Starting phenix.real_space_refine on Sun Apr 7 02:50:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkr_14049/04_2024/7qkr_14049_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkr_14049/04_2024/7qkr_14049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkr_14049/04_2024/7qkr_14049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkr_14049/04_2024/7qkr_14049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkr_14049/04_2024/7qkr_14049_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkr_14049/04_2024/7qkr_14049_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 47 5.16 5 C 6047 2.51 5 N 1549 2.21 5 O 1756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 401": "NH1" <-> "NH2" Residue "A TYR 1165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1193": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9403 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1203, 9403 Unusual residues: {' MG': 1, '9Z9': 1, 'ANP': 1, 'I6H': 1} Classifications: {'peptide': 1199, 'undetermined': 4} Link IDs: {'PTRANS': 27, 'TRANS': 1171, None: 4} Not linked: pdbres="ALA A1288 " pdbres="I6H A1301 " Not linked: pdbres="I6H A1301 " pdbres="ANP A1302 " Not linked: pdbres="ANP A1302 " pdbres=" MG A1303 " Not linked: pdbres=" MG A1303 " pdbres="9Z9 A1304 " Chain breaks: 2 Time building chain proxies: 5.56, per 1000 atoms: 0.59 Number of scatterers: 9403 At special positions: 0 Unit cell: (137.268, 97.092, 102.951, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 3 15.00 Mg 1 11.99 O 1756 8.00 N 1549 7.00 C 6047 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=0, symmetry=0 Time building additional restraints: 4.21 Conformation dependent library (CDL) restraints added in 1.7 seconds 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 4 sheets defined 65.3% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 33 through 41 Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.786A pdb=" N MET A 58 " --> pdb=" O ASP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 79 removed outlier: 3.637A pdb=" N CYS A 65 " --> pdb=" O TRP A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 100 Processing helix chain 'A' and resid 105 through 157 Processing helix chain 'A' and resid 161 through 166 Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 180 through 186 Processing helix chain 'A' and resid 189 through 211 Processing helix chain 'A' and resid 213 through 228 Processing helix chain 'A' and resid 231 through 260 Processing helix chain 'A' and resid 262 through 268 Processing helix chain 'A' and resid 271 through 325 removed outlier: 3.615A pdb=" N LEU A 275 " --> pdb=" O HIS A 271 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP A 304 " --> pdb=" O MET A 300 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N SER A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 371 removed outlier: 3.614A pdb=" N ILE A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE A 355 " --> pdb=" O ILE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 441 removed outlier: 3.914A pdb=" N ILE A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 464 through 469 Processing helix chain 'A' and resid 485 through 493 removed outlier: 4.323A pdb=" N GLY A 492 " --> pdb=" O ASN A 488 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 516 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.709A pdb=" N GLN A 525 " --> pdb=" O GLU A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 557 removed outlier: 4.266A pdb=" N SER A 557 " --> pdb=" O ARG A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 587 removed outlier: 3.816A pdb=" N GLY A 577 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE A 578 " --> pdb=" O ARG A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 602 removed outlier: 3.534A pdb=" N ILE A 602 " --> pdb=" O LEU A 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 599 through 602' Processing helix chain 'A' and resid 622 through 628 Processing helix chain 'A' and resid 631 through 645 Processing helix chain 'A' and resid 699 through 705 Processing helix chain 'A' and resid 707 through 711 Processing helix chain 'A' and resid 716 through 741 removed outlier: 3.617A pdb=" N ALA A 720 " --> pdb=" O CYS A 716 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 746 through 800 Proline residue: A 750 - end of helix removed outlier: 3.574A pdb=" N TYR A 759 " --> pdb=" O ILE A 756 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 763 " --> pdb=" O THR A 760 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE A 766 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N CYS A 768 " --> pdb=" O MET A 765 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 769 " --> pdb=" O ILE A 766 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 770 " --> pdb=" O GLY A 767 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N THR A 778 " --> pdb=" O LEU A 775 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ARG A 795 " --> pdb=" O MET A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 809 Processing helix chain 'A' and resid 815 through 832 Proline residue: A 826 - end of helix removed outlier: 4.135A pdb=" N GLU A 830 " --> pdb=" O PRO A 826 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLY A 831 " --> pdb=" O GLN A 827 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU A 832 " --> pdb=" O ASP A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 857 Processing helix chain 'A' and resid 859 through 893 removed outlier: 4.083A pdb=" N VAL A 864 " --> pdb=" O ARG A 860 " (cutoff:3.500A) Proline residue: A 870 - end of helix removed outlier: 3.615A pdb=" N GLY A 876 " --> pdb=" O LEU A 872 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A 890 " --> pdb=" O PHE A 886 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU A 891 " --> pdb=" O GLU A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 905 Processing helix chain 'A' and resid 908 through 914 Processing helix chain 'A' and resid 917 through 970 removed outlier: 3.540A pdb=" N LYS A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG A 941 " --> pdb=" O ARG A 937 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR A 942 " --> pdb=" O SER A 938 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 945 " --> pdb=" O ARG A 941 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASN A 953 " --> pdb=" O ILE A 949 " (cutoff:3.500A) Proline residue: A 954 - end of helix Processing helix chain 'A' and resid 975 through 1017 removed outlier: 3.527A pdb=" N GLU A 994 " --> pdb=" O GLN A 990 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE A 995 " --> pdb=" O SER A 991 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 996 " --> pdb=" O ALA A 992 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 997 " --> pdb=" O GLY A 993 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TYR A 998 " --> pdb=" O GLU A 994 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA A 999 " --> pdb=" O PHE A 995 " (cutoff:3.500A) Proline residue: A1000 - end of helix removed outlier: 3.618A pdb=" N LYS A1004 " --> pdb=" O PRO A1000 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A1006 " --> pdb=" O MET A1002 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLN A1007 " --> pdb=" O GLY A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1054 No H-bonds generated for 'chain 'A' and resid 1052 through 1054' Processing helix chain 'A' and resid 1085 through 1090 Processing helix chain 'A' and resid 1108 through 1110 No H-bonds generated for 'chain 'A' and resid 1108 through 1110' Processing helix chain 'A' and resid 1113 through 1119 Processing helix chain 'A' and resid 1134 through 1141 removed outlier: 4.478A pdb=" N GLY A1141 " --> pdb=" O ASN A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1161 Processing helix chain 'A' and resid 1165 through 1169 Processing helix chain 'A' and resid 1188 through 1201 Processing helix chain 'A' and resid 1218 through 1232 removed outlier: 3.823A pdb=" N MET A1222 " --> pdb=" O SER A1218 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL A1223 " --> pdb=" O GLU A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1246 through 1249 removed outlier: 4.059A pdb=" N ASN A1249 " --> pdb=" O THR A1246 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1246 through 1249' Processing helix chain 'A' and resid 1267 through 1273 Processing helix chain 'A' and resid 1276 through 1287 Processing sheet with id= A, first strand: chain 'A' and resid 416 through 418 Processing sheet with id= B, first strand: chain 'A' and resid 615 through 620 removed outlier: 6.908A pdb=" N VAL A 610 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR A 619 " --> pdb=" O ILE A 608 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE A 608 " --> pdb=" O THR A 619 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N THR A 592 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU A 426 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL A 594 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1065 through 1067 Processing sheet with id= D, first strand: chain 'A' and resid 1260 through 1265 removed outlier: 6.750A pdb=" N VAL A1255 " --> pdb=" O VAL A1262 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER A1264 " --> pdb=" O ILE A1253 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE A1253 " --> pdb=" O SER A1264 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL A1252 " --> pdb=" O TYR A1072 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR A1237 " --> pdb=" O VAL A1073 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU A1075 " --> pdb=" O THR A1237 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR A1239 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N GLY A1077 " --> pdb=" O THR A1239 " (cutoff:3.500A) 566 hydrogen bonds defined for protein. 1446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.34 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1531 1.27 - 1.40: 2263 1.40 - 1.54: 5587 1.54 - 1.67: 107 1.67 - 1.81: 78 Bond restraints: 9566 Sorted by residual: bond pdb=" N3B ANP A1302 " pdb=" PG ANP A1302 " ideal model delta sigma weight residual 1.795 1.627 0.168 2.00e-02 2.50e+03 7.09e+01 bond pdb=" O3A ANP A1302 " pdb=" PB ANP A1302 " ideal model delta sigma weight residual 1.700 1.598 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" N ILE A1042 " pdb=" CA ILE A1042 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.14e-02 7.69e+03 1.34e+01 bond pdb=" C THR A 233 " pdb=" O THR A 233 " ideal model delta sigma weight residual 1.237 1.199 0.038 1.17e-02 7.31e+03 1.03e+01 bond pdb=" N ILE A1033 " pdb=" CA ILE A1033 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.24e-02 6.50e+03 9.80e+00 ... (remaining 9561 not shown) Histogram of bond angle deviations from ideal: 99.50 - 115.34: 6096 115.34 - 131.17: 6839 131.17 - 147.01: 18 147.01 - 162.85: 0 162.85 - 178.68: 1 Bond angle restraints: 12954 Sorted by residual: angle pdb=" CA ARG A1260 " pdb=" C ARG A1260 " pdb=" O ARG A1260 " ideal model delta sigma weight residual 121.11 116.58 4.53 1.17e+00 7.31e-01 1.50e+01 angle pdb=" N ILE A 234 " pdb=" CA ILE A 234 " pdb=" C ILE A 234 " ideal model delta sigma weight residual 110.53 106.91 3.62 9.40e-01 1.13e+00 1.49e+01 angle pdb=" CA ILE A 756 " pdb=" C ILE A 756 " pdb=" O ILE A 756 " ideal model delta sigma weight residual 121.27 117.28 3.99 1.04e+00 9.25e-01 1.47e+01 angle pdb=" CA VAL A1262 " pdb=" C VAL A1262 " pdb=" O VAL A1262 " ideal model delta sigma weight residual 120.85 116.80 4.05 1.06e+00 8.90e-01 1.46e+01 angle pdb=" N GLY A 620 " pdb=" CA GLY A 620 " pdb=" C GLY A 620 " ideal model delta sigma weight residual 110.45 115.34 -4.89 1.30e+00 5.92e-01 1.42e+01 ... (remaining 12949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.63: 5466 23.63 - 47.25: 314 47.25 - 70.87: 36 70.87 - 94.50: 16 94.50 - 118.12: 3 Dihedral angle restraints: 5835 sinusoidal: 2373 harmonic: 3462 Sorted by residual: dihedral pdb=" C23 9Z9 A1304 " pdb=" C21 9Z9 A1304 " pdb=" C22 9Z9 A1304 " pdb=" O20 9Z9 A1304 " ideal model delta sinusoidal sigma weight residual 177.26 59.14 118.12 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C22 9Z9 A1304 " pdb=" C23 9Z9 A1304 " pdb=" C48 9Z9 A1304 " pdb=" O49 9Z9 A1304 " ideal model delta sinusoidal sigma weight residual 177.15 -65.26 -117.59 1 3.00e+01 1.11e-03 1.56e+01 dihedral pdb=" C22 9Z9 A1304 " pdb=" C23 9Z9 A1304 " pdb=" C24 9Z9 A1304 " pdb=" O25 9Z9 A1304 " ideal model delta sinusoidal sigma weight residual -163.69 -61.22 -102.47 1 3.00e+01 1.11e-03 1.30e+01 ... (remaining 5832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1341 0.084 - 0.169: 149 0.169 - 0.253: 22 0.253 - 0.338: 6 0.338 - 0.422: 1 Chirality restraints: 1519 Sorted by residual: chirality pdb=" C3' ANP A1302 " pdb=" C2' ANP A1302 " pdb=" C4' ANP A1302 " pdb=" O3' ANP A1302 " both_signs ideal model delta sigma weight residual False -2.36 -2.78 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA THR A 231 " pdb=" N THR A 231 " pdb=" C THR A 231 " pdb=" CB THR A 231 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA PHE A 341 " pdb=" N PHE A 341 " pdb=" C PHE A 341 " pdb=" CB PHE A 341 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1516 not shown) Planarity restraints: 1611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1193 " 0.202 9.50e-02 1.11e+02 9.04e-02 5.01e+00 pdb=" NE ARG A1193 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A1193 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A1193 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A1193 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1216 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C LEU A1216 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU A1216 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP A1217 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 228 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" C LEU A 228 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU A 228 " 0.013 2.00e-02 2.50e+03 pdb=" N SER A 229 " 0.011 2.00e-02 2.50e+03 ... (remaining 1608 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 60 2.65 - 3.21: 8968 3.21 - 3.77: 14365 3.77 - 4.34: 20532 4.34 - 4.90: 33648 Nonbonded interactions: 77573 Sorted by model distance: nonbonded pdb=" O3G ANP A1302 " pdb="MG MG A1303 " model vdw 2.084 2.170 nonbonded pdb=" OG SER A 435 " pdb="MG MG A1303 " model vdw 2.127 2.170 nonbonded pdb=" OD1 ASN A 706 " pdb=" NZ LYS A 791 " model vdw 2.310 2.520 nonbonded pdb=" N GLY A1040 " pdb=" OD2 ASP A1104 " model vdw 2.344 2.520 nonbonded pdb=" OE2 GLU A 142 " pdb=" NH2 ARG A 889 " model vdw 2.348 2.520 ... (remaining 77568 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: 1.520 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: 5.380 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.180 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 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 : 0.007 0.168 9566 Z= 0.422 Angle : 0.856 9.852 12954 Z= 0.599 Chirality : 0.057 0.422 1519 Planarity : 0.005 0.090 1611 Dihedral : 15.132 118.125 3615 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.40 % Allowed : 3.86 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.24), residues: 1193 helix: 0.85 (0.19), residues: 802 sheet: -1.67 (0.74), residues: 48 loop : -1.15 (0.30), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 316 HIS 0.005 0.001 HIS A 103 PHE 0.030 0.001 PHE A 119 TYR 0.021 0.001 TYR A 248 ARG 0.004 0.000 ARG A1274 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 0.985 Fit side-chains REVERT: A 322 MET cc_start: 0.8410 (mtp) cc_final: 0.8075 (mtp) REVERT: A 345 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7478 (mp) REVERT: A 534 VAL cc_start: 0.8751 (p) cc_final: 0.8357 (m) outliers start: 4 outliers final: 3 residues processed: 135 average time/residue: 0.2535 time to fit residues: 46.4312 Evaluate side-chains 96 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 865 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 GLN A 580 GLN A1282 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9566 Z= 0.236 Angle : 0.505 5.976 12954 Z= 0.266 Chirality : 0.039 0.133 1519 Planarity : 0.004 0.039 1611 Dihedral : 8.919 106.371 1465 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.29 % Allowed : 9.50 % Favored : 89.22 % 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 (0.24), residues: 1193 helix: 1.03 (0.18), residues: 804 sheet: -1.72 (0.74), residues: 47 loop : -1.03 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 316 HIS 0.005 0.001 HIS A 103 PHE 0.020 0.002 PHE A 119 TYR 0.026 0.001 TYR A 248 ARG 0.008 0.000 ARG A 642 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 1.164 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 108 average time/residue: 0.2491 time to fit residues: 37.4044 Evaluate side-chains 99 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1034 ASP Chi-restraints excluded: chain A residue 1154 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 109 optimal weight: 0.0030 chunk 117 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9566 Z= 0.218 Angle : 0.466 5.485 12954 Z= 0.247 Chirality : 0.038 0.134 1519 Planarity : 0.004 0.038 1611 Dihedral : 7.790 102.226 1463 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.38 % Allowed : 10.88 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.24), residues: 1193 helix: 1.13 (0.19), residues: 803 sheet: -1.67 (0.73), residues: 47 loop : -0.85 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 316 HIS 0.004 0.001 HIS A 103 PHE 0.015 0.001 PHE A 979 TYR 0.025 0.001 TYR A 248 ARG 0.002 0.000 ARG A 810 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: A 534 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8145 (m) outliers start: 14 outliers final: 11 residues processed: 105 average time/residue: 0.2632 time to fit residues: 38.8833 Evaluate side-chains 103 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain A residue 1264 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 56 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 115 optimal weight: 0.2980 chunk 57 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9566 Z= 0.204 Angle : 0.451 5.452 12954 Z= 0.239 Chirality : 0.038 0.138 1519 Planarity : 0.004 0.037 1611 Dihedral : 7.422 98.725 1463 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.29 % Allowed : 11.77 % Favored : 86.94 % 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: 0.70 (0.24), residues: 1193 helix: 1.17 (0.19), residues: 804 sheet: -1.59 (0.72), residues: 47 loop : -0.80 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 316 HIS 0.004 0.001 HIS A 103 PHE 0.016 0.001 PHE A 308 TYR 0.024 0.001 TYR A 248 ARG 0.002 0.000 ARG A 810 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 534 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8199 (m) REVERT: A 792 MET cc_start: 0.8290 (mmp) cc_final: 0.7854 (mmp) REVERT: A 805 MET cc_start: 0.8141 (mmm) cc_final: 0.7820 (mmp) outliers start: 13 outliers final: 10 residues processed: 100 average time/residue: 0.2200 time to fit residues: 31.2280 Evaluate side-chains 98 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1154 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 98 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9566 Z= 0.204 Angle : 0.451 5.452 12954 Z= 0.239 Chirality : 0.038 0.138 1519 Planarity : 0.004 0.037 1611 Dihedral : 7.422 98.725 1463 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.09 % Allowed : 12.27 % Favored : 86.65 % 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: 0.70 (0.24), residues: 1193 helix: 1.17 (0.19), residues: 804 sheet: -1.59 (0.72), residues: 47 loop : -0.80 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 316 HIS 0.004 0.001 HIS A 103 PHE 0.016 0.001 PHE A 308 TYR 0.024 0.001 TYR A 248 ARG 0.002 0.000 ARG A 810 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: A 534 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8200 (m) REVERT: A 792 MET cc_start: 0.8291 (mmp) cc_final: 0.7854 (mmp) REVERT: A 805 MET cc_start: 0.8140 (mmm) cc_final: 0.7821 (mmp) outliers start: 11 outliers final: 10 residues processed: 95 average time/residue: 0.2201 time to fit residues: 29.7043 Evaluate side-chains 98 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1154 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9566 Z= 0.204 Angle : 0.451 5.452 12954 Z= 0.239 Chirality : 0.038 0.138 1519 Planarity : 0.004 0.037 1611 Dihedral : 7.422 98.725 1463 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.09 % Allowed : 12.27 % Favored : 86.65 % 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: 0.70 (0.24), residues: 1193 helix: 1.17 (0.19), residues: 804 sheet: -1.59 (0.72), residues: 47 loop : -0.80 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 316 HIS 0.004 0.001 HIS A 103 PHE 0.016 0.001 PHE A 308 TYR 0.024 0.001 TYR A 248 ARG 0.002 0.000 ARG A 810 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: A 534 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8200 (m) REVERT: A 792 MET cc_start: 0.8291 (mmp) cc_final: 0.7854 (mmp) REVERT: A 805 MET cc_start: 0.8140 (mmm) cc_final: 0.7821 (mmp) outliers start: 11 outliers final: 10 residues processed: 95 average time/residue: 0.2291 time to fit residues: 30.9716 Evaluate side-chains 98 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1154 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.5980 chunk 13 optimal weight: 0.0770 chunk 66 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 64 optimal weight: 0.4980 chunk 115 optimal weight: 2.9990 chunk 72 optimal weight: 0.0470 chunk 70 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9566 Z= 0.141 Angle : 0.432 5.454 12954 Z= 0.230 Chirality : 0.037 0.137 1519 Planarity : 0.004 0.036 1611 Dihedral : 7.141 97.577 1463 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.48 % Allowed : 11.97 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.25), residues: 1193 helix: 1.31 (0.19), residues: 803 sheet: -1.49 (0.72), residues: 47 loop : -0.71 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 316 HIS 0.003 0.001 HIS A 103 PHE 0.015 0.001 PHE A 308 TYR 0.022 0.001 TYR A 248 ARG 0.002 0.000 ARG A 810 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 534 VAL cc_start: 0.8639 (OUTLIER) cc_final: 0.8137 (m) REVERT: A 792 MET cc_start: 0.8157 (mmp) cc_final: 0.7812 (mmp) REVERT: A 805 MET cc_start: 0.8099 (mmm) cc_final: 0.7823 (mmp) outliers start: 15 outliers final: 10 residues processed: 106 average time/residue: 0.2312 time to fit residues: 35.0116 Evaluate side-chains 98 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1154 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.9990 chunk 46 optimal weight: 0.0170 chunk 69 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.6422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9566 Z= 0.142 Angle : 0.432 5.454 12954 Z= 0.230 Chirality : 0.037 0.137 1519 Planarity : 0.004 0.036 1611 Dihedral : 6.973 97.576 1461 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.09 % Allowed : 12.56 % Favored : 86.35 % 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: 0.89 (0.25), residues: 1193 helix: 1.31 (0.19), residues: 803 sheet: -1.49 (0.72), residues: 47 loop : -0.71 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 316 HIS 0.003 0.001 HIS A 103 PHE 0.015 0.001 PHE A 308 TYR 0.022 0.001 TYR A 248 ARG 0.002 0.000 ARG A 810 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: A 534 VAL cc_start: 0.8640 (OUTLIER) cc_final: 0.8137 (m) REVERT: A 792 MET cc_start: 0.8157 (mmp) cc_final: 0.7810 (mmp) REVERT: A 805 MET cc_start: 0.8099 (mmm) cc_final: 0.7823 (mmp) outliers start: 11 outliers final: 10 residues processed: 96 average time/residue: 0.2294 time to fit residues: 31.4465 Evaluate side-chains 97 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1154 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 33 optimal weight: 0.0670 chunk 97 optimal weight: 0.1980 chunk 70 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9566 Z= 0.150 Angle : 0.430 5.454 12954 Z= 0.229 Chirality : 0.037 0.143 1519 Planarity : 0.004 0.036 1611 Dihedral : 7.085 97.569 1461 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.19 % Allowed : 12.46 % Favored : 86.35 % 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: 0.90 (0.25), residues: 1193 helix: 1.32 (0.19), residues: 803 sheet: -1.49 (0.72), residues: 47 loop : -0.71 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 316 HIS 0.003 0.001 HIS A 103 PHE 0.016 0.001 PHE A 308 TYR 0.022 0.001 TYR A 248 ARG 0.002 0.000 ARG A 810 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: A 534 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8137 (m) REVERT: A 792 MET cc_start: 0.8156 (mmp) cc_final: 0.7812 (mmp) REVERT: A 805 MET cc_start: 0.8099 (mmm) cc_final: 0.7824 (mmp) outliers start: 12 outliers final: 10 residues processed: 96 average time/residue: 0.2291 time to fit residues: 31.0217 Evaluate side-chains 97 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1154 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9566 Z= 0.270 Angle : 0.483 7.196 12954 Z= 0.253 Chirality : 0.039 0.139 1519 Planarity : 0.004 0.036 1611 Dihedral : 6.825 92.705 1461 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.09 % Allowed : 12.66 % Favored : 86.25 % 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: 0.83 (0.24), residues: 1193 helix: 1.22 (0.19), residues: 804 sheet: -1.42 (0.70), residues: 48 loop : -0.62 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 304 HIS 0.004 0.001 HIS A 103 PHE 0.017 0.002 PHE A 979 TYR 0.027 0.001 TYR A 248 ARG 0.002 0.000 ARG A1035 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 792 MET cc_start: 0.8307 (mmp) cc_final: 0.7897 (mmp) outliers start: 11 outliers final: 10 residues processed: 102 average time/residue: 0.2445 time to fit residues: 34.6492 Evaluate side-chains 99 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1154 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1137 ASN A1282 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.129489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.095196 restraints weight = 11364.977| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.81 r_work: 0.2895 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9566 Z= 0.176 Angle : 0.456 7.393 12954 Z= 0.241 Chirality : 0.037 0.136 1519 Planarity : 0.004 0.037 1611 Dihedral : 6.770 91.662 1461 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.09 % Allowed : 12.86 % Favored : 86.05 % 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: 0.93 (0.25), residues: 1193 helix: 1.28 (0.19), residues: 804 sheet: -1.43 (0.72), residues: 47 loop : -0.56 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 304 HIS 0.003 0.001 HIS A 103 PHE 0.015 0.001 PHE A 308 TYR 0.026 0.001 TYR A 248 ARG 0.002 0.000 ARG A 810 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2102.20 seconds wall clock time: 39 minutes 14.83 seconds (2354.83 seconds total)