Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 02:56:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s38_24819/04_2023/7s38_24819_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s38_24819/04_2023/7s38_24819.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s38_24819/04_2023/7s38_24819_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s38_24819/04_2023/7s38_24819_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s38_24819/04_2023/7s38_24819_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s38_24819/04_2023/7s38_24819.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s38_24819/04_2023/7s38_24819.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s38_24819/04_2023/7s38_24819_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s38_24819/04_2023/7s38_24819_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.092 sd= 0.966 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 138 5.49 5 S 25 5.16 5 C 8392 2.51 5 N 2442 2.21 5 O 2990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 13987 Number of models: 1 Model: "" Number of chains: 4 Chain: "N" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 540 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "P" Number of atoms: 11065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1353, 11065 Classifications: {'peptide': 1353} Link IDs: {'PTRANS': 35, 'TRANS': 1317} Chain breaks: 1 Chain: "R" Number of atoms: 1855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1855 Classifications: {'RNA': 87} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 42, 'rna3p_pyr': 33} Link IDs: {'rna2p': 12, 'rna3p': 74} Chain: "T" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 527 Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 7.89, per 1000 atoms: 0.56 Number of scatterers: 13987 At special positions: 0 Unit cell: (123.9, 112.35, 107.1, 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 25 16.00 P 138 15.00 O 2990 8.00 N 2442 7.00 C 8392 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 - 3.50 Amino acid : False - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.56 Conformation dependent library (CDL) restraints added in 1.9 seconds 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2574 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 8 sheets defined 46.6% alpha, 7.1% beta 48 base pairs and 94 stacking pairs defined. Time for finding SS restraints: 6.10 Creating SS restraints... Processing helix chain 'P' and resid 60 through 93 removed outlier: 5.019A pdb=" N ASN P 88 " --> pdb=" O GLU P 84 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLU P 89 " --> pdb=" O ILE P 85 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS P 92 " --> pdb=" O ASN P 88 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL P 93 " --> pdb=" O GLU P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 102 Processing helix chain 'P' and resid 122 through 131 Processing helix chain 'P' and resid 135 through 144 Processing helix chain 'P' and resid 151 through 163 Processing helix chain 'P' and resid 176 through 178 No H-bonds generated for 'chain 'P' and resid 176 through 178' Processing helix chain 'P' and resid 181 through 195 Processing helix chain 'P' and resid 208 through 212 Processing helix chain 'P' and resid 218 through 227 Processing helix chain 'P' and resid 237 through 246 Processing helix chain 'P' and resid 253 through 256 No H-bonds generated for 'chain 'P' and resid 253 through 256' Processing helix chain 'P' and resid 269 through 282 removed outlier: 4.532A pdb=" N ASP P 272 " --> pdb=" O ASP P 269 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP P 273 " --> pdb=" O THR P 270 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU P 279 " --> pdb=" O ASP P 276 " (cutoff:3.500A) Processing helix chain 'P' and resid 284 through 305 removed outlier: 4.417A pdb=" N ASP P 288 " --> pdb=" O GLN P 285 " (cutoff:3.500A) Processing helix chain 'P' and resid 316 through 342 Processing helix chain 'P' and resid 347 through 351 Processing helix chain 'P' and resid 359 through 363 Processing helix chain 'P' and resid 369 through 382 Proline residue: P 378 - end of helix Processing helix chain 'P' and resid 389 through 394 Processing helix chain 'P' and resid 405 through 409 removed outlier: 3.771A pdb=" N GLY P 408 " --> pdb=" O PHE P 405 " (cutoff:3.500A) Processing helix chain 'P' and resid 412 through 425 Processing helix chain 'P' and resid 431 through 435 Processing helix chain 'P' and resid 437 through 445 Processing helix chain 'P' and resid 478 through 481 No H-bonds generated for 'chain 'P' and resid 478 through 481' Processing helix chain 'P' and resid 484 through 495 Processing helix chain 'P' and resid 513 through 526 removed outlier: 4.274A pdb=" N LYS P 526 " --> pdb=" O ASN P 522 " (cutoff:3.500A) Processing helix chain 'P' and resid 542 through 551 Processing helix chain 'P' and resid 561 through 567 Processing helix chain 'P' and resid 592 through 601 Processing helix chain 'P' and resid 604 through 608 removed outlier: 3.680A pdb=" N ASP P 608 " --> pdb=" O LYS P 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 604 through 608' Processing helix chain 'P' and resid 613 through 625 Processing helix chain 'P' and resid 629 through 635 Processing helix chain 'P' and resid 637 through 639 No H-bonds generated for 'chain 'P' and resid 637 through 639' Processing helix chain 'P' and resid 647 through 653 Processing helix chain 'P' and resid 664 through 668 Processing helix chain 'P' and resid 679 through 684 Processing helix chain 'P' and resid 693 through 698 Processing helix chain 'P' and resid 704 through 710 Processing helix chain 'P' and resid 712 through 715 No H-bonds generated for 'chain 'P' and resid 712 through 715' Processing helix chain 'P' and resid 720 through 725 Processing helix chain 'P' and resid 731 through 750 Processing helix chain 'P' and resid 775 through 791 Processing helix chain 'P' and resid 795 through 798 No H-bonds generated for 'chain 'P' and resid 795 through 798' Processing helix chain 'P' and resid 805 through 807 No H-bonds generated for 'chain 'P' and resid 805 through 807' Processing helix chain 'P' and resid 809 through 816 Processing helix chain 'P' and resid 852 through 854 No H-bonds generated for 'chain 'P' and resid 852 through 854' Processing helix chain 'P' and resid 861 through 864 removed outlier: 3.651A pdb=" N ARG P 864 " --> pdb=" O ASP P 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 861 through 864' Processing helix chain 'P' and resid 873 through 888 removed outlier: 3.800A pdb=" N LYS P 878 " --> pdb=" O GLU P 874 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ASN P 881 " --> pdb=" O LYS P 877 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N TYR P 882 " --> pdb=" O LYS P 878 " (cutoff:3.500A) Processing helix chain 'P' and resid 894 through 900 Processing helix chain 'P' and resid 903 through 905 No H-bonds generated for 'chain 'P' and resid 903 through 905' Processing helix chain 'P' and resid 910 through 921 Processing helix chain 'P' and resid 926 through 939 Processing helix chain 'P' and resid 960 through 969 Processing helix chain 'P' and resid 981 through 1000 Processing helix chain 'P' and resid 1002 through 1008 removed outlier: 4.655A pdb=" N SER P1006 " --> pdb=" O LYS P1003 " (cutoff:3.500A) Processing helix chain 'P' and resid 1018 through 1021 No H-bonds generated for 'chain 'P' and resid 1018 through 1021' Processing helix chain 'P' and resid 1042 through 1044 No H-bonds generated for 'chain 'P' and resid 1042 through 1044' Processing helix chain 'P' and resid 1078 through 1088 Processing helix chain 'P' and resid 1128 through 1131 No H-bonds generated for 'chain 'P' and resid 1128 through 1131' Processing helix chain 'P' and resid 1171 through 1176 Processing helix chain 'P' and resid 1178 through 1185 Processing helix chain 'P' and resid 1192 through 1194 No H-bonds generated for 'chain 'P' and resid 1192 through 1194' Processing helix chain 'P' and resid 1230 through 1240 Processing helix chain 'P' and resid 1249 through 1261 Processing helix chain 'P' and resid 1263 through 1279 removed outlier: 3.513A pdb=" N PHE P1276 " --> pdb=" O ILE P1273 " (cutoff:3.500A) Processing helix chain 'P' and resid 1284 through 1296 Processing helix chain 'P' and resid 1302 through 1315 removed outlier: 4.508A pdb=" N THR P1314 " --> pdb=" O ILE P1310 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU P1315 " --> pdb=" O HIS P1311 " (cutoff:3.500A) Processing helix chain 'P' and resid 1341 through 1344 Processing sheet with id= A, first strand: chain 'P' and resid 954 through 957 removed outlier: 6.430A pdb=" N ASN P1093 " --> pdb=" O ALA P 50 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU P 52 " --> pdb=" O ASN P1093 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL P1095 " --> pdb=" O LEU P 52 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'P' and resid 29 through 33 Processing sheet with id= C, first strand: chain 'P' and resid 34 through 36 removed outlier: 7.124A pdb=" N GLU P1357 " --> pdb=" O LEU P 35 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU P1203 " --> pdb=" O ILE P1348 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'P' and resid 837 through 840 Processing sheet with id= E, first strand: chain 'P' and resid 1049 through 1051 Processing sheet with id= F, first strand: chain 'P' and resid 1196 through 1199 removed outlier: 3.627A pdb=" N ILE P1196 " --> pdb=" O LEU P1144 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE P1166 " --> pdb=" O ALA P1140 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER P1142 " --> pdb=" O LEU P1164 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU P1164 " --> pdb=" O SER P1142 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU P1144 " --> pdb=" O GLU P1162 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLU P1162 " --> pdb=" O LEU P1144 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL P1146 " --> pdb=" O VAL P1160 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL P1160 " --> pdb=" O VAL P1146 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS P1148 " --> pdb=" O LYS P1158 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LYS P1158 " --> pdb=" O LYS P1148 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU P1150 " --> pdb=" O LYS P1156 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS P1156 " --> pdb=" O GLU P1150 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'P' and resid 1324 through 1326 Processing sheet with id= H, first strand: chain 'P' and resid 1063 through 1065 404 hydrogen bonds defined for protein. 1065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 116 hydrogen bonds 228 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 94 stacking parallelities Total time for adding SS restraints: 7.42 Time building geometry restraints manager: 6.89 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: 2639 1.33 - 1.45: 4045 1.45 - 1.57: 7518 1.57 - 1.69: 284 1.69 - 1.81: 46 Bond restraints: 14532 Sorted by residual: bond pdb=" C2' 2YR T 6 " pdb=" C3' 2YR T 6 " ideal model delta sigma weight residual 1.224 1.518 -0.294 2.00e-02 2.50e+03 2.16e+02 bond pdb=" C4' 2YR T 6 " pdb=" O4' 2YR T 6 " ideal model delta sigma weight residual 1.271 1.462 -0.191 2.00e-02 2.50e+03 9.11e+01 bond pdb=" C1' 2YR T 6 " pdb=" N1 2YR T 6 " ideal model delta sigma weight residual 1.348 1.532 -0.184 2.00e-02 2.50e+03 8.42e+01 bond pdb=" C5 2YR T 6 " pdb=" C6 2YR T 6 " ideal model delta sigma weight residual 1.499 1.335 0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" C2 2YR T 6 " pdb=" N3 2YR T 6 " ideal model delta sigma weight residual 1.491 1.359 0.132 2.00e-02 2.50e+03 4.37e+01 ... (remaining 14527 not shown) Histogram of bond angle deviations from ideal: 98.34 - 105.46: 798 105.46 - 112.59: 7363 112.59 - 119.71: 5334 119.71 - 126.84: 6239 126.84 - 133.96: 468 Bond angle restraints: 20202 Sorted by residual: angle pdb=" C2' DT N 28 " pdb=" C1' DT N 28 " pdb=" N1 DT N 28 " ideal model delta sigma weight residual 113.50 119.21 -5.71 1.50e+00 4.44e-01 1.45e+01 angle pdb=" N ALA P1034 " pdb=" CA ALA P1034 " pdb=" C ALA P1034 " ideal model delta sigma weight residual 110.80 118.82 -8.02 2.13e+00 2.20e-01 1.42e+01 angle pdb=" C2' DT T 19 " pdb=" C1' DT T 19 " pdb=" N1 DT T 19 " ideal model delta sigma weight residual 113.50 118.89 -5.39 1.50e+00 4.44e-01 1.29e+01 angle pdb=" C2' DT T 16 " pdb=" C1' DT T 16 " pdb=" N1 DT T 16 " ideal model delta sigma weight residual 113.50 118.88 -5.38 1.50e+00 4.44e-01 1.29e+01 angle pdb=" C2' DT T 21 " pdb=" C1' DT T 21 " pdb=" N1 DT T 21 " ideal model delta sigma weight residual 113.50 118.80 -5.30 1.50e+00 4.44e-01 1.25e+01 ... (remaining 20197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7557 17.93 - 35.86: 604 35.86 - 53.80: 234 53.80 - 71.73: 78 71.73 - 89.66: 12 Dihedral angle restraints: 8485 sinusoidal: 4505 harmonic: 3980 Sorted by residual: dihedral pdb=" CA ASP P 644 " pdb=" C ASP P 644 " pdb=" N ASP P 645 " pdb=" CA ASP P 645 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA PHE P1134 " pdb=" C PHE P1134 " pdb=" N ASP P1135 " pdb=" CA ASP P1135 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" O4' C R 11 " pdb=" C1' C R 11 " pdb=" N1 C R 11 " pdb=" C2 C R 11 " ideal model delta sinusoidal sigma weight residual -128.00 -72.86 -55.14 1 1.70e+01 3.46e-03 1.42e+01 ... (remaining 8482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1639 0.045 - 0.090: 509 0.090 - 0.134: 120 0.134 - 0.179: 30 0.179 - 0.224: 5 Chirality restraints: 2303 Sorted by residual: chirality pdb=" C3' 2YR T 6 " pdb=" C2' 2YR T 6 " pdb=" C4' 2YR T 6 " pdb=" O3' 2YR T 6 " both_signs ideal model delta sigma weight residual False -2.39 -2.62 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB VAL P 27 " pdb=" CA VAL P 27 " pdb=" CG1 VAL P 27 " pdb=" CG2 VAL P 27 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CB ILE P 43 " pdb=" CA ILE P 43 " pdb=" CG1 ILE P 43 " pdb=" CG2 ILE P 43 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.21e-01 ... (remaining 2300 not shown) Planarity restraints: 2081 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A R 69 " 0.028 2.00e-02 2.50e+03 2.40e-02 1.59e+01 pdb=" N9 A R 69 " -0.060 2.00e-02 2.50e+03 pdb=" C8 A R 69 " -0.007 2.00e-02 2.50e+03 pdb=" N7 A R 69 " 0.006 2.00e-02 2.50e+03 pdb=" C5 A R 69 " 0.008 2.00e-02 2.50e+03 pdb=" C6 A R 69 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A R 69 " 0.001 2.00e-02 2.50e+03 pdb=" N1 A R 69 " -0.006 2.00e-02 2.50e+03 pdb=" C2 A R 69 " -0.008 2.00e-02 2.50e+03 pdb=" N3 A R 69 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A R 69 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU P 302 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C LEU P 302 " -0.067 2.00e-02 2.50e+03 pdb=" O LEU P 302 " 0.025 2.00e-02 2.50e+03 pdb=" N SER P 303 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C R 70 " 0.023 2.00e-02 2.50e+03 2.52e-02 1.42e+01 pdb=" N1 C R 70 " -0.055 2.00e-02 2.50e+03 pdb=" C2 C R 70 " 0.043 2.00e-02 2.50e+03 pdb=" O2 C R 70 " -0.015 2.00e-02 2.50e+03 pdb=" N3 C R 70 " -0.007 2.00e-02 2.50e+03 pdb=" C4 C R 70 " -0.001 2.00e-02 2.50e+03 pdb=" N4 C R 70 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C R 70 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C R 70 " 0.004 2.00e-02 2.50e+03 ... (remaining 2078 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2016 2.77 - 3.30: 12742 3.30 - 3.83: 23981 3.83 - 4.37: 29428 4.37 - 4.90: 46213 Nonbonded interactions: 114380 Sorted by model distance: nonbonded pdb=" O ARG P 557 " pdb=" OG SER P 590 " model vdw 2.233 2.440 nonbonded pdb=" OD1 ASP P 276 " pdb=" NZ LYS P 599 " model vdw 2.246 2.520 nonbonded pdb=" NZ LYS P 742 " pdb=" OP1 C R 67 " model vdw 2.249 2.520 nonbonded pdb=" OP1 DG N 25 " pdb=" NH1 ARG P1114 " model vdw 2.263 2.520 nonbonded pdb=" NH2 ARG P 820 " pdb=" OD1 ASP P 825 " model vdw 2.268 2.520 ... (remaining 114375 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 0.000 Extract box with map and model: 4.750 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 45.560 Find NCS groups from input model: 0.340 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 : 0.008 0.294 14532 Z= 0.482 Angle : 0.988 10.435 20202 Z= 0.544 Chirality : 0.047 0.224 2303 Planarity : 0.006 0.039 2081 Dihedral : 15.519 89.659 5911 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 0.08 % 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: -1.38 (0.20), residues: 1349 helix: -0.83 (0.18), residues: 649 sheet: -0.48 (0.47), residues: 106 loop : -0.93 (0.23), residues: 594 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 258 average time/residue: 0.3518 time to fit residues: 122.2491 Evaluate side-chains 97 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 1.541 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1525 time to fit residues: 2.3135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 59 optimal weight: 0.0970 chunk 115 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 113 HIS P 224 ASN P 357 ASN P1254 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 14532 Z= 0.183 Angle : 0.539 8.454 20202 Z= 0.288 Chirality : 0.037 0.131 2303 Planarity : 0.004 0.038 2081 Dihedral : 16.330 91.112 3032 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 1.48 % 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: -0.19 (0.22), residues: 1349 helix: 0.48 (0.20), residues: 655 sheet: -0.42 (0.43), residues: 136 loop : -0.66 (0.25), residues: 558 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 116 average time/residue: 0.3566 time to fit residues: 57.4823 Evaluate side-chains 75 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 1.661 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1254 time to fit residues: 3.8596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 90 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 357 ASN P 758 ASN P1054 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 14532 Z= 0.246 Angle : 0.532 7.966 20202 Z= 0.284 Chirality : 0.037 0.141 2303 Planarity : 0.004 0.060 2081 Dihedral : 16.399 95.031 3032 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 1.32 % 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: 0.11 (0.22), residues: 1349 helix: 0.78 (0.20), residues: 663 sheet: -0.34 (0.43), residues: 136 loop : -0.58 (0.26), residues: 550 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 89 average time/residue: 0.3357 time to fit residues: 42.9056 Evaluate side-chains 63 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 1.393 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1261 time to fit residues: 2.9389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 134 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 113 HIS P 193 ASN ** P 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 14532 Z= 0.326 Angle : 0.566 7.841 20202 Z= 0.301 Chirality : 0.039 0.146 2303 Planarity : 0.004 0.033 2081 Dihedral : 16.544 97.761 3032 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 1.23 % 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: -0.04 (0.22), residues: 1349 helix: 0.65 (0.20), residues: 668 sheet: -0.42 (0.43), residues: 136 loop : -0.66 (0.26), residues: 545 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 3 residues processed: 82 average time/residue: 0.3140 time to fit residues: 37.8491 Evaluate side-chains 62 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 1.461 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1533 time to fit residues: 2.7844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 chunk 98 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 309 ASN P 342 GLN P 803 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 14532 Z= 0.169 Angle : 0.481 8.216 20202 Z= 0.257 Chirality : 0.035 0.133 2303 Planarity : 0.003 0.039 2081 Dihedral : 16.544 96.997 3032 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 0.58 % 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: 0.22 (0.22), residues: 1349 helix: 0.87 (0.20), residues: 673 sheet: -0.34 (0.45), residues: 128 loop : -0.54 (0.26), residues: 548 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 1.617 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 70 average time/residue: 0.3433 time to fit residues: 35.9255 Evaluate side-chains 55 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 1.748 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1538 time to fit residues: 2.4978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 83 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 74 optimal weight: 0.0670 chunk 137 optimal weight: 5.9990 overall best weight: 2.1124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 14532 Z= 0.292 Angle : 0.533 7.728 20202 Z= 0.283 Chirality : 0.038 0.144 2303 Planarity : 0.003 0.033 2081 Dihedral : 16.531 98.234 3032 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 0.58 % 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: 0.18 (0.22), residues: 1349 helix: 0.86 (0.20), residues: 669 sheet: -0.21 (0.44), residues: 134 loop : -0.62 (0.25), residues: 546 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 1.560 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 68 average time/residue: 0.2904 time to fit residues: 30.4703 Evaluate side-chains 58 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 1.525 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1327 time to fit residues: 2.7957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 88 optimal weight: 0.0670 chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 14532 Z= 0.319 Angle : 0.542 8.080 20202 Z= 0.289 Chirality : 0.038 0.141 2303 Planarity : 0.004 0.032 2081 Dihedral : 16.688 98.962 3032 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 0.41 % 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: 0.12 (0.22), residues: 1349 helix: 0.82 (0.20), residues: 673 sheet: -0.31 (0.46), residues: 126 loop : -0.66 (0.25), residues: 550 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 1.494 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 61 average time/residue: 0.3224 time to fit residues: 29.2846 Evaluate side-chains 55 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 1.579 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1377 time to fit residues: 2.2461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 14532 Z= 0.203 Angle : 0.493 8.072 20202 Z= 0.265 Chirality : 0.036 0.139 2303 Planarity : 0.003 0.032 2081 Dihedral : 16.587 97.755 3032 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 0.08 % 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: 0.28 (0.23), residues: 1349 helix: 0.94 (0.20), residues: 673 sheet: -0.25 (0.47), residues: 126 loop : -0.55 (0.26), residues: 550 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 1.560 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.3387 time to fit residues: 30.4966 Evaluate side-chains 53 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.882 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 0.4980 chunk 132 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 698 HIS ** P1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 14532 Z= 0.240 Angle : 0.506 7.873 20202 Z= 0.271 Chirality : 0.037 0.141 2303 Planarity : 0.003 0.031 2081 Dihedral : 16.518 97.787 3032 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 0.16 % 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: 0.26 (0.23), residues: 1349 helix: 0.94 (0.20), residues: 673 sheet: -0.28 (0.47), residues: 126 loop : -0.60 (0.26), residues: 550 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 57 average time/residue: 0.3095 time to fit residues: 26.7264 Evaluate side-chains 54 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 1.440 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1306 time to fit residues: 2.3155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 14532 Z= 0.187 Angle : 0.480 7.856 20202 Z= 0.257 Chirality : 0.036 0.140 2303 Planarity : 0.003 0.032 2081 Dihedral : 16.485 97.287 3032 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.23), residues: 1349 helix: 1.03 (0.20), residues: 672 sheet: -0.24 (0.47), residues: 126 loop : -0.56 (0.26), residues: 551 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.3161 time to fit residues: 27.6151 Evaluate side-chains 53 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.566 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 107 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 116 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.0060 chunk 102 optimal weight: 0.5980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.099476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.065554 restraints weight = 33753.692| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.17 r_work: 0.2856 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 14532 Z= 0.134 Angle : 0.457 7.723 20202 Z= 0.245 Chirality : 0.035 0.145 2303 Planarity : 0.003 0.031 2081 Dihedral : 16.374 96.647 3032 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.23), residues: 1349 helix: 1.12 (0.20), residues: 673 sheet: -0.06 (0.49), residues: 117 loop : -0.54 (0.25), residues: 559 =============================================================================== Job complete usr+sys time: 2676.68 seconds wall clock time: 49 minutes 52.80 seconds (2992.80 seconds total)