Starting phenix.real_space_refine on Fri Feb 16 01:48:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s38_24819/02_2024/7s38_24819_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s38_24819/02_2024/7s38_24819.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s38_24819/02_2024/7s38_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_24819/02_2024/7s38_24819_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s38_24819/02_2024/7s38_24819_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s38_24819/02_2024/7s38_24819.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s38_24819/02_2024/7s38_24819.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s38_24819/02_2024/7s38_24819_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s38_24819/02_2024/7s38_24819_updated.pdb" } 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= 0.092 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 8.09, per 1000 atoms: 0.58 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: 6.62 Conformation dependent library (CDL) restraints added in 2.1 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: 8.09 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: 8.30 Time building geometry restraints manager: 7.03 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 - 31.55: 8224 31.55 - 63.10: 533 63.10 - 94.65: 59 94.65 - 126.20: 0 126.20 - 157.75: 1 Dihedral angle restraints: 8817 sinusoidal: 4837 harmonic: 3980 Sorted by residual: dihedral pdb=" C3' 2YR T 6 " pdb=" C4' 2YR T 6 " pdb=" C5' 2YR T 6 " pdb=" O5' 2YR T 6 " ideal model delta sinusoidal sigma weight residual 191.74 33.99 157.75 1 3.00e+01 1.11e-03 2.05e+01 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 ... (remaining 8814 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: 0.010 Normalize map: mean=0, sd=1: 0.940 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: 4.120 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 48.190 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.730 ------------------------------------------------------------------------------- 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 : 17.812 157.752 6243 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 % Allowed : 4.69 % Favored : 95.23 % 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: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P1126 HIS 0.010 0.002 HIS P 160 PHE 0.024 0.002 PHE P1235 TYR 0.025 0.002 TYR P1242 ARG 0.010 0.001 ARG P1210 *********************** 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 : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 303 SER cc_start: 0.8172 (t) cc_final: 0.7852 (p) REVERT: P 338 LEU cc_start: 0.8379 (mt) cc_final: 0.8103 (mt) REVERT: P 465 MET cc_start: 0.8631 (ppp) cc_final: 0.8138 (ppp) REVERT: P 569 PHE cc_start: 0.7699 (m-80) cc_final: 0.7251 (m-80) REVERT: P 816 LEU cc_start: 0.8928 (mt) cc_final: 0.8595 (mt) REVERT: P 1339 THR cc_start: 0.8692 (p) cc_final: 0.8445 (p) outliers start: 1 outliers final: 1 residues processed: 258 average time/residue: 0.3507 time to fit residues: 121.9017 Evaluate side-chains 99 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 1008 PHE 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: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14532 Z= 0.181 Angle : 0.538 8.513 20202 Z= 0.288 Chirality : 0.037 0.133 2303 Planarity : 0.004 0.046 2081 Dihedral : 19.903 150.101 3366 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.48 % Allowed : 10.70 % Favored : 87.82 % 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: 0.46 (0.20), residues: 657 sheet: -0.43 (0.43), residues: 136 loop : -0.62 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 883 HIS 0.004 0.001 HIS P 167 PHE 0.015 0.001 PHE P 185 TYR 0.012 0.001 TYR P 836 ARG 0.014 0.001 ARG P 307 *********************** 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 121 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 90 MET cc_start: 0.9031 (tpp) cc_final: 0.8691 (tpp) REVERT: P 303 SER cc_start: 0.8055 (t) cc_final: 0.7818 (p) REVERT: P 529 TYR cc_start: 0.6108 (p90) cc_final: 0.5625 (p90) REVERT: P 816 LEU cc_start: 0.9121 (mt) cc_final: 0.8711 (mt) REVERT: P 836 TYR cc_start: 0.7435 (m-80) cc_final: 0.5662 (m-80) REVERT: P 1213 MET cc_start: 0.8611 (mtp) cc_final: 0.8397 (mtm) outliers start: 18 outliers final: 7 residues processed: 117 average time/residue: 0.3327 time to fit residues: 54.6081 Evaluate side-chains 78 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 692 ASN Chi-restraints excluded: chain P residue 834 SER Chi-restraints excluded: chain P residue 887 LEU Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1257 LEU Chi-restraints excluded: chain P residue 1299 ASP 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: 0.0970 chunk 111 optimal weight: 0.0980 chunk 90 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 357 ASN P 758 ASN P1054 ASN P1254 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14532 Z= 0.165 Angle : 0.493 8.131 20202 Z= 0.263 Chirality : 0.035 0.132 2303 Planarity : 0.003 0.044 2081 Dihedral : 19.887 148.768 3364 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.23 % Allowed : 11.44 % Favored : 87.33 % 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: 0.86 (0.20), residues: 663 sheet: -0.30 (0.43), residues: 137 loop : -0.56 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 883 HIS 0.003 0.001 HIS P 167 PHE 0.029 0.001 PHE P 569 TYR 0.011 0.001 TYR P 155 ARG 0.007 0.000 ARG P 424 *********************** 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 91 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 303 SER cc_start: 0.8122 (t) cc_final: 0.7843 (p) REVERT: P 523 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8468 (mm-30) REVERT: P 693 PHE cc_start: 0.8246 (t80) cc_final: 0.8015 (t80) REVERT: P 816 LEU cc_start: 0.9164 (mt) cc_final: 0.8790 (mt) REVERT: P 836 TYR cc_start: 0.7321 (m-80) cc_final: 0.5901 (m-80) REVERT: P 1037 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8107 (p90) REVERT: P 1213 MET cc_start: 0.8582 (mtp) cc_final: 0.8327 (mtm) outliers start: 15 outliers final: 7 residues processed: 89 average time/residue: 0.3502 time to fit residues: 43.6041 Evaluate side-chains 72 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 692 ASN Chi-restraints excluded: chain P residue 834 SER Chi-restraints excluded: chain P residue 887 LEU Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1018 VAL Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1257 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 113 HIS ** P 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 342 GLN P1254 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3479 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= 0.298 Angle : 0.556 6.270 20202 Z= 0.296 Chirality : 0.038 0.148 2303 Planarity : 0.004 0.034 2081 Dihedral : 20.021 154.908 3364 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.56 % Allowed : 11.77 % Favored : 86.67 % 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: 0.16 (0.22), residues: 1349 helix: 0.83 (0.20), residues: 661 sheet: -0.30 (0.46), residues: 117 loop : -0.57 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P1126 HIS 0.003 0.001 HIS P 420 PHE 0.019 0.002 PHE P1008 TYR 0.021 0.002 TYR P1336 ARG 0.004 0.001 ARG P 220 *********************** 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 92 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 73 time to evaluate : 1.401 Fit side-chains revert: symmetry clash REVERT: P 185 PHE cc_start: 0.7822 (t80) cc_final: 0.7614 (t80) REVERT: P 631 MET cc_start: 0.8978 (tpt) cc_final: 0.8771 (tpt) REVERT: P 782 LYS cc_start: 0.9044 (ttmt) cc_final: 0.8778 (mttm) REVERT: P 816 LEU cc_start: 0.9290 (mt) cc_final: 0.8780 (mt) REVERT: P 836 TYR cc_start: 0.7283 (m-80) cc_final: 0.5853 (m-80) REVERT: P 1037 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8090 (p90) REVERT: P 1213 MET cc_start: 0.8739 (mtp) cc_final: 0.8487 (mtm) outliers start: 19 outliers final: 7 residues processed: 92 average time/residue: 0.2825 time to fit residues: 38.5338 Evaluate side-chains 68 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 643 PHE Chi-restraints excluded: chain P residue 692 ASN Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1015 VAL Chi-restraints excluded: chain P residue 1018 VAL Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1257 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 121 optimal weight: 0.1980 chunk 98 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 0.0370 chunk 127 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 309 ASN P 803 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14532 Z= 0.135 Angle : 0.468 6.748 20202 Z= 0.251 Chirality : 0.035 0.135 2303 Planarity : 0.003 0.032 2081 Dihedral : 20.038 155.954 3364 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.91 % Allowed : 12.92 % Favored : 86.17 % 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: 0.36 (0.22), residues: 1349 helix: 1.04 (0.20), residues: 668 sheet: -0.28 (0.46), residues: 129 loop : -0.53 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 883 HIS 0.002 0.000 HIS P 328 PHE 0.015 0.001 PHE P 569 TYR 0.014 0.001 TYR P 594 ARG 0.009 0.000 ARG P 671 *********************** 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 80 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 631 MET cc_start: 0.8972 (tpt) cc_final: 0.8763 (tpt) REVERT: P 816 LEU cc_start: 0.9179 (mt) cc_final: 0.8788 (mt) REVERT: P 836 TYR cc_start: 0.7205 (m-80) cc_final: 0.6003 (m-80) REVERT: P 1037 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8206 (p90) REVERT: P 1155 LYS cc_start: 0.8252 (mmtt) cc_final: 0.8048 (mmtt) REVERT: P 1213 MET cc_start: 0.8661 (mtp) cc_final: 0.8404 (mtm) outliers start: 11 outliers final: 4 residues processed: 79 average time/residue: 0.3077 time to fit residues: 35.9134 Evaluate side-chains 62 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 428 ASP Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1018 VAL Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1257 LEU 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: 0.0470 chunk 28 optimal weight: 30.0000 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 193 ASN ** P1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 14532 Z= 0.372 Angle : 0.597 7.480 20202 Z= 0.315 Chirality : 0.040 0.159 2303 Planarity : 0.004 0.035 2081 Dihedral : 20.105 153.794 3364 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.48 % Allowed : 13.00 % Favored : 85.51 % 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: 0.10 (0.22), residues: 1349 helix: 0.73 (0.20), residues: 676 sheet: -0.03 (0.48), residues: 115 loop : -0.63 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P1126 HIS 0.004 0.001 HIS P 167 PHE 0.056 0.002 PHE P 185 TYR 0.023 0.002 TYR P1336 ARG 0.009 0.001 ARG P 671 *********************** 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 82 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 64 time to evaluate : 1.653 Fit side-chains revert: symmetry clash REVERT: P 534 MET cc_start: 0.5967 (ptt) cc_final: 0.5714 (ptt) REVERT: P 816 LEU cc_start: 0.9297 (mt) cc_final: 0.8956 (mt) REVERT: P 1037 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.7945 (p90) REVERT: P 1213 MET cc_start: 0.8732 (mtp) cc_final: 0.8456 (mtm) outliers start: 18 outliers final: 11 residues processed: 79 average time/residue: 0.2651 time to fit residues: 32.1959 Evaluate side-chains 70 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 428 ASP Chi-restraints excluded: chain P residue 643 PHE Chi-restraints excluded: chain P residue 661 ARG Chi-restraints excluded: chain P residue 670 ILE Chi-restraints excluded: chain P residue 692 ASN Chi-restraints excluded: chain P residue 830 ILE Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1015 VAL Chi-restraints excluded: chain P residue 1018 VAL Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1257 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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: 0.8383 moved from start: 0.4165 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= 0.254 Angle : 0.520 7.950 20202 Z= 0.275 Chirality : 0.037 0.139 2303 Planarity : 0.003 0.033 2081 Dihedral : 20.177 156.249 3364 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.91 % Allowed : 14.16 % Favored : 84.94 % 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 (0.23), residues: 1349 helix: 0.84 (0.20), residues: 675 sheet: -0.22 (0.47), residues: 126 loop : -0.59 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 883 HIS 0.003 0.001 HIS P 328 PHE 0.015 0.002 PHE P 185 TYR 0.015 0.001 TYR P 155 ARG 0.006 0.000 ARG P 671 *********************** 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 71 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 1.360 Fit side-chains REVERT: P 816 LEU cc_start: 0.9265 (mt) cc_final: 0.8910 (mt) REVERT: P 1037 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.8085 (p90) REVERT: P 1213 MET cc_start: 0.8727 (mtp) cc_final: 0.8448 (mtm) outliers start: 11 outliers final: 7 residues processed: 70 average time/residue: 0.2888 time to fit residues: 30.3062 Evaluate side-chains 64 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 428 ASP Chi-restraints excluded: chain P residue 643 PHE Chi-restraints excluded: chain P residue 830 ILE Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1018 VAL Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1257 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 805 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14532 Z= 0.230 Angle : 0.506 7.676 20202 Z= 0.268 Chirality : 0.036 0.139 2303 Planarity : 0.003 0.032 2081 Dihedral : 20.150 156.732 3364 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.99 % Allowed : 14.57 % Favored : 84.44 % 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: 0.24 (0.23), residues: 1349 helix: 0.89 (0.20), residues: 674 sheet: -0.20 (0.47), residues: 126 loop : -0.56 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 883 HIS 0.003 0.001 HIS P 328 PHE 0.016 0.002 PHE P 185 TYR 0.014 0.001 TYR P 155 ARG 0.006 0.000 ARG P 671 *********************** 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 72 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 1.478 Fit side-chains REVERT: P 228 GLN cc_start: 0.8196 (tp40) cc_final: 0.7969 (tm-30) REVERT: P 816 LEU cc_start: 0.9262 (mt) cc_final: 0.8907 (mt) REVERT: P 1037 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8072 (p90) REVERT: P 1213 MET cc_start: 0.8707 (mtp) cc_final: 0.8416 (mtm) REVERT: P 1364 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.6357 (pp30) outliers start: 12 outliers final: 8 residues processed: 71 average time/residue: 0.2673 time to fit residues: 29.5896 Evaluate side-chains 66 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 428 ASP Chi-restraints excluded: chain P residue 643 PHE Chi-restraints excluded: chain P residue 692 ASN Chi-restraints excluded: chain P residue 830 ILE Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1015 VAL Chi-restraints excluded: chain P residue 1018 VAL Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1257 LEU Chi-restraints excluded: chain P residue 1364 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 57 optimal weight: 0.0470 chunk 103 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 124 optimal weight: 0.1980 chunk 131 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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: 0.8335 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14532 Z= 0.143 Angle : 0.469 7.649 20202 Z= 0.249 Chirality : 0.035 0.136 2303 Planarity : 0.003 0.032 2081 Dihedral : 20.049 157.374 3364 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.74 % Allowed : 14.73 % Favored : 84.53 % 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: 0.40 (0.23), residues: 1349 helix: 1.05 (0.20), residues: 674 sheet: -0.23 (0.46), residues: 133 loop : -0.50 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 883 HIS 0.002 0.000 HIS P 328 PHE 0.018 0.001 PHE P 185 TYR 0.011 0.001 TYR P 155 ARG 0.006 0.000 ARG P 220 *********************** 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 67 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 1.519 Fit side-chains REVERT: P 702 LEU cc_start: 0.7460 (mm) cc_final: 0.7010 (mm) REVERT: P 816 LEU cc_start: 0.9210 (mt) cc_final: 0.8869 (mt) REVERT: P 1037 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.8109 (p90) REVERT: P 1364 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6323 (pp30) outliers start: 9 outliers final: 7 residues processed: 67 average time/residue: 0.2818 time to fit residues: 29.1222 Evaluate side-chains 64 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 428 ASP Chi-restraints excluded: chain P residue 643 PHE Chi-restraints excluded: chain P residue 830 ILE Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1015 VAL Chi-restraints excluded: chain P residue 1018 VAL Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1257 LEU Chi-restraints excluded: chain P residue 1364 GLN 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: 0.0980 chunk 66 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 146 optimal weight: 5.9990 chunk 134 optimal weight: 0.0050 chunk 116 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 698 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14532 Z= 0.167 Angle : 0.475 7.350 20202 Z= 0.253 Chirality : 0.035 0.134 2303 Planarity : 0.003 0.033 2081 Dihedral : 19.943 154.120 3364 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.91 % Allowed : 14.57 % Favored : 84.53 % 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: 0.45 (0.23), residues: 1349 helix: 1.08 (0.20), residues: 676 sheet: -0.14 (0.47), residues: 131 loop : -0.49 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 883 HIS 0.003 0.001 HIS P 328 PHE 0.019 0.001 PHE P 185 TYR 0.012 0.001 TYR P 155 ARG 0.006 0.000 ARG P 220 ********************** 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 69 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 1.507 Fit side-chains REVERT: P 816 LEU cc_start: 0.9251 (mt) cc_final: 0.8927 (mt) REVERT: P 1037 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7982 (p90) REVERT: P 1245 LEU cc_start: 0.6783 (mt) cc_final: 0.6575 (mt) REVERT: P 1364 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6328 (pp30) outliers start: 11 outliers final: 8 residues processed: 68 average time/residue: 0.2971 time to fit residues: 30.6988 Evaluate side-chains 66 residues out of total 1215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 428 ASP Chi-restraints excluded: chain P residue 643 PHE Chi-restraints excluded: chain P residue 692 ASN Chi-restraints excluded: chain P residue 830 ILE Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1015 VAL Chi-restraints excluded: chain P residue 1018 VAL Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1257 LEU Chi-restraints excluded: chain P residue 1364 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.0020 chunk 116 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 803 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.099402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.065251 restraints weight = 33737.257| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.17 r_work: 0.2848 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14532 Z= 0.156 Angle : 0.466 7.218 20202 Z= 0.248 Chirality : 0.035 0.133 2303 Planarity : 0.003 0.032 2081 Dihedral : 19.915 153.389 3364 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.74 % Allowed : 14.65 % Favored : 84.61 % 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: 0.51 (0.23), residues: 1349 helix: 1.12 (0.20), residues: 675 sheet: -0.16 (0.47), residues: 131 loop : -0.44 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 883 HIS 0.003 0.001 HIS P 328 PHE 0.017 0.001 PHE P 185 TYR 0.012 0.001 TYR P 155 ARG 0.006 0.000 ARG P 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2850.64 seconds wall clock time: 52 minutes 55.08 seconds (3175.08 seconds total)