3.27 - 3.82: 23450 3.82 - 4.36: 27512 4.36 - 4.90: 42953 Nonbonded interactions: 107458 Sorted by model distance: nonbonded pdb=" OG SER A 236 " pdb=" OE1 GLU A 238 " model vdw 2.188 3.040 nonbonded pdb=" O CYS A 334 " pdb=" OG1 THR A 338 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR A 595 " pdb=" O LEU A 781 " model vdw 2.277 3.040 nonbonded pdb=" O TYR A 11 " pdb=" NE2 GLN A1044 " model vdw 2.292 3.120 nonbonded pdb=" O ILE A1073 " pdb=" ND2 ASN A1265 " model vdw 2.299 3.120 ... (remaining 107453 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=1.00 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: 0.010 Normalize map: mean=0, sd=1: 2.820 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: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 37.880 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 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 : 0.005 0.133 13304 Z= 0.328 Angle : 1.222 28.234 18434 Z= 0.573 Chirality : 0.072 0.762 2053 Planarity : 0.008 0.189 1998 Dihedral : 21.535 175.662 5409 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.26 % Allowed : 26.93 % Favored : 72.81 % 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: -1.30 (0.22), residues: 1298 helix: -0.61 (0.19), residues: 613 sheet: -0.69 (0.42), residues: 148 loop : -1.03 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP A 483 HIS 0.024 0.002 HIS A 479 PHE 0.029 0.002 PHE A 999 TYR 0.039 0.002 TYR A 971 ARG 0.014 0.001 ARG A 386 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 999 PHE cc_start: 0.6747 (t80) cc_final: 0.5837 (t80) outliers start: 3 outliers final: 1 residues processed: 105 average time/residue: 0.2694 time to fit residues: 41.8488 Evaluate side-chains 90 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 972 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 42 optimal weight: 40.0000 chunk 66 optimal weight: 5.9990 chunk 81 optimal weight: 0.0980 chunk 126 optimal weight: 7.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN A 913 ASN A 929 GLN ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 GLN ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1295 ASN A1303 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13304 Z= 0.372 Angle : 0.734 10.305 18434 Z= 0.392 Chirality : 0.043 0.166 2053 Planarity : 0.005 0.099 1998 Dihedral : 22.119 175.115 2718 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.34 % Allowed : 22.98 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.04 (0.23), residues: 1298 helix: 0.71 (0.20), residues: 625 sheet: -0.95 (0.45), residues: 134 loop : -0.54 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1258 HIS 0.011 0.002 HIS A 479 PHE 0.023 0.002 PHE A 198 TYR 0.023 0.002 TYR A 61 ARG 0.008 0.001 ARG A 386 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 75 time to evaluate : 1.336 Fit side-chains revert: symmetry clash REVERT: A 319 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8643 (mm) outliers start: 39 outliers final: 17 residues processed: 103 average time/residue: 0.2573 time to fit residues: 40.2203 Evaluate side-chains 88 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 973 SER Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 85 optimal weight: 0.0670 chunk 34 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN A 969 GLN ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13304 Z= 0.197 Angle : 0.623 10.426 18434 Z= 0.329 Chirality : 0.039 0.161 2053 Planarity : 0.004 0.064 1998 Dihedral : 22.005 179.189 2716 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.49 % Allowed : 22.73 % Favored : 74.79 % 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: 0.37 (0.24), residues: 1298 helix: 1.13 (0.21), residues: 626 sheet: -0.91 (0.44), residues: 137 loop : -0.38 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1298 HIS 0.009 0.001 HIS A 479 PHE 0.020 0.001 PHE A 999 TYR 0.018 0.001 TYR A 595 ARG 0.005 0.000 ARG A 386 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8592 (mm) REVERT: A 1270 ILE cc_start: 0.8440 (pt) cc_final: 0.8180 (pt) outliers start: 29 outliers final: 14 residues processed: 105 average time/residue: 0.2899 time to fit residues: 45.9179 Evaluate side-chains 85 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1248 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 9.9990 chunk 95 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 120 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 GLN ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 13304 Z= 0.476 Angle : 0.771 10.222 18434 Z= 0.414 Chirality : 0.045 0.182 2053 Planarity : 0.005 0.054 1998 Dihedral : 22.330 179.636 2716 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.37 % Allowed : 22.64 % Favored : 72.98 % 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: 0.07 (0.23), residues: 1298 helix: 0.89 (0.20), residues: 629 sheet: -0.85 (0.44), residues: 135 loop : -0.63 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 483 HIS 0.007 0.002 HIS A1105 PHE 0.023 0.002 PHE A 198 TYR 0.024 0.003 TYR A 61 ARG 0.004 0.001 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 72 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8739 (mm) REVERT: A 1299 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8596 (tp) outliers start: 51 outliers final: 30 residues processed: 116 average time/residue: 0.2578 time to fit residues: 44.4886 Evaluate side-chains 101 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 PHE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1049 PHE Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1301 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13304 Z= 0.174 Angle : 0.645 11.958 18434 Z= 0.335 Chirality : 0.040 0.351 2053 Planarity : 0.004 0.043 1998 Dihedral : 21.999 179.650 2716 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.49 % Allowed : 24.36 % Favored : 73.16 % 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: 0.47 (0.24), residues: 1298 helix: 1.28 (0.21), residues: 628 sheet: -1.00 (0.42), residues: 144 loop : -0.37 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 765 HIS 0.006 0.001 HIS A 479 PHE 0.014 0.001 PHE A 165 TYR 0.022 0.001 TYR A 595 ARG 0.005 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8706 (mm) outliers start: 29 outliers final: 17 residues processed: 107 average time/residue: 0.2568 time to fit residues: 41.4667 Evaluate side-chains 90 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 PHE Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1174 ARG Chi-restraints excluded: chain A residue 1248 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 26 optimal weight: 0.0470 chunk 78 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 111 optimal weight: 0.0770 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 overall best weight: 2.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 GLN ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13304 Z= 0.256 Angle : 0.651 11.581 18434 Z= 0.342 Chirality : 0.041 0.311 2053 Planarity : 0.004 0.049 1998 Dihedral : 21.997 177.958 2716 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.26 % Allowed : 24.10 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.24), residues: 1298 helix: 1.37 (0.21), residues: 621 sheet: -0.87 (0.43), residues: 135 loop : -0.40 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 765 HIS 0.005 0.001 HIS A 479 PHE 0.018 0.001 PHE A 513 TYR 0.032 0.002 TYR A 971 ARG 0.004 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 77 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8766 (mm) outliers start: 38 outliers final: 31 residues processed: 106 average time/residue: 0.2531 time to fit residues: 40.6105 Evaluate side-chains 106 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 74 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 PHE Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1174 ARG Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1301 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 13304 Z= 0.214 Angle : 0.631 11.874 18434 Z= 0.330 Chirality : 0.040 0.207 2053 Planarity : 0.004 0.047 1998 Dihedral : 21.914 179.334 2716 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.09 % Allowed : 24.19 % Favored : 72.73 % 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: 0.60 (0.24), residues: 1298 helix: 1.42 (0.21), residues: 621 sheet: -1.00 (0.41), residues: 149 loop : -0.32 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1298 HIS 0.004 0.001 HIS A 479 PHE 0.015 0.001 PHE A 513 TYR 0.040 0.002 TYR A 971 ARG 0.003 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 77 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8786 (mm) REVERT: A 1224 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.6454 (pp30) outliers start: 36 outliers final: 27 residues processed: 105 average time/residue: 0.2680 time to fit residues: 42.0032 Evaluate side-chains 102 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 PHE Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1049 PHE Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1224 GLN Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1301 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 105 optimal weight: 0.0970 chunk 121 optimal weight: 5.9990 overall best weight: 2.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 ASN ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13304 Z= 0.220 Angle : 0.644 12.422 18434 Z= 0.336 Chirality : 0.040 0.207 2053 Planarity : 0.004 0.047 1998 Dihedral : 21.906 178.983 2716 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.34 % Allowed : 24.01 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.24), residues: 1298 helix: 1.45 (0.21), residues: 619 sheet: -0.81 (0.43), residues: 139 loop : -0.35 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1298 HIS 0.004 0.001 HIS A 479 PHE 0.015 0.001 PHE A 513 TYR 0.043 0.002 TYR A 971 ARG 0.003 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 73 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8797 (mm) REVERT: A 1224 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.6419 (pp30) outliers start: 39 outliers final: 31 residues processed: 102 average time/residue: 0.2593 time to fit residues: 39.7413 Evaluate side-chains 105 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 72 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 PHE Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1049 PHE Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1224 GLN Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1301 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 0.1980 chunk 117 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN ** A 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 13304 Z= 0.190 Angle : 0.638 12.542 18434 Z= 0.332 Chirality : 0.040 0.199 2053 Planarity : 0.004 0.048 1998 Dihedral : 21.845 179.708 2716 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.17 % Allowed : 24.36 % Favored : 72.47 % 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: 0.67 (0.24), residues: 1298 helix: 1.43 (0.21), residues: 626 sheet: -0.64 (0.44), residues: 135 loop : -0.36 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1298 HIS 0.008 0.001 HIS A1096 PHE 0.016 0.001 PHE A1079 TYR 0.041 0.002 TYR A 971 ARG 0.005 0.000 ARG A1174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 76 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8799 (mm) REVERT: A 1224 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6448 (pp30) outliers start: 37 outliers final: 26 residues processed: 105 average time/residue: 0.2579 time to fit residues: 40.3038 Evaluate side-chains 99 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 PHE Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1224 GLN Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1301 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 85 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN ** A 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 GLN ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13304 Z= 0.201 Angle : 0.648 13.211 18434 Z= 0.336 Chirality : 0.040 0.201 2053 Planarity : 0.004 0.047 1998 Dihedral : 21.849 179.181 2716 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.74 % Allowed : 24.36 % Favored : 72.90 % 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: 0.68 (0.24), residues: 1298 helix: 1.43 (0.21), residues: 626 sheet: -0.58 (0.44), residues: 135 loop : -0.36 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 765 HIS 0.008 0.001 HIS A1096 PHE 0.050 0.001 PHE A 165 TYR 0.029 0.001 TYR A 971 ARG 0.010 0.000 ARG A 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 74 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8805 (mm) REVERT: A 1224 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.6470 (pp30) outliers start: 32 outliers final: 28 residues processed: 96 average time/residue: 0.2493 time to fit residues: 36.4969 Evaluate side-chains 102 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 PHE Chi-restraints excluded: chain A residue 1014 GLN Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1224 GLN Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1301 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 GLN ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.068832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.046739 restraints weight = 69526.254| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 5.23 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 13304 Z= 0.229 Angle : 0.649 13.002 18434 Z= 0.338 Chirality : 0.040 0.206 2053 Planarity : 0.004 0.044 1998 Dihedral : 21.864 178.503 2716 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.92 % Allowed : 24.27 % Favored : 72.81 % 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: 0.69 (0.24), residues: 1298 helix: 1.49 (0.21), residues: 619 sheet: -0.57 (0.44), residues: 135 loop : -0.40 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 765 HIS 0.007 0.001 HIS A1096 PHE 0.046 0.001 PHE A 165 TYR 0.020 0.002 TYR A 61 ARG 0.009 0.000 ARG A 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2430.24 seconds wall clock time: 45 minutes 50.84 seconds (2750.84 seconds total)