Starting phenix.real_space_refine on Sun Apr 7 05:36:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwf_36681/04_2024/8jwf_36681_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwf_36681/04_2024/8jwf_36681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwf_36681/04_2024/8jwf_36681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwf_36681/04_2024/8jwf_36681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwf_36681/04_2024/8jwf_36681_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwf_36681/04_2024/8jwf_36681_neut_updated.pdb" } resolution = 3.64 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= -0.003 sd= 0.050 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 S 40 5.16 5 C 6300 2.51 5 N 1600 2.21 5 O 1771 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 1116": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9717 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1204, 9691 Classifications: {'peptide': 1204} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 1177} Chain breaks: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'YMZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.61, per 1000 atoms: 0.58 Number of scatterers: 9717 At special positions: 0 Unit cell: (70.4, 116.6, 144.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 F 6 9.00 O 1771 8.00 N 1600 7.00 C 6300 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: 4.13 Conformation dependent library (CDL) restraints added in 1.7 seconds 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2286 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 5 sheets defined 61.8% alpha, 2.7% 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 15 through 23 Processing helix chain 'A' and resid 28 through 38 removed outlier: 3.776A pdb=" N ASN A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 51 through 69 removed outlier: 4.503A pdb=" N PHE A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER A 67 " --> pdb=" O CYS A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 86 removed outlier: 4.093A pdb=" N GLY A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 137 removed outlier: 4.576A pdb=" N ILE A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N SER A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 148 through 162 removed outlier: 3.744A pdb=" N LEU A 155 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP A 156 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 172 through 190 removed outlier: 3.574A pdb=" N TYR A 184 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ILE A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 225 removed outlier: 5.562A pdb=" N VAL A 201 " --> pdb=" O CYS A 197 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N PHE A 202 " --> pdb=" O ILE A 198 " (cutoff:3.500A) Proline residue: A 203 - end of helix removed outlier: 3.547A pdb=" N CYS A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS A 215 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 239 Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 250 through 304 removed outlier: 3.882A pdb=" N LEU A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU A 287 " --> pdb=" O ASN A 283 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 357 removed outlier: 3.540A pdb=" N SER A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR A 334 " --> pdb=" O MET A 330 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Proline residue: A 338 - end of helix removed outlier: 3.545A pdb=" N LEU A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 426 Processing helix chain 'A' and resid 450 through 456 removed outlier: 3.983A pdb=" N LYS A 456 " --> pdb=" O TRP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 488 removed outlier: 4.555A pdb=" N SER A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 479 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 removed outlier: 3.915A pdb=" N GLU A 523 " --> pdb=" O MET A 520 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N TYR A 524 " --> pdb=" O LYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 536 Processing helix chain 'A' and resid 542 through 547 Processing helix chain 'A' and resid 565 through 578 Processing helix chain 'A' and resid 589 through 592 removed outlier: 4.279A pdb=" N SER A 592 " --> pdb=" O ALA A 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 589 through 592' Processing helix chain 'A' and resid 595 through 606 Processing helix chain 'A' and resid 624 through 626 No H-bonds generated for 'chain 'A' and resid 624 through 626' Processing helix chain 'A' and resid 677 through 680 No H-bonds generated for 'chain 'A' and resid 677 through 680' Processing helix chain 'A' and resid 686 through 693 Processing helix chain 'A' and resid 772 through 783 removed outlier: 4.046A pdb=" N ILE A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 801 removed outlier: 4.062A pdb=" N ILE A 791 " --> pdb=" O LYS A 787 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 818 removed outlier: 4.041A pdb=" N ALA A 807 " --> pdb=" O TYR A 803 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 808 " --> pdb=" O PRO A 804 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 816 " --> pdb=" O ARG A 812 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 818 " --> pdb=" O VAL A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 873 removed outlier: 3.918A pdb=" N TYR A 833 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 843 " --> pdb=" O ILE A 839 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 865 " --> pdb=" O LYS A 861 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 866 " --> pdb=" O THR A 862 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR A 873 " --> pdb=" O GLU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 880 Processing helix chain 'A' and resid 886 through 902 removed outlier: 4.589A pdb=" N VAL A 897 " --> pdb=" O ILE A 893 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N HIS A 898 " --> pdb=" O ASN A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 928 removed outlier: 3.836A pdb=" N VAL A 909 " --> pdb=" O VAL A 905 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 910 " --> pdb=" O ASN A 906 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE A 926 " --> pdb=" O MET A 922 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR A 927 " --> pdb=" O VAL A 923 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE A 928 " --> pdb=" O MET A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 946 Processing helix chain 'A' and resid 949 through 961 Processing helix chain 'A' and resid 982 through 991 removed outlier: 3.783A pdb=" N PHE A 990 " --> pdb=" O ILE A 986 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 998 Processing helix chain 'A' and resid 1002 through 1035 removed outlier: 3.530A pdb=" N CYS A1006 " --> pdb=" O GLU A1002 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE A1009 " --> pdb=" O PHE A1005 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR A1015 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LYS A1018 " --> pdb=" O ASP A1014 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY A1019 " --> pdb=" O TYR A1015 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG A1022 " --> pdb=" O LYS A1018 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA A1029 " --> pdb=" O ILE A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1055 removed outlier: 3.955A pdb=" N ARG A1055 " --> pdb=" O PHE A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1081 Processing helix chain 'A' and resid 1088 through 1097 removed outlier: 3.825A pdb=" N GLU A1095 " --> pdb=" O LYS A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1121 No H-bonds generated for 'chain 'A' and resid 1119 through 1121' Processing helix chain 'A' and resid 1167 through 1173 removed outlier: 5.761A pdb=" N MET A1171 " --> pdb=" O SER A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1241 No H-bonds generated for 'chain 'A' and resid 1239 through 1241' Processing helix chain 'A' and resid 1244 through 1249 removed outlier: 4.602A pdb=" N ASN A1249 " --> pdb=" O ARG A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1269 Processing helix chain 'A' and resid 1278 through 1288 Processing helix chain 'A' and resid 1307 through 1309 No H-bonds generated for 'chain 'A' and resid 1307 through 1309' Processing helix chain 'A' and resid 1315 through 1328 removed outlier: 3.561A pdb=" N ALA A1325 " --> pdb=" O ALA A1321 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ARG A1328 " --> pdb=" O ARG A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1344 through 1359 Processing helix chain 'A' and resid 1372 through 1377 removed outlier: 4.853A pdb=" N ARG A1377 " --> pdb=" O ALA A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1416 Processing sheet with id= A, first strand: chain 'A' and resid 457 through 460 removed outlier: 5.901A pdb=" N ILE A 583 " --> pdb=" O GLY A 458 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL A 460 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE A 585 " --> pdb=" O VAL A 460 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 1126 through 1128 Processing sheet with id= C, first strand: chain 'A' and resid 1366 through 1368 removed outlier: 6.793A pdb=" N THR A1157 " --> pdb=" O THR A1367 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A1382 " --> pdb=" O ALA A1158 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A1160 " --> pdb=" O VAL A1382 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A1384 " --> pdb=" O VAL A1160 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 1251 through 1254 removed outlier: 7.313A pdb=" N ILE A1332 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N VAL A1254 " --> pdb=" O ILE A1332 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N LEU A1334 " --> pdb=" O VAL A1254 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 633 through 636 removed outlier: 3.500A pdb=" N GLU A 672 " --> pdb=" O VAL A 634 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N SER A 636 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE A 670 " --> pdb=" O SER A 636 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1323 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: 3.00 Time building geometry restraints manager: 4.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2717 1.33 - 1.45: 1744 1.45 - 1.58: 5368 1.58 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 9896 Sorted by residual: bond pdb=" CAR YMZ A1500 " pdb=" NAP YMZ A1500 " ideal model delta sigma weight residual 1.298 1.373 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" CA LYS A1104 " pdb=" CB LYS A1104 " ideal model delta sigma weight residual 1.528 1.569 -0.041 1.35e-02 5.49e+03 9.11e+00 bond pdb=" C GLU A1267 " pdb=" N ASN A1268 " ideal model delta sigma weight residual 1.335 1.371 -0.036 1.31e-02 5.83e+03 7.46e+00 bond pdb=" N ILE A1107 " pdb=" CA ILE A1107 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.25e-02 6.40e+03 5.60e+00 bond pdb=" CAJ YMZ A1500 " pdb=" CAU YMZ A1500 " ideal model delta sigma weight residual 1.414 1.369 0.045 2.00e-02 2.50e+03 5.16e+00 ... (remaining 9891 not shown) Histogram of bond angle deviations from ideal: 98.36 - 105.47: 114 105.47 - 112.58: 5080 112.58 - 119.69: 3399 119.69 - 126.81: 4684 126.81 - 133.92: 60 Bond angle restraints: 13337 Sorted by residual: angle pdb=" N SER A1105 " pdb=" CA SER A1105 " pdb=" C SER A1105 " ideal model delta sigma weight residual 111.28 117.83 -6.55 1.09e+00 8.42e-01 3.61e+01 angle pdb=" C ILE A 336 " pdb=" N LEU A 337 " pdb=" CA LEU A 337 " ideal model delta sigma weight residual 120.58 125.66 -5.08 1.32e+00 5.74e-01 1.48e+01 angle pdb=" N ILE A1107 " pdb=" CA ILE A1107 " pdb=" CB ILE A1107 " ideal model delta sigma weight residual 111.23 104.98 6.25 1.65e+00 3.67e-01 1.43e+01 angle pdb=" O SER A1105 " pdb=" C SER A1105 " pdb=" N ASN A1106 " ideal model delta sigma weight residual 122.12 126.06 -3.94 1.06e+00 8.90e-01 1.38e+01 angle pdb=" CA LYS A1104 " pdb=" C LYS A1104 " pdb=" O LYS A1104 " ideal model delta sigma weight residual 120.43 124.43 -4.00 1.12e+00 7.97e-01 1.28e+01 ... (remaining 13332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.51: 5864 23.51 - 47.02: 108 47.02 - 70.53: 6 70.53 - 94.04: 7 94.04 - 117.55: 2 Dihedral angle restraints: 5987 sinusoidal: 2447 harmonic: 3540 Sorted by residual: dihedral pdb=" CA GLY A 182 " pdb=" C GLY A 182 " pdb=" N LEU A 183 " pdb=" CA LEU A 183 " ideal model delta harmonic sigma weight residual 180.00 -153.06 -26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA SER A1168 " pdb=" C SER A1168 " pdb=" N THR A1169 " pdb=" CA THR A1169 " ideal model delta harmonic sigma weight residual 180.00 155.11 24.89 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA LEU A 593 " pdb=" C LEU A 593 " pdb=" N ASP A 594 " pdb=" CA ASP A 594 " ideal model delta harmonic sigma weight residual 180.00 158.28 21.72 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 5984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1388 0.081 - 0.162: 137 0.162 - 0.243: 1 0.243 - 0.324: 1 0.324 - 0.405: 2 Chirality restraints: 1529 Sorted by residual: chirality pdb=" CA LYS A1104 " pdb=" N LYS A1104 " pdb=" C LYS A1104 " pdb=" CB LYS A1104 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CA ILE A1107 " pdb=" N ILE A1107 " pdb=" C ILE A1107 " pdb=" CB ILE A1107 " both_signs ideal model delta sigma weight residual False 2.43 2.80 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA ASN A1106 " pdb=" N ASN A1106 " pdb=" C ASN A1106 " pdb=" CB ASN A1106 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1526 not shown) Planarity restraints: 1654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A1104 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.12e+00 pdb=" C LYS A1104 " 0.052 2.00e-02 2.50e+03 pdb=" O LYS A1104 " -0.021 2.00e-02 2.50e+03 pdb=" N SER A1105 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 885 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO A 886 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 886 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 886 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 108 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C LEU A 108 " -0.038 2.00e-02 2.50e+03 pdb=" O LEU A 108 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 109 " 0.013 2.00e-02 2.50e+03 ... (remaining 1651 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1124 2.75 - 3.28: 10746 3.28 - 3.82: 14648 3.82 - 4.36: 17643 4.36 - 4.90: 29443 Nonbonded interactions: 73604 Sorted by model distance: nonbonded pdb=" O LEU A 540 " pdb=" NH1 ARG A 570 " model vdw 2.208 2.520 nonbonded pdb=" N PHE A 385 " pdb=" OE2 GLU A 394 " model vdw 2.222 2.520 nonbonded pdb=" O LEU A 518 " pdb=" NZ LYS A 522 " model vdw 2.229 2.520 nonbonded pdb=" O ASP A1014 " pdb=" NZ LYS A1018 " model vdw 2.231 2.520 nonbonded pdb=" O GLU A 824 " pdb=" OG SER A 827 " model vdw 2.233 2.440 ... (remaining 73599 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 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.070 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 29.510 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 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 0.075 9896 Z= 0.423 Angle : 0.797 6.822 13337 Z= 0.463 Chirality : 0.048 0.405 1529 Planarity : 0.005 0.056 1654 Dihedral : 10.453 117.551 3701 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.09 % Allowed : 1.47 % Favored : 98.43 % 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: -3.42 (0.21), residues: 1190 helix: -1.69 (0.16), residues: 707 sheet: -2.94 (0.78), residues: 34 loop : -3.03 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 186 HIS 0.010 0.002 HIS A 892 PHE 0.027 0.003 PHE A 868 TYR 0.026 0.003 TYR A 851 ARG 0.010 0.001 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 PHE cc_start: 0.8392 (m-10) cc_final: 0.8108 (t80) REVERT: A 344 MET cc_start: 0.6850 (mtp) cc_final: 0.6413 (mtt) REVERT: A 348 GLU cc_start: 0.7574 (pp20) cc_final: 0.7366 (pm20) REVERT: A 575 ARG cc_start: 0.8149 (ttp80) cc_final: 0.7500 (ttp80) REVERT: A 580 ASN cc_start: 0.7986 (m110) cc_final: 0.7691 (m-40) REVERT: A 785 TYR cc_start: 0.8580 (m-80) cc_final: 0.8004 (m-80) REVERT: A 959 ILE cc_start: 0.9243 (tt) cc_final: 0.9011 (mm) REVERT: A 1027 ASN cc_start: 0.7975 (m-40) cc_final: 0.7746 (m110) REVERT: A 1091 LYS cc_start: 0.8466 (mttt) cc_final: 0.7999 (mttm) REVERT: A 1414 TYR cc_start: 0.8348 (m-10) cc_final: 0.8125 (m-10) outliers start: 1 outliers final: 0 residues processed: 196 average time/residue: 0.2665 time to fit residues: 69.8322 Evaluate side-chains 103 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9896 Z= 0.207 Angle : 0.615 10.458 13337 Z= 0.319 Chirality : 0.042 0.148 1529 Planarity : 0.004 0.036 1654 Dihedral : 6.651 68.387 1318 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.29 % Allowed : 7.92 % Favored : 90.79 % 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: -1.25 (0.24), residues: 1190 helix: 0.20 (0.19), residues: 712 sheet: -1.62 (0.81), residues: 40 loop : -2.50 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 453 HIS 0.006 0.001 HIS A 892 PHE 0.017 0.002 PHE A 257 TYR 0.020 0.002 TYR A 477 ARG 0.006 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8347 (tt0) REVERT: A 202 PHE cc_start: 0.8384 (m-10) cc_final: 0.8164 (t80) REVERT: A 354 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.7087 (t80) REVERT: A 404 LYS cc_start: 0.7922 (mttt) cc_final: 0.7510 (tptp) REVERT: A 575 ARG cc_start: 0.7942 (ttp80) cc_final: 0.7495 (ttp80) REVERT: A 580 ASN cc_start: 0.8011 (m110) cc_final: 0.7662 (m-40) REVERT: A 922 MET cc_start: 0.8140 (mmp) cc_final: 0.7891 (mmp) REVERT: A 1091 LYS cc_start: 0.8236 (mttt) cc_final: 0.7794 (mttm) outliers start: 14 outliers final: 9 residues processed: 129 average time/residue: 0.2459 time to fit residues: 44.1525 Evaluate side-chains 106 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1120 ASN Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1293 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 0.0570 chunk 33 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 HIS A 676 HIS A 874 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9896 Z= 0.166 Angle : 0.542 12.367 13337 Z= 0.284 Chirality : 0.041 0.146 1529 Planarity : 0.003 0.035 1654 Dihedral : 5.771 71.464 1318 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.93 % Allowed : 8.75 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.25), residues: 1190 helix: 0.81 (0.20), residues: 711 sheet: -0.72 (0.89), residues: 41 loop : -2.28 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 453 HIS 0.006 0.001 HIS A 143 PHE 0.014 0.001 PHE A 257 TYR 0.037 0.001 TYR A 477 ARG 0.005 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.9470 (mm-30) cc_final: 0.9214 (mm-30) REVERT: A 143 HIS cc_start: 0.7949 (m-70) cc_final: 0.7429 (t-170) REVERT: A 161 GLN cc_start: 0.8725 (mm-40) cc_final: 0.8349 (tt0) REVERT: A 202 PHE cc_start: 0.8517 (m-10) cc_final: 0.8284 (t80) REVERT: A 354 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.7099 (t80) REVERT: A 404 LYS cc_start: 0.7982 (mttt) cc_final: 0.7549 (tptp) REVERT: A 430 TYR cc_start: 0.6030 (m-80) cc_final: 0.5516 (m-80) REVERT: A 575 ARG cc_start: 0.7980 (ttp80) cc_final: 0.7522 (ttp80) REVERT: A 580 ASN cc_start: 0.7936 (m110) cc_final: 0.7599 (m-40) REVERT: A 841 MET cc_start: 0.7701 (tpp) cc_final: 0.7221 (tpt) REVERT: A 922 MET cc_start: 0.8109 (mmp) cc_final: 0.7818 (mmp) REVERT: A 1091 LYS cc_start: 0.8240 (mttt) cc_final: 0.7918 (mttm) outliers start: 21 outliers final: 11 residues processed: 125 average time/residue: 0.2409 time to fit residues: 42.4552 Evaluate side-chains 109 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1135 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 0.0470 chunk 109 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 57 optimal weight: 30.0000 chunk 103 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 542 HIS A 630 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9896 Z= 0.172 Angle : 0.537 11.739 13337 Z= 0.281 Chirality : 0.041 0.135 1529 Planarity : 0.003 0.039 1654 Dihedral : 5.469 66.587 1318 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.84 % Allowed : 10.77 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.25), residues: 1190 helix: 1.17 (0.20), residues: 703 sheet: -0.59 (0.91), residues: 41 loop : -2.04 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 453 HIS 0.021 0.002 HIS A 542 PHE 0.013 0.001 PHE A 257 TYR 0.040 0.001 TYR A 477 ARG 0.003 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.9457 (mm-30) cc_final: 0.9251 (mm-30) REVERT: A 161 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8351 (tt0) REVERT: A 202 PHE cc_start: 0.8550 (m-10) cc_final: 0.8287 (t80) REVERT: A 354 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.7155 (t80) REVERT: A 404 LYS cc_start: 0.8023 (mttt) cc_final: 0.7571 (tptp) REVERT: A 430 TYR cc_start: 0.5920 (m-10) cc_final: 0.5342 (m-80) REVERT: A 575 ARG cc_start: 0.8077 (ttp80) cc_final: 0.7688 (ttp80) REVERT: A 578 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6720 (mmt) REVERT: A 580 ASN cc_start: 0.7911 (m110) cc_final: 0.7584 (m-40) REVERT: A 922 MET cc_start: 0.8018 (mmp) cc_final: 0.7657 (mmp) REVERT: A 1091 LYS cc_start: 0.8199 (mttt) cc_final: 0.7916 (mttm) outliers start: 20 outliers final: 13 residues processed: 116 average time/residue: 0.2488 time to fit residues: 40.0751 Evaluate side-chains 114 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1336 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 5.9990 chunk 65 optimal weight: 0.0470 chunk 1 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 HIS A 607 ASN A 853 ASN A1243 ASN A1370 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9896 Z= 0.321 Angle : 0.657 9.054 13337 Z= 0.348 Chirality : 0.045 0.141 1529 Planarity : 0.004 0.040 1654 Dihedral : 5.824 67.979 1318 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.50 % Allowed : 10.31 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.25), residues: 1190 helix: 0.76 (0.19), residues: 706 sheet: -0.80 (0.91), residues: 41 loop : -2.06 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 453 HIS 0.007 0.002 HIS A 278 PHE 0.019 0.002 PHE A 58 TYR 0.030 0.002 TYR A 813 ARG 0.004 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 108 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.9444 (mm-30) cc_final: 0.9220 (mm-30) REVERT: A 161 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8444 (tt0) REVERT: A 202 PHE cc_start: 0.8618 (m-10) cc_final: 0.8355 (t80) REVERT: A 354 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.7066 (t80) REVERT: A 404 LYS cc_start: 0.8088 (mttt) cc_final: 0.7636 (tptp) REVERT: A 575 ARG cc_start: 0.8291 (ttp80) cc_final: 0.7959 (ttp80) REVERT: A 578 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6762 (mmt) REVERT: A 580 ASN cc_start: 0.7870 (m110) cc_final: 0.7598 (m-40) REVERT: A 788 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8114 (t70) REVERT: A 922 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7819 (mmp) REVERT: A 1091 LYS cc_start: 0.8426 (mttt) cc_final: 0.7909 (mttm) REVERT: A 1121 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8513 (pt) outliers start: 38 outliers final: 25 residues processed: 130 average time/residue: 0.2296 time to fit residues: 41.8344 Evaluate side-chains 132 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 102 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 452 TRP Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1336 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.6980 chunk 104 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9896 Z= 0.218 Angle : 0.566 8.514 13337 Z= 0.300 Chirality : 0.042 0.135 1529 Planarity : 0.004 0.043 1654 Dihedral : 5.668 66.881 1318 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.95 % Allowed : 12.62 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1190 helix: 0.94 (0.19), residues: 712 sheet: -0.64 (0.92), residues: 41 loop : -1.99 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 453 HIS 0.024 0.002 HIS A 542 PHE 0.012 0.001 PHE A 257 TYR 0.014 0.001 TYR A1097 ARG 0.003 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 102 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.9448 (mm-30) cc_final: 0.9201 (mm-30) REVERT: A 156 ASP cc_start: 0.8989 (m-30) cc_final: 0.8735 (p0) REVERT: A 161 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8418 (tt0) REVERT: A 202 PHE cc_start: 0.8609 (m-10) cc_final: 0.8354 (t80) REVERT: A 354 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.6980 (t80) REVERT: A 404 LYS cc_start: 0.8063 (mttt) cc_final: 0.7618 (tptp) REVERT: A 575 ARG cc_start: 0.8183 (ttp80) cc_final: 0.7860 (ttp80) REVERT: A 578 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6923 (mmt) REVERT: A 580 ASN cc_start: 0.7853 (m110) cc_final: 0.7574 (m-40) REVERT: A 922 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7581 (mmp) REVERT: A 1091 LYS cc_start: 0.8317 (mttt) cc_final: 0.7823 (mttm) outliers start: 32 outliers final: 25 residues processed: 119 average time/residue: 0.2290 time to fit residues: 38.7337 Evaluate side-chains 127 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 452 TRP Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1336 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.0570 chunk 13 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 998 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9896 Z= 0.165 Angle : 0.526 7.697 13337 Z= 0.276 Chirality : 0.040 0.134 1529 Planarity : 0.003 0.045 1654 Dihedral : 5.323 62.180 1318 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.67 % Allowed : 13.54 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1190 helix: 1.32 (0.19), residues: 707 sheet: -0.50 (0.94), residues: 41 loop : -1.86 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 453 HIS 0.005 0.001 HIS A 278 PHE 0.013 0.001 PHE A 43 TYR 0.012 0.001 TYR A1097 ARG 0.003 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 103 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8383 (tt0) REVERT: A 202 PHE cc_start: 0.8569 (m-10) cc_final: 0.8352 (t80) REVERT: A 354 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.6950 (t80) REVERT: A 404 LYS cc_start: 0.8054 (mttt) cc_final: 0.7612 (tptp) REVERT: A 575 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7849 (ttp80) REVERT: A 578 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.7043 (mmt) REVERT: A 580 ASN cc_start: 0.7857 (m110) cc_final: 0.7573 (m-40) REVERT: A 788 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.8033 (t70) REVERT: A 922 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7608 (mmp) REVERT: A 1027 ASN cc_start: 0.8256 (m110) cc_final: 0.8003 (m110) REVERT: A 1091 LYS cc_start: 0.8362 (mttt) cc_final: 0.7853 (mttm) outliers start: 29 outliers final: 19 residues processed: 120 average time/residue: 0.2373 time to fit residues: 40.1775 Evaluate side-chains 124 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 452 TRP Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1336 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 22 optimal weight: 0.0980 chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 HIS A 998 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9896 Z= 0.180 Angle : 0.552 10.640 13337 Z= 0.285 Chirality : 0.040 0.134 1529 Planarity : 0.003 0.045 1654 Dihedral : 5.141 57.251 1318 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.41 % Allowed : 13.08 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1190 helix: 1.34 (0.19), residues: 707 sheet: -0.49 (0.95), residues: 41 loop : -1.75 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 453 HIS 0.005 0.001 HIS A 278 PHE 0.011 0.001 PHE A 157 TYR 0.013 0.001 TYR A1015 ARG 0.002 0.000 ARG A1319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 107 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.9392 (ttmt) cc_final: 0.9190 (ttmt) REVERT: A 161 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8380 (tt0) REVERT: A 202 PHE cc_start: 0.8606 (m-10) cc_final: 0.8383 (t80) REVERT: A 354 TYR cc_start: 0.7642 (OUTLIER) cc_final: 0.6971 (t80) REVERT: A 404 LYS cc_start: 0.8002 (mttt) cc_final: 0.7560 (tptp) REVERT: A 575 ARG cc_start: 0.8203 (ttp80) cc_final: 0.7930 (ttp80) REVERT: A 578 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.7141 (mmt) REVERT: A 580 ASN cc_start: 0.7896 (m110) cc_final: 0.7622 (m-40) REVERT: A 690 MET cc_start: 0.9190 (mmp) cc_final: 0.8946 (mmm) REVERT: A 834 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8367 (tt) REVERT: A 922 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7602 (mmp) REVERT: A 1027 ASN cc_start: 0.8278 (m110) cc_final: 0.8003 (m110) REVERT: A 1091 LYS cc_start: 0.8374 (mttt) cc_final: 0.7854 (mttm) outliers start: 37 outliers final: 26 residues processed: 129 average time/residue: 0.2287 time to fit residues: 41.5563 Evaluate side-chains 133 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 103 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1336 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 998 ASN A1304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9896 Z= 0.176 Angle : 0.550 8.951 13337 Z= 0.284 Chirality : 0.040 0.138 1529 Planarity : 0.003 0.045 1654 Dihedral : 5.058 54.890 1318 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.95 % Allowed : 13.54 % Favored : 83.52 % 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: 0.33 (0.25), residues: 1190 helix: 1.43 (0.20), residues: 701 sheet: -0.46 (0.95), residues: 41 loop : -1.74 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 453 HIS 0.005 0.001 HIS A 542 PHE 0.022 0.001 PHE A 170 TYR 0.012 0.001 TYR A1097 ARG 0.002 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 103 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8379 (tt0) REVERT: A 202 PHE cc_start: 0.8594 (m-10) cc_final: 0.8385 (t80) REVERT: A 354 TYR cc_start: 0.7643 (OUTLIER) cc_final: 0.6971 (t80) REVERT: A 404 LYS cc_start: 0.7999 (mttt) cc_final: 0.7541 (tptp) REVERT: A 575 ARG cc_start: 0.8219 (ttp80) cc_final: 0.7938 (ttp80) REVERT: A 578 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.7172 (mmt) REVERT: A 580 ASN cc_start: 0.7892 (m110) cc_final: 0.7617 (m-40) REVERT: A 834 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8355 (tt) REVERT: A 922 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7611 (mmp) REVERT: A 1027 ASN cc_start: 0.8272 (m110) cc_final: 0.8008 (m110) REVERT: A 1091 LYS cc_start: 0.8352 (mttt) cc_final: 0.7814 (mttm) outliers start: 32 outliers final: 24 residues processed: 123 average time/residue: 0.2283 time to fit residues: 39.7735 Evaluate side-chains 126 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1336 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 119 optimal weight: 0.0060 chunk 110 optimal weight: 0.8980 chunk 95 optimal weight: 0.0040 chunk 9 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 30.0000 chunk 75 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.3812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9896 Z= 0.182 Angle : 0.571 8.583 13337 Z= 0.294 Chirality : 0.041 0.134 1529 Planarity : 0.003 0.045 1654 Dihedral : 4.954 51.191 1318 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.76 % Allowed : 13.72 % Favored : 83.52 % 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: 0.34 (0.25), residues: 1190 helix: 1.42 (0.20), residues: 699 sheet: -0.54 (0.94), residues: 41 loop : -1.68 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 453 HIS 0.005 0.001 HIS A 278 PHE 0.013 0.001 PHE A 43 TYR 0.012 0.001 TYR A1097 ARG 0.003 0.000 ARG A 570 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 103 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 PHE cc_start: 0.8569 (m-10) cc_final: 0.8358 (t80) REVERT: A 354 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.6981 (t80) REVERT: A 404 LYS cc_start: 0.7984 (mttt) cc_final: 0.7533 (tptp) REVERT: A 575 ARG cc_start: 0.8256 (ttp80) cc_final: 0.7948 (ttp80) REVERT: A 578 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.7041 (mmt) REVERT: A 580 ASN cc_start: 0.7843 (m110) cc_final: 0.7562 (m-40) REVERT: A 834 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8364 (tt) REVERT: A 922 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7622 (mmp) REVERT: A 961 LYS cc_start: 0.9024 (tptt) cc_final: 0.8761 (tppt) REVERT: A 1017 ASN cc_start: 0.8289 (m-40) cc_final: 0.7851 (p0) REVERT: A 1027 ASN cc_start: 0.8274 (m110) cc_final: 0.8001 (m110) REVERT: A 1091 LYS cc_start: 0.8345 (mttt) cc_final: 0.7803 (mttm) outliers start: 30 outliers final: 24 residues processed: 121 average time/residue: 0.2279 time to fit residues: 39.0497 Evaluate side-chains 127 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1336 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 97 optimal weight: 0.0870 chunk 12 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 826 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.139415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.100496 restraints weight = 22541.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.104174 restraints weight = 8706.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.106486 restraints weight = 4781.478| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9896 Z= 0.160 Angle : 0.551 9.028 13337 Z= 0.283 Chirality : 0.040 0.135 1529 Planarity : 0.003 0.046 1654 Dihedral : 4.705 45.131 1318 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.39 % Allowed : 14.46 % Favored : 83.15 % 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: 0.43 (0.25), residues: 1190 helix: 1.46 (0.19), residues: 708 sheet: -0.46 (0.94), residues: 41 loop : -1.64 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 453 HIS 0.005 0.001 HIS A 278 PHE 0.025 0.001 PHE A 170 TYR 0.038 0.001 TYR A 477 ARG 0.002 0.000 ARG A 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1992.85 seconds wall clock time: 37 minutes 31.48 seconds (2251.48 seconds total)