Starting phenix.real_space_refine on Tue Sep 24 18:55:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlu_22380/09_2024/7jlu_22380.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlu_22380/09_2024/7jlu_22380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlu_22380/09_2024/7jlu_22380.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlu_22380/09_2024/7jlu_22380.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlu_22380/09_2024/7jlu_22380.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlu_22380/09_2024/7jlu_22380.cif" } resolution = 3.8 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= 0.001 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 Ca 1 9.91 5 S 52 5.16 5 C 5499 2.51 5 N 1460 2.21 5 O 1580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8592 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5884 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 31, 'TRANS': 694} Chain breaks: 3 Chain: "B" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2707 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 24, 'TRANS': 328} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.56, per 1000 atoms: 0.76 Number of scatterers: 8592 At special positions: 0 Unit cell: (96.6758, 108.878, 94.7986, 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) Ca 1 19.99 S 52 16.00 O 1580 8.00 N 1460 7.00 C 5499 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 974.3 milliseconds 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 5 sheets defined 31.7% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 540 through 546 removed outlier: 3.885A pdb=" N TYR A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 554 Processing helix chain 'A' and resid 663 through 669 removed outlier: 3.549A pdb=" N LEU A 669 " --> pdb=" O VAL A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 3.853A pdb=" N ILE A 736 " --> pdb=" O PRO A 733 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU A 737 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 763 Processing helix chain 'A' and resid 803 through 808 removed outlier: 3.638A pdb=" N ASN A 806 " --> pdb=" O SER A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 831 removed outlier: 3.658A pdb=" N GLY A 830 " --> pdb=" O SER A 827 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 831 " --> pdb=" O ILE A 828 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 827 through 831' Processing helix chain 'A' and resid 896 through 901 removed outlier: 3.827A pdb=" N ILE A 899 " --> pdb=" O PRO A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 949 removed outlier: 3.520A pdb=" N LEU A 949 " --> pdb=" O VAL A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 976 removed outlier: 3.855A pdb=" N LEU A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 981 Processing helix chain 'A' and resid 1044 through 1052 removed outlier: 3.590A pdb=" N MET A1048 " --> pdb=" O ALA A1044 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU A1049 " --> pdb=" O LEU A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 removed outlier: 4.007A pdb=" N TYR A1072 " --> pdb=" O TYR A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1079 removed outlier: 3.570A pdb=" N ILE A1078 " --> pdb=" O LEU A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1100 removed outlier: 4.271A pdb=" N GLU A1087 " --> pdb=" O SER A1083 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A1088 " --> pdb=" O GLU A1084 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A1090 " --> pdb=" O LEU A1086 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLN A1092 " --> pdb=" O ASN A1088 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN A1093 " --> pdb=" O SER A1089 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP A1095 " --> pdb=" O LYS A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1149 removed outlier: 4.141A pdb=" N THR A1148 " --> pdb=" O TYR A1145 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU A1149 " --> pdb=" O TRP A1146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1145 through 1149' Processing helix chain 'A' and resid 1166 through 1178 removed outlier: 3.629A pdb=" N ASP A1170 " --> pdb=" O ALA A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1190 removed outlier: 3.716A pdb=" N GLU A1189 " --> pdb=" O TYR A1186 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR A1190 " --> pdb=" O TRP A1187 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 103 Processing helix chain 'B' and resid 121 through 136 removed outlier: 3.706A pdb=" N VAL B 125 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 168 Processing helix chain 'B' and resid 184 through 192 Processing helix chain 'B' and resid 195 through 199 removed outlier: 3.517A pdb=" N GLY B 198 " --> pdb=" O LEU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 223 removed outlier: 3.570A pdb=" N GLU B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 243 Processing helix chain 'B' and resid 245 through 252 Processing helix chain 'B' and resid 278 through 284 removed outlier: 4.160A pdb=" N ASP B 284 " --> pdb=" O ASN B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 298 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 317 through 325 removed outlier: 3.600A pdb=" N GLU B 321 " --> pdb=" O PRO B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 350 removed outlier: 3.656A pdb=" N GLN B 350 " --> pdb=" O TRP B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 358 through 366 Processing helix chain 'B' and resid 384 through 389 Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 398 through 407 removed outlier: 3.911A pdb=" N THR B 402 " --> pdb=" O TYR B 398 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 415 removed outlier: 3.895A pdb=" N ARG B 412 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU B 413 " --> pdb=" O GLY B 409 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 414 " --> pdb=" O ALA B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 452 Processing sheet with id=AA1, first strand: chain 'A' and resid 529 through 531 removed outlier: 3.625A pdb=" N LEU A 529 " --> pdb=" O ILE A 559 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 561 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 531 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU A 560 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU A 605 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N SER A 631 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N MET A 607 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 689 through 690 removed outlier: 3.805A pdb=" N ILE A 690 " --> pdb=" O GLU A 711 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 744 through 748 removed outlier: 7.046A pdb=" N VAL A 795 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 790 " --> pdb=" O GLU A 814 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N CYS A 816 " --> pdb=" O LEU A 790 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 792 " --> pdb=" O CYS A 816 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU A 813 " --> pdb=" O LYS A 838 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LEU A 840 " --> pdb=" O LEU A 813 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE A 815 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE A 884 " --> pdb=" O CYS A 909 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N SER A 911 " --> pdb=" O ILE A 884 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N MET A 886 " --> pdb=" O SER A 911 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP A1040 " --> pdb=" O ILE A1018 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N HIS A1120 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A1238 " --> pdb=" O PHE A1162 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A1162 " --> pdb=" O VAL A1238 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A1246 " --> pdb=" O PHE A1154 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE A1154 " --> pdb=" O PHE A1246 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY A1153 " --> pdb=" O VAL A1289 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A1289 " --> pdb=" O GLY A1153 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A1155 " --> pdb=" O ASN A1287 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN A1287 " --> pdb=" O ALA A1155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1139 through 1140 removed outlier: 3.590A pdb=" N CYS A1271 " --> pdb=" O THR A1206 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS A1223 " --> pdb=" O ALA A1207 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 174 through 176 removed outlier: 5.398A pdb=" N LEU B 109 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU B 141 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR B 111 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP B 143 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASP B 110 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N VAL B 230 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 112 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU B 227 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE B 256 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N MET B 229 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ILE B 258 " --> pdb=" O MET B 229 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL B 231 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ARG B 303 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE B 256 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU B 305 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 258 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU B 302 " --> pdb=" O GLU B 429 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL B 431 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE B 304 " --> pdb=" O VAL B 431 " (cutoff:3.500A) 263 hydrogen bonds defined for protein. 699 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: 2.80 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2793 1.34 - 1.46: 1911 1.46 - 1.58: 3998 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 8780 Sorted by residual: bond pdb=" N THR A1136 " pdb=" CA THR A1136 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.20e+00 bond pdb=" CA THR B 147 " pdb=" C THR B 147 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.24e-02 6.50e+03 8.96e-01 bond pdb=" CB GLU B 251 " pdb=" CG GLU B 251 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.43e-01 bond pdb=" CA ASN A 744 " pdb=" CB ASN A 744 " ideal model delta sigma weight residual 1.535 1.554 -0.019 2.09e-02 2.29e+03 8.33e-01 bond pdb=" CB ASP B 150 " pdb=" CG ASP B 150 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.91e-01 ... (remaining 8775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 11613 2.30 - 4.59: 257 4.59 - 6.89: 28 6.89 - 9.19: 6 9.19 - 11.49: 1 Bond angle restraints: 11905 Sorted by residual: angle pdb=" CA LEU B 334 " pdb=" CB LEU B 334 " pdb=" CG LEU B 334 " ideal model delta sigma weight residual 116.30 127.79 -11.49 3.50e+00 8.16e-02 1.08e+01 angle pdb=" CA GLU B 251 " pdb=" CB GLU B 251 " pdb=" CG GLU B 251 " ideal model delta sigma weight residual 114.10 120.41 -6.31 2.00e+00 2.50e-01 9.95e+00 angle pdb=" CB MET A1241 " pdb=" CG MET A1241 " pdb=" SD MET A1241 " ideal model delta sigma weight residual 112.70 120.82 -8.12 3.00e+00 1.11e-01 7.33e+00 angle pdb=" CB MET B 383 " pdb=" CG MET B 383 " pdb=" SD MET B 383 " ideal model delta sigma weight residual 112.70 120.76 -8.06 3.00e+00 1.11e-01 7.22e+00 angle pdb=" C ALA B 351 " pdb=" N ASN B 352 " pdb=" CA ASN B 352 " ideal model delta sigma weight residual 121.54 126.63 -5.09 1.91e+00 2.74e-01 7.09e+00 ... (remaining 11900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4548 17.96 - 35.92: 634 35.92 - 53.89: 117 53.89 - 71.85: 18 71.85 - 89.81: 7 Dihedral angle restraints: 5324 sinusoidal: 2162 harmonic: 3162 Sorted by residual: dihedral pdb=" CA SER A 590 " pdb=" C SER A 590 " pdb=" N ASN A 591 " pdb=" CA ASN A 591 " ideal model delta harmonic sigma weight residual -180.00 -157.98 -22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA TRP A 900 " pdb=" C TRP A 900 " pdb=" N MET A 901 " pdb=" CA MET A 901 " ideal model delta harmonic sigma weight residual 180.00 160.61 19.39 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA ARG A1133 " pdb=" C ARG A1133 " pdb=" N SER A1134 " pdb=" CA SER A1134 " ideal model delta harmonic sigma weight residual -180.00 -160.87 -19.13 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 777 0.033 - 0.066: 367 0.066 - 0.099: 137 0.099 - 0.131: 60 0.131 - 0.164: 9 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CA GLU A 743 " pdb=" N GLU A 743 " pdb=" C GLU A 743 " pdb=" CB GLU A 743 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" CG LEU A 630 " pdb=" CB LEU A 630 " pdb=" CD1 LEU A 630 " pdb=" CD2 LEU A 630 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CB THR A1299 " pdb=" CA THR A1299 " pdb=" OG1 THR A1299 " pdb=" CG2 THR A1299 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 1347 not shown) Planarity restraints: 1515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 900 " 0.017 2.00e-02 2.50e+03 1.46e-02 5.32e+00 pdb=" CG TRP A 900 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 900 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 900 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 900 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 900 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 900 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 900 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 900 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 900 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 800 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO A 801 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 801 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 801 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 385 " -0.006 2.00e-02 2.50e+03 1.22e-02 2.59e+00 pdb=" CG PHE B 385 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE B 385 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 385 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE B 385 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 385 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 385 " -0.000 2.00e-02 2.50e+03 ... (remaining 1512 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 475 2.73 - 3.27: 8625 3.27 - 3.81: 13132 3.81 - 4.36: 15685 4.36 - 4.90: 26632 Nonbonded interactions: 64549 Sorted by model distance: nonbonded pdb=" OG SER A1080 " pdb=" OD1 ASP A1081 " model vdw 2.187 3.040 nonbonded pdb=" O LEU A 551 " pdb=" OG1 THR A 554 " model vdw 2.200 3.040 nonbonded pdb=" OD1 ASP A1040 " pdb=" N GLU A1041 " model vdw 2.241 3.120 nonbonded pdb=" O GLU A 543 " pdb=" OG SER A 547 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR B 418 " pdb=" OE1 GLU B 435 " model vdw 2.269 3.040 ... (remaining 64544 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 17.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.580 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 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 : 0.003 0.031 8780 Z= 0.193 Angle : 0.780 11.487 11905 Z= 0.392 Chirality : 0.046 0.164 1350 Planarity : 0.004 0.043 1515 Dihedral : 16.633 89.810 3272 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 0.21 % Allowed : 0.42 % Favored : 99.37 % 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: -1.56 (0.26), residues: 1067 helix: 0.08 (0.35), residues: 246 sheet: 0.28 (0.37), residues: 203 loop : -2.08 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 900 HIS 0.008 0.001 HIS B 430 PHE 0.026 0.002 PHE B 385 TYR 0.020 0.002 TYR A1186 ARG 0.020 0.001 ARG A 882 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 551 LEU cc_start: 0.7731 (mm) cc_final: 0.7458 (mt) REVERT: A 586 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7289 (mtp180) REVERT: A 607 MET cc_start: 0.6620 (mmm) cc_final: 0.6395 (mtt) REVERT: A 677 MET cc_start: 0.8016 (mmt) cc_final: 0.7815 (mmt) REVERT: A 1138 MET cc_start: 0.7502 (ttt) cc_final: 0.7211 (ttt) outliers start: 2 outliers final: 0 residues processed: 102 average time/residue: 0.1860 time to fit residues: 27.5131 Evaluate side-chains 84 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 0.0000 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 0.0070 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.6008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1090 GLN ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 HIS B 328 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8780 Z= 0.261 Angle : 0.690 7.106 11905 Z= 0.350 Chirality : 0.047 0.165 1350 Planarity : 0.005 0.051 1515 Dihedral : 5.201 31.837 1177 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 1.26 % Allowed : 12.00 % Favored : 86.74 % 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: -1.59 (0.26), residues: 1067 helix: -0.21 (0.32), residues: 258 sheet: 0.20 (0.37), residues: 217 loop : -2.03 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 582 HIS 0.006 0.001 HIS B 430 PHE 0.022 0.002 PHE A 704 TYR 0.014 0.002 TYR A1145 ARG 0.005 0.001 ARG A1233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.896 Fit side-chains REVERT: A 584 GLU cc_start: 0.7458 (mp0) cc_final: 0.7192 (mp0) REVERT: A 677 MET cc_start: 0.8202 (mmt) cc_final: 0.7833 (mmt) REVERT: B 107 LEU cc_start: 0.7756 (mp) cc_final: 0.7461 (mt) outliers start: 12 outliers final: 9 residues processed: 87 average time/residue: 0.1705 time to fit residues: 22.3975 Evaluate side-chains 86 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 718 HIS Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain B residue 148 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 ASN ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 HIS B 328 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8780 Z= 0.304 Angle : 0.689 6.338 11905 Z= 0.356 Chirality : 0.048 0.156 1350 Planarity : 0.005 0.056 1515 Dihedral : 5.224 23.112 1173 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 2.42 % Allowed : 18.11 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.25), residues: 1067 helix: -0.37 (0.31), residues: 270 sheet: -0.16 (0.37), residues: 215 loop : -2.39 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 582 HIS 0.005 0.001 HIS A 663 PHE 0.021 0.002 PHE A 704 TYR 0.014 0.002 TYR A 575 ARG 0.004 0.001 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 78 time to evaluate : 1.003 Fit side-chains REVERT: A 677 MET cc_start: 0.8236 (mmt) cc_final: 0.7840 (mmt) REVERT: A 718 HIS cc_start: 0.7264 (OUTLIER) cc_final: 0.7027 (m-70) REVERT: A 1070 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7877 (p0) REVERT: B 107 LEU cc_start: 0.7850 (mp) cc_final: 0.7596 (mt) outliers start: 23 outliers final: 13 residues processed: 94 average time/residue: 0.1712 time to fit residues: 24.3581 Evaluate side-chains 93 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 718 HIS Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1070 ASN Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1269 GLU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 402 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8780 Z= 0.177 Angle : 0.621 8.480 11905 Z= 0.315 Chirality : 0.045 0.151 1350 Planarity : 0.005 0.053 1515 Dihedral : 4.914 24.149 1173 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 2.63 % Allowed : 20.74 % Favored : 76.63 % 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: -1.86 (0.26), residues: 1067 helix: -0.28 (0.32), residues: 274 sheet: -0.27 (0.36), residues: 229 loop : -2.22 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 900 HIS 0.004 0.001 HIS A 663 PHE 0.019 0.001 PHE A 704 TYR 0.015 0.001 TYR A 575 ARG 0.005 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 85 time to evaluate : 0.910 Fit side-chains REVERT: A 661 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7377 (tm-30) REVERT: A 677 MET cc_start: 0.8234 (mmt) cc_final: 0.7908 (mmt) REVERT: A 718 HIS cc_start: 0.7149 (OUTLIER) cc_final: 0.6901 (m-70) REVERT: A 1126 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6803 (mp0) REVERT: A 1229 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7328 (tmm) REVERT: B 107 LEU cc_start: 0.7812 (mp) cc_final: 0.7578 (mt) REVERT: B 305 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7697 (mp) outliers start: 25 outliers final: 11 residues processed: 103 average time/residue: 0.1556 time to fit residues: 24.3799 Evaluate side-chains 94 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 718 HIS Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1126 GLU Chi-restraints excluded: chain A residue 1229 MET Chi-restraints excluded: chain A residue 1246 PHE Chi-restraints excluded: chain A residue 1269 GLU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 402 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1178 HIS ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8780 Z= 0.185 Angle : 0.612 10.138 11905 Z= 0.309 Chirality : 0.045 0.144 1350 Planarity : 0.004 0.052 1515 Dihedral : 4.802 23.712 1173 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 2.53 % Allowed : 20.95 % Favored : 76.53 % 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: -1.78 (0.26), residues: 1067 helix: -0.06 (0.32), residues: 273 sheet: -0.07 (0.36), residues: 219 loop : -2.30 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 900 HIS 0.003 0.001 HIS A 663 PHE 0.019 0.001 PHE A 704 TYR 0.013 0.001 TYR A 575 ARG 0.006 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 0.913 Fit side-chains REVERT: A 661 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7304 (tm-30) REVERT: A 718 HIS cc_start: 0.7090 (OUTLIER) cc_final: 0.6849 (m-70) REVERT: A 1229 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7365 (tmm) REVERT: B 107 LEU cc_start: 0.7807 (mp) cc_final: 0.7571 (mt) REVERT: B 305 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7703 (mp) outliers start: 24 outliers final: 16 residues processed: 99 average time/residue: 0.1761 time to fit residues: 25.9177 Evaluate side-chains 99 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 635 LYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 718 HIS Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1101 ILE Chi-restraints excluded: chain A residue 1178 HIS Chi-restraints excluded: chain A residue 1229 MET Chi-restraints excluded: chain A residue 1246 PHE Chi-restraints excluded: chain A residue 1269 GLU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 402 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 99 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: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS B 350 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8780 Z= 0.319 Angle : 0.678 8.368 11905 Z= 0.351 Chirality : 0.047 0.153 1350 Planarity : 0.005 0.055 1515 Dihedral : 5.136 23.337 1173 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 3.47 % Allowed : 21.26 % Favored : 75.26 % 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: -1.93 (0.26), residues: 1067 helix: -0.13 (0.32), residues: 265 sheet: -0.20 (0.37), residues: 213 loop : -2.35 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 900 HIS 0.018 0.002 HIS A1178 PHE 0.022 0.002 PHE A 704 TYR 0.016 0.002 TYR A 575 ARG 0.005 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 79 time to evaluate : 0.951 Fit side-chains REVERT: A 677 MET cc_start: 0.8228 (mmt) cc_final: 0.7847 (mmt) REVERT: A 718 HIS cc_start: 0.7303 (OUTLIER) cc_final: 0.7035 (m-70) REVERT: A 1229 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7317 (tmm) REVERT: A 1302 MET cc_start: 0.5500 (mtt) cc_final: 0.5053 (mmm) REVERT: B 305 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7657 (mp) outliers start: 33 outliers final: 21 residues processed: 105 average time/residue: 0.1629 time to fit residues: 25.7692 Evaluate side-chains 103 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 79 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 635 LYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 718 HIS Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1101 ILE Chi-restraints excluded: chain A residue 1178 HIS Chi-restraints excluded: chain A residue 1229 MET Chi-restraints excluded: chain A residue 1269 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 402 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 103 optimal weight: 0.4980 chunk 64 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 47 optimal weight: 0.3980 chunk 63 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN A1178 HIS ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8780 Z= 0.151 Angle : 0.620 12.121 11905 Z= 0.309 Chirality : 0.045 0.169 1350 Planarity : 0.004 0.052 1515 Dihedral : 4.769 24.509 1173 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 2.63 % Allowed : 22.74 % Favored : 74.63 % 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: -1.77 (0.26), residues: 1067 helix: 0.04 (0.33), residues: 263 sheet: -0.18 (0.37), residues: 215 loop : -2.24 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 900 HIS 0.003 0.001 HIS A 663 PHE 0.019 0.001 PHE A 704 TYR 0.011 0.001 TYR A1145 ARG 0.006 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 85 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 677 MET cc_start: 0.8149 (mmt) cc_final: 0.7640 (mmt) REVERT: A 718 HIS cc_start: 0.7122 (OUTLIER) cc_final: 0.6835 (m-70) REVERT: A 1229 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7343 (tmm) REVERT: A 1302 MET cc_start: 0.5492 (mtt) cc_final: 0.5155 (mmm) REVERT: B 305 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7716 (mp) outliers start: 25 outliers final: 16 residues processed: 106 average time/residue: 0.1735 time to fit residues: 27.3957 Evaluate side-chains 98 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 635 LYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 718 HIS Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1178 HIS Chi-restraints excluded: chain A residue 1229 MET Chi-restraints excluded: chain A residue 1246 PHE Chi-restraints excluded: chain A residue 1269 GLU Chi-restraints excluded: chain A residue 1271 CYS Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 402 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1178 HIS ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8780 Z= 0.168 Angle : 0.618 11.222 11905 Z= 0.309 Chirality : 0.044 0.143 1350 Planarity : 0.004 0.051 1515 Dihedral : 4.704 23.026 1173 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 2.74 % Allowed : 22.74 % Favored : 74.53 % 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: -1.70 (0.26), residues: 1067 helix: 0.04 (0.34), residues: 264 sheet: -0.13 (0.37), residues: 215 loop : -2.16 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 900 HIS 0.007 0.001 HIS A1178 PHE 0.019 0.001 PHE A 704 TYR 0.012 0.001 TYR A 575 ARG 0.007 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 81 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 718 HIS cc_start: 0.7077 (OUTLIER) cc_final: 0.6797 (m-70) REVERT: A 1126 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: A 1229 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7299 (tmm) REVERT: A 1302 MET cc_start: 0.5504 (mtt) cc_final: 0.5146 (mmm) REVERT: B 305 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7724 (mp) outliers start: 26 outliers final: 18 residues processed: 103 average time/residue: 0.1676 time to fit residues: 26.3733 Evaluate side-chains 101 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 635 LYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 718 HIS Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1126 GLU Chi-restraints excluded: chain A residue 1178 HIS Chi-restraints excluded: chain A residue 1229 MET Chi-restraints excluded: chain A residue 1269 GLU Chi-restraints excluded: chain A residue 1271 CYS Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 402 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 57 optimal weight: 0.2980 chunk 41 optimal weight: 0.0980 chunk 75 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1178 HIS ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8780 Z= 0.149 Angle : 0.617 10.928 11905 Z= 0.305 Chirality : 0.044 0.141 1350 Planarity : 0.004 0.050 1515 Dihedral : 4.611 23.202 1173 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 2.74 % Allowed : 23.47 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.26), residues: 1067 helix: -0.02 (0.33), residues: 270 sheet: -0.13 (0.37), residues: 215 loop : -2.12 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 900 HIS 0.008 0.001 HIS A1178 PHE 0.019 0.001 PHE A 704 TYR 0.011 0.001 TYR A 575 ARG 0.007 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 80 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: A 718 HIS cc_start: 0.7074 (OUTLIER) cc_final: 0.6790 (m-70) REVERT: A 1126 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: A 1229 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7302 (tmm) REVERT: A 1302 MET cc_start: 0.5523 (mtt) cc_final: 0.5195 (mmm) outliers start: 26 outliers final: 19 residues processed: 103 average time/residue: 0.1690 time to fit residues: 26.3316 Evaluate side-chains 102 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 635 LYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 718 HIS Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1126 GLU Chi-restraints excluded: chain A residue 1178 HIS Chi-restraints excluded: chain A residue 1229 MET Chi-restraints excluded: chain A residue 1269 GLU Chi-restraints excluded: chain A residue 1271 CYS Chi-restraints excluded: chain B residue 103 HIS Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 402 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 98 optimal weight: 0.0270 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 overall best weight: 1.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1070 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1178 HIS ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8780 Z= 0.215 Angle : 0.649 13.783 11905 Z= 0.324 Chirality : 0.045 0.146 1350 Planarity : 0.004 0.051 1515 Dihedral : 4.711 22.162 1173 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 2.84 % Allowed : 23.47 % Favored : 73.68 % 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: -1.76 (0.26), residues: 1067 helix: -0.10 (0.33), residues: 270 sheet: -0.18 (0.37), residues: 215 loop : -2.17 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 900 HIS 0.011 0.001 HIS A1178 PHE 0.019 0.001 PHE A 704 TYR 0.015 0.001 TYR A 575 ARG 0.007 0.000 ARG A 621 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 83 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 718 HIS cc_start: 0.7107 (OUTLIER) cc_final: 0.6835 (m-70) REVERT: A 1040 ASP cc_start: 0.8528 (t0) cc_final: 0.7765 (p0) REVERT: A 1126 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: A 1229 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7306 (tmm) REVERT: A 1241 MET cc_start: 0.8330 (mmm) cc_final: 0.8117 (mmm) REVERT: A 1302 MET cc_start: 0.5615 (mtt) cc_final: 0.5322 (mmm) REVERT: B 305 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7735 (mp) outliers start: 27 outliers final: 19 residues processed: 107 average time/residue: 0.1789 time to fit residues: 29.1714 Evaluate side-chains 103 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 635 LYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 718 HIS Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1126 GLU Chi-restraints excluded: chain A residue 1178 HIS Chi-restraints excluded: chain A residue 1229 MET Chi-restraints excluded: chain A residue 1269 GLU Chi-restraints excluded: chain A residue 1271 CYS Chi-restraints excluded: chain B residue 103 HIS Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 402 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 85 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 4 optimal weight: 0.0870 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1070 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1178 HIS ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.112284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099994 restraints weight = 18542.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.102553 restraints weight = 9697.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.104236 restraints weight = 5990.744| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8780 Z= 0.188 Angle : 0.654 13.555 11905 Z= 0.323 Chirality : 0.045 0.144 1350 Planarity : 0.004 0.051 1515 Dihedral : 4.707 23.145 1173 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 2.63 % Allowed : 23.89 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.26), residues: 1067 helix: -0.10 (0.33), residues: 270 sheet: -0.18 (0.37), residues: 215 loop : -2.16 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 900 HIS 0.004 0.001 HIS A1178 PHE 0.019 0.001 PHE A 704 TYR 0.014 0.001 TYR A 575 ARG 0.007 0.000 ARG A 621 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1994.69 seconds wall clock time: 37 minutes 17.21 seconds (2237.21 seconds total)