Starting phenix.real_space_refine on Thu Mar 14 21:12:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4a_35167/03_2024/8i4a_35167_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4a_35167/03_2024/8i4a_35167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4a_35167/03_2024/8i4a_35167.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4a_35167/03_2024/8i4a_35167.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4a_35167/03_2024/8i4a_35167_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4a_35167/03_2024/8i4a_35167_updated.pdb" } resolution = 3.4 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= 0.001 sd= 0.045 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: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 6340 2.51 5 N 1645 2.21 5 O 1735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 41": "OE1" <-> "OE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A GLU 505": "OE1" <-> "OE2" Residue "A GLU 521": "OE1" <-> "OE2" Residue "A GLU 568": "OE1" <-> "OE2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A GLU 584": "OE1" <-> "OE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A GLU 884": "OE1" <-> "OE2" Residue "A GLU 1020": "OE1" <-> "OE2" Residue "A GLU 1022": "OE1" <-> "OE2" Residue "A GLU 1069": "OE1" <-> "OE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "A GLU 1172": "OE1" <-> "OE2" Residue "A GLU 1213": "OE1" <-> "OE2" Residue "A GLU 1266": "OE1" <-> "OE2" Residue "A GLU 1280": "OE1" <-> "OE2" Residue "A GLU 1286": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9763 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1219, 9763 Unusual residues: {'H9F': 1} Classifications: {'peptide': 1218, 'undetermined': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 1178, None: 1} Not linked: pdbres="PRO A1298 " pdbres="H9F A1401 " Chain breaks: 2 Time building chain proxies: 5.77, per 1000 atoms: 0.59 Number of scatterers: 9763 At special positions: 0 Unit cell: (77.04, 114.49, 146.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1735 8.00 N 1645 7.00 C 6340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.26 Conformation dependent library (CDL) restraints added in 1.9 seconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2306 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 5 sheets defined 59.1% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.701A pdb=" N ASN A 28 " --> pdb=" O TRP A 25 " (cutoff:3.500A) Proline residue: A 29 - end of helix Processing helix chain 'A' and resid 53 through 74 Processing helix chain 'A' and resid 80 through 92 removed outlier: 5.267A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 122 Proline residue: A 110 - end of helix removed outlier: 3.596A pdb=" N ASN A 122 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 149 Processing helix chain 'A' and resid 153 through 178 removed outlier: 4.012A pdb=" N HIS A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 removed outlier: 3.591A pdb=" N LYS A 188 " --> pdb=" O MET A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 199 No H-bonds generated for 'chain 'A' and resid 196 through 199' Processing helix chain 'A' and resid 204 through 217 removed outlier: 4.067A pdb=" N VAL A 208 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N THR A 209 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N HIS A 213 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA A 217 " --> pdb=" O PHE A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 232 removed outlier: 3.687A pdb=" N THR A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 252 Proline residue: A 249 - end of helix Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 266 through 281 removed outlier: 4.652A pdb=" N ALA A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 289 Processing helix chain 'A' and resid 292 through 341 removed outlier: 4.328A pdb=" N LYS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 365 removed outlier: 3.896A pdb=" N PHE A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 390 Processing helix chain 'A' and resid 451 through 458 Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 501 through 510 removed outlier: 3.901A pdb=" N VAL A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 537 through 551 Processing helix chain 'A' and resid 567 through 576 Processing helix chain 'A' and resid 581 through 584 removed outlier: 3.975A pdb=" N GLU A 584 " --> pdb=" O ILE A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 581 through 584' Processing helix chain 'A' and resid 594 through 599 removed outlier: 3.799A pdb=" N LYS A 598 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 621 Processing helix chain 'A' and resid 627 through 631 Processing helix chain 'A' and resid 699 through 708 removed outlier: 4.051A pdb=" N GLY A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 743 removed outlier: 3.724A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 804 Processing helix chain 'A' and resid 810 through 815 Processing helix chain 'A' and resid 818 through 823 Processing helix chain 'A' and resid 828 through 834 removed outlier: 3.764A pdb=" N ASP A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 860 removed outlier: 4.191A pdb=" N LEU A 841 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 844 " --> pdb=" O PHE A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 867 Proline residue: A 867 - end of helix Processing helix chain 'A' and resid 873 through 883 Processing helix chain 'A' and resid 892 through 895 No H-bonds generated for 'chain 'A' and resid 892 through 895' Processing helix chain 'A' and resid 898 through 909 Processing helix chain 'A' and resid 911 through 916 Processing helix chain 'A' and resid 921 through 931 Processing helix chain 'A' and resid 938 through 966 removed outlier: 3.969A pdb=" N SER A 945 " --> pdb=" O PHE A 941 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG A 951 " --> pdb=" O TRP A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 1018 removed outlier: 4.246A pdb=" N MET A 990 " --> pdb=" O ALA A 986 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLN A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP A1018 " --> pdb=" O ILE A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1088 Processing helix chain 'A' and resid 1110 through 1112 No H-bonds generated for 'chain 'A' and resid 1110 through 1112' Processing helix chain 'A' and resid 1133 through 1136 No H-bonds generated for 'chain 'A' and resid 1133 through 1136' Processing helix chain 'A' and resid 1143 through 1152 Processing helix chain 'A' and resid 1156 through 1159 No H-bonds generated for 'chain 'A' and resid 1156 through 1159' Processing helix chain 'A' and resid 1172 through 1174 No H-bonds generated for 'chain 'A' and resid 1172 through 1174' Processing helix chain 'A' and resid 1179 through 1193 Processing helix chain 'A' and resid 1209 through 1222 Processing helix chain 'A' and resid 1258 through 1263 Processing helix chain 'A' and resid 1268 through 1274 Processing helix chain 'A' and resid 1279 through 1295 Processing sheet with id= A, first strand: chain 'A' and resid 433 through 435 Processing sheet with id= B, first strand: chain 'A' and resid 440 through 443 removed outlier: 6.285A pdb=" N THR A 587 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL A 443 " --> pdb=" O THR A 587 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU A 589 " --> pdb=" O VAL A 443 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP A 559 " --> pdb=" O VAL A 478 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1063 through 1065 Processing sheet with id= D, first strand: chain 'A' and resid 1252 through 1256 removed outlier: 6.636A pdb=" N VAL A1246 " --> pdb=" O LYS A1253 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR A1255 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL A1228 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ILE A1073 " --> pdb=" O VAL A1228 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N THR A1230 " --> pdb=" O ILE A1073 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER A1118 " --> pdb=" O ILE A1199 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ASP A1201 " --> pdb=" O SER A1118 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE A1120 " --> pdb=" O ASP A1201 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 603 through 607 removed outlier: 3.618A pdb=" N GLN A 613 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LYS A 607 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N MET A 611 " --> pdb=" O LYS A 607 " (cutoff:3.500A) 502 hydrogen bonds defined for protein. 1395 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: 3.35 Time building geometry restraints manager: 4.59 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: 2977 1.33 - 1.46: 1849 1.46 - 1.58: 5079 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 9975 Sorted by residual: bond pdb=" C5 H9F A1401 " pdb=" N8 H9F A1401 " ideal model delta sigma weight residual 1.348 1.451 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C2 H9F A1401 " pdb=" N7 H9F A1401 " ideal model delta sigma weight residual 1.360 1.451 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C3 H9F A1401 " pdb=" N5 H9F A1401 " ideal model delta sigma weight residual 1.365 1.452 -0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C6 H9F A1401 " pdb=" N6 H9F A1401 " ideal model delta sigma weight residual 1.364 1.450 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C4 H9F A1401 " pdb=" C5 H9F A1401 " ideal model delta sigma weight residual 1.456 1.386 0.070 2.00e-02 2.50e+03 1.21e+01 ... (remaining 9970 not shown) Histogram of bond angle deviations from ideal: 96.47 - 103.99: 119 103.99 - 111.50: 4608 111.50 - 119.02: 3664 119.02 - 126.54: 4977 126.54 - 134.06: 147 Bond angle restraints: 13515 Sorted by residual: angle pdb=" C LEU A 835 " pdb=" N LEU A 836 " pdb=" CA LEU A 836 " ideal model delta sigma weight residual 119.83 113.58 6.25 1.11e+00 8.12e-01 3.17e+01 angle pdb=" C LEU A 892 " pdb=" N GLU A 893 " pdb=" CA GLU A 893 " ideal model delta sigma weight residual 122.56 114.37 8.19 1.72e+00 3.38e-01 2.27e+01 angle pdb=" CA LEU A1214 " pdb=" CB LEU A1214 " pdb=" CG LEU A1214 " ideal model delta sigma weight residual 116.30 132.88 -16.58 3.50e+00 8.16e-02 2.24e+01 angle pdb=" N ILE A 805 " pdb=" CA ILE A 805 " pdb=" C ILE A 805 " ideal model delta sigma weight residual 113.42 108.41 5.01 1.17e+00 7.31e-01 1.84e+01 angle pdb=" C LYS A 305 " pdb=" N GLU A 306 " pdb=" CA GLU A 306 " ideal model delta sigma weight residual 121.92 114.56 7.36 1.73e+00 3.34e-01 1.81e+01 ... (remaining 13510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.63: 5593 23.63 - 47.26: 341 47.26 - 70.89: 32 70.89 - 94.52: 8 94.52 - 118.15: 3 Dihedral angle restraints: 5977 sinusoidal: 2418 harmonic: 3559 Sorted by residual: dihedral pdb=" CA PHE A 352 " pdb=" C PHE A 352 " pdb=" N VAL A 353 " pdb=" CA VAL A 353 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA CYS A 253 " pdb=" C CYS A 253 " pdb=" N PHE A 254 " pdb=" CA PHE A 254 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA TRP A 291 " pdb=" C TRP A 291 " pdb=" N GLU A 292 " pdb=" CA GLU A 292 " ideal model delta harmonic sigma weight residual -180.00 -159.01 -20.99 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 5974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1165 0.060 - 0.120: 346 0.120 - 0.179: 47 0.179 - 0.239: 2 0.239 - 0.299: 1 Chirality restraints: 1561 Sorted by residual: chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CG LEU A 582 " pdb=" CB LEU A 582 " pdb=" CD1 LEU A 582 " pdb=" CD2 LEU A 582 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB VAL A 889 " pdb=" CA VAL A 889 " pdb=" CG1 VAL A 889 " pdb=" CG2 VAL A 889 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1558 not shown) Planarity restraints: 1676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 869 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.79e+00 pdb=" N PRO A 870 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 870 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 870 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 218 " 0.039 5.00e-02 4.00e+02 5.92e-02 5.61e+00 pdb=" N PRO A 219 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 219 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 219 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1123 " 0.035 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO A1124 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A1124 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1124 " 0.029 5.00e-02 4.00e+02 ... (remaining 1673 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 253 2.67 - 3.23: 9973 3.23 - 3.79: 15250 3.79 - 4.34: 20503 4.34 - 4.90: 33456 Nonbonded interactions: 79435 Sorted by model distance: nonbonded pdb=" NH2 ARG A 272 " pdb=" O PHE A 825 " model vdw 2.115 2.520 nonbonded pdb=" OG SER A 794 " pdb=" OD1 ASP A 833 " model vdw 2.123 2.440 nonbonded pdb=" NE2 GLN A1183 " pdb=" O ALA A1203 " model vdw 2.137 2.520 nonbonded pdb=" O VAL A 410 " pdb=" OG1 THR A 434 " model vdw 2.210 2.440 nonbonded pdb=" OD1 ASP A 953 " pdb=" NE2 GLN A 994 " model vdw 2.227 2.520 ... (remaining 79430 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 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: 3.320 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 30.850 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 : 0.012 0.103 9975 Z= 0.735 Angle : 0.937 16.579 13515 Z= 0.503 Chirality : 0.055 0.299 1561 Planarity : 0.005 0.060 1676 Dihedral : 15.095 118.154 3671 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.46 (0.24), residues: 1212 helix: -0.84 (0.18), residues: 781 sheet: -1.03 (0.61), residues: 76 loop : -0.79 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 64 HIS 0.008 0.001 HIS A1060 PHE 0.036 0.003 PHE A 98 TYR 0.016 0.002 TYR A1016 ARG 0.010 0.001 ARG A1220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.117 Fit side-chains REVERT: A 611 MET cc_start: 0.4865 (tpt) cc_final: 0.3322 (tmm) REVERT: A 921 GLU cc_start: 0.8464 (pt0) cc_final: 0.8226 (pt0) REVERT: A 1049 MET cc_start: 0.8412 (mtp) cc_final: 0.7824 (mmm) REVERT: A 1069 GLU cc_start: 0.7498 (pt0) cc_final: 0.7177 (pt0) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1979 time to fit residues: 30.5675 Evaluate side-chains 85 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 40.0000 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 387 GLN A 845 GLN A 924 GLN A1134 ASN ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9975 Z= 0.227 Angle : 0.568 8.331 13515 Z= 0.292 Chirality : 0.042 0.155 1561 Planarity : 0.004 0.053 1676 Dihedral : 7.948 86.929 1350 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.56 % Allowed : 6.12 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.25), residues: 1212 helix: 0.01 (0.19), residues: 788 sheet: -0.75 (0.60), residues: 76 loop : -0.41 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 64 HIS 0.004 0.001 HIS A 152 PHE 0.027 0.002 PHE A 324 TYR 0.017 0.001 TYR A 157 ARG 0.003 0.000 ARG A 915 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 611 MET cc_start: 0.4594 (tpt) cc_final: 0.3189 (tmm) REVERT: A 893 GLU cc_start: 0.8405 (pp20) cc_final: 0.8203 (tm-30) REVERT: A 912 TRP cc_start: 0.8267 (m-10) cc_final: 0.7949 (m-10) REVERT: A 1131 MET cc_start: 0.8286 (tpp) cc_final: 0.7971 (tpp) outliers start: 6 outliers final: 3 residues processed: 105 average time/residue: 0.2159 time to fit residues: 32.9348 Evaluate side-chains 97 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 1168 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 40.0000 chunk 34 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 GLN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9975 Z= 0.320 Angle : 0.573 6.313 13515 Z= 0.296 Chirality : 0.043 0.157 1561 Planarity : 0.004 0.052 1676 Dihedral : 7.493 89.311 1350 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.41 % Allowed : 9.79 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1212 helix: 0.17 (0.19), residues: 788 sheet: -0.60 (0.60), residues: 76 loop : -0.31 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.004 0.001 HIS A 152 PHE 0.020 0.002 PHE A 324 TYR 0.012 0.002 TYR A 917 ARG 0.004 0.000 ARG A 915 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7623 (mm) REVERT: A 893 GLU cc_start: 0.8521 (pp20) cc_final: 0.8276 (tm-30) REVERT: A 1049 MET cc_start: 0.8359 (mtt) cc_final: 0.7900 (mmm) outliers start: 15 outliers final: 9 residues processed: 103 average time/residue: 0.1958 time to fit residues: 30.0004 Evaluate side-chains 101 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1220 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 0.4980 chunk 110 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9975 Z= 0.176 Angle : 0.505 6.365 13515 Z= 0.258 Chirality : 0.040 0.149 1561 Planarity : 0.004 0.048 1676 Dihedral : 7.038 88.600 1350 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.51 % Allowed : 11.21 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.21 (0.25), residues: 1212 helix: 0.50 (0.19), residues: 786 sheet: -0.52 (0.55), residues: 86 loop : -0.22 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 89 HIS 0.002 0.000 HIS A 152 PHE 0.017 0.001 PHE A 324 TYR 0.016 0.001 TYR A1016 ARG 0.003 0.000 ARG A 915 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 611 MET cc_start: 0.4069 (tpp) cc_final: 0.2617 (tmm) REVERT: A 1049 MET cc_start: 0.8124 (mtt) cc_final: 0.7745 (mmm) REVERT: A 1069 GLU cc_start: 0.7668 (pt0) cc_final: 0.7389 (pt0) REVERT: A 1131 MET cc_start: 0.8081 (tpp) cc_final: 0.7764 (tpp) outliers start: 16 outliers final: 10 residues processed: 115 average time/residue: 0.1984 time to fit residues: 33.8546 Evaluate side-chains 108 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1220 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 20.0000 chunk 104 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.2980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 GLN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9975 Z= 0.238 Angle : 0.532 8.126 13515 Z= 0.271 Chirality : 0.041 0.152 1561 Planarity : 0.004 0.049 1676 Dihedral : 6.896 88.454 1350 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.69 % Allowed : 12.90 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.31 (0.25), residues: 1212 helix: 0.55 (0.19), residues: 786 sheet: -0.32 (0.56), residues: 86 loop : -0.14 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 89 HIS 0.003 0.000 HIS A 798 PHE 0.015 0.001 PHE A 325 TYR 0.017 0.001 TYR A1016 ARG 0.005 0.000 ARG A 915 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7546 (mm) REVERT: A 611 MET cc_start: 0.4307 (tpp) cc_final: 0.2998 (tmm) REVERT: A 836 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7452 (mt) REVERT: A 1049 MET cc_start: 0.8048 (mtt) cc_final: 0.7763 (mmm) REVERT: A 1069 GLU cc_start: 0.7677 (pt0) cc_final: 0.7314 (pt0) REVERT: A 1131 MET cc_start: 0.8041 (tpp) cc_final: 0.7716 (tpp) outliers start: 18 outliers final: 10 residues processed: 110 average time/residue: 0.2082 time to fit residues: 33.7963 Evaluate side-chains 110 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1220 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 30.0000 chunk 112 optimal weight: 0.0470 overall best weight: 1.1280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9975 Z= 0.227 Angle : 0.519 8.050 13515 Z= 0.265 Chirality : 0.040 0.151 1561 Planarity : 0.004 0.050 1676 Dihedral : 6.813 88.258 1350 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.35 % Allowed : 13.94 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.25), residues: 1212 helix: 0.66 (0.19), residues: 786 sheet: -0.13 (0.57), residues: 86 loop : -0.13 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 89 HIS 0.003 0.000 HIS A 798 PHE 0.015 0.001 PHE A 325 TYR 0.018 0.001 TYR A1016 ARG 0.004 0.000 ARG A 915 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7433 (t0) REVERT: A 307 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7534 (mm) REVERT: A 611 MET cc_start: 0.4336 (tpp) cc_final: 0.3321 (tmm) REVERT: A 836 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7253 (mp) REVERT: A 1049 MET cc_start: 0.8007 (mtt) cc_final: 0.7750 (mmm) REVERT: A 1069 GLU cc_start: 0.7647 (pt0) cc_final: 0.7253 (pt0) REVERT: A 1131 MET cc_start: 0.7979 (tpp) cc_final: 0.7660 (tpp) outliers start: 25 outliers final: 16 residues processed: 118 average time/residue: 0.1925 time to fit residues: 33.7553 Evaluate side-chains 118 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1220 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 116 optimal weight: 0.9990 chunk 72 optimal weight: 0.0010 chunk 71 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 69 optimal weight: 0.8980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9975 Z= 0.161 Angle : 0.499 7.734 13515 Z= 0.252 Chirality : 0.039 0.145 1561 Planarity : 0.003 0.049 1676 Dihedral : 6.669 87.207 1350 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.98 % Allowed : 14.60 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.73 (0.25), residues: 1212 helix: 0.87 (0.19), residues: 787 sheet: -0.00 (0.56), residues: 86 loop : -0.03 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 89 HIS 0.002 0.000 HIS A 798 PHE 0.013 0.001 PHE A 325 TYR 0.020 0.001 TYR A1016 ARG 0.002 0.000 ARG A 915 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7498 (t0) REVERT: A 611 MET cc_start: 0.4409 (tpp) cc_final: 0.3491 (tmm) REVERT: A 1006 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7633 (ttm) REVERT: A 1049 MET cc_start: 0.7963 (mtt) cc_final: 0.7705 (mmm) REVERT: A 1069 GLU cc_start: 0.7617 (pt0) cc_final: 0.7277 (pt0) REVERT: A 1112 ASP cc_start: 0.8254 (m-30) cc_final: 0.7669 (p0) REVERT: A 1122 GLN cc_start: 0.8909 (mt0) cc_final: 0.8608 (mt0) REVERT: A 1131 MET cc_start: 0.8024 (tpp) cc_final: 0.7707 (tpp) outliers start: 21 outliers final: 16 residues processed: 120 average time/residue: 0.2057 time to fit residues: 35.9574 Evaluate side-chains 124 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1220 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 0.0980 chunk 106 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 108 optimal weight: 0.2980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 GLN ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9975 Z= 0.165 Angle : 0.502 8.401 13515 Z= 0.255 Chirality : 0.039 0.150 1561 Planarity : 0.003 0.050 1676 Dihedral : 6.607 86.660 1350 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.07 % Allowed : 14.88 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.87 (0.25), residues: 1212 helix: 0.97 (0.19), residues: 788 sheet: 0.09 (0.56), residues: 86 loop : 0.01 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 89 HIS 0.002 0.000 HIS A 798 PHE 0.013 0.001 PHE A 325 TYR 0.020 0.001 TYR A1016 ARG 0.005 0.000 ARG A 915 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7440 (t0) REVERT: A 307 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7429 (mm) REVERT: A 611 MET cc_start: 0.4335 (tpp) cc_final: 0.2642 (mtt) REVERT: A 836 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7145 (mp) REVERT: A 1006 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7659 (ttm) REVERT: A 1050 TYR cc_start: 0.7286 (OUTLIER) cc_final: 0.6880 (m-80) REVERT: A 1069 GLU cc_start: 0.7612 (pt0) cc_final: 0.7246 (pt0) REVERT: A 1112 ASP cc_start: 0.8223 (m-30) cc_final: 0.7711 (p0) REVERT: A 1131 MET cc_start: 0.8018 (tpp) cc_final: 0.7697 (tpp) outliers start: 22 outliers final: 16 residues processed: 118 average time/residue: 0.1990 time to fit residues: 34.6579 Evaluate side-chains 123 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1220 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 47 optimal weight: 0.0870 chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 98 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 108 optimal weight: 0.0980 chunk 71 optimal weight: 0.9990 chunk 114 optimal weight: 0.0770 chunk 70 optimal weight: 0.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 GLN ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9975 Z= 0.133 Angle : 0.500 9.054 13515 Z= 0.250 Chirality : 0.038 0.148 1561 Planarity : 0.003 0.049 1676 Dihedral : 6.482 85.554 1350 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.98 % Allowed : 15.07 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.08 (0.25), residues: 1212 helix: 1.15 (0.19), residues: 788 sheet: 0.36 (0.58), residues: 81 loop : -0.00 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 89 HIS 0.001 0.000 HIS A 572 PHE 0.012 0.001 PHE A 325 TYR 0.023 0.001 TYR A1016 ARG 0.003 0.000 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7484 (t0) REVERT: A 241 MET cc_start: 0.8448 (tpt) cc_final: 0.7779 (tpt) REVERT: A 307 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7233 (mm) REVERT: A 611 MET cc_start: 0.4284 (tpp) cc_final: 0.2627 (mtt) REVERT: A 836 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7208 (mp) REVERT: A 1006 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7644 (ttm) REVERT: A 1050 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.6860 (m-80) REVERT: A 1069 GLU cc_start: 0.7560 (pt0) cc_final: 0.7196 (pt0) REVERT: A 1112 ASP cc_start: 0.8133 (m-30) cc_final: 0.7730 (p0) REVERT: A 1131 MET cc_start: 0.7915 (tpp) cc_final: 0.7611 (tpp) outliers start: 21 outliers final: 14 residues processed: 126 average time/residue: 0.2151 time to fit residues: 39.1908 Evaluate side-chains 121 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1220 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.0370 chunk 79 optimal weight: 0.9980 chunk 120 optimal weight: 20.0000 chunk 110 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 76 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 387 GLN A 909 GLN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9975 Z= 0.169 Angle : 0.521 9.245 13515 Z= 0.261 Chirality : 0.040 0.151 1561 Planarity : 0.003 0.049 1676 Dihedral : 6.486 85.143 1350 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.79 % Allowed : 15.54 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.15 (0.25), residues: 1212 helix: 1.19 (0.19), residues: 791 sheet: 0.38 (0.63), residues: 71 loop : 0.08 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 89 HIS 0.005 0.000 HIS A1060 PHE 0.012 0.001 PHE A 325 TYR 0.018 0.001 TYR A1016 ARG 0.003 0.000 ARG A 824 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7455 (t0) REVERT: A 76 GLN cc_start: 0.7138 (pt0) cc_final: 0.6641 (pt0) REVERT: A 307 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7489 (mm) REVERT: A 611 MET cc_start: 0.4283 (tpp) cc_final: 0.2599 (mtt) REVERT: A 836 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7505 (mt) REVERT: A 1006 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7603 (ttm) REVERT: A 1112 ASP cc_start: 0.8179 (m-30) cc_final: 0.7690 (p0) REVERT: A 1131 MET cc_start: 0.7925 (tpp) cc_final: 0.7608 (tpp) outliers start: 19 outliers final: 13 residues processed: 112 average time/residue: 0.1981 time to fit residues: 33.3960 Evaluate side-chains 118 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1220 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.0670 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 GLN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.210670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124257 restraints weight = 10501.520| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.65 r_work: 0.3132 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9975 Z= 0.166 Angle : 0.512 8.982 13515 Z= 0.257 Chirality : 0.039 0.150 1561 Planarity : 0.003 0.048 1676 Dihedral : 6.476 84.975 1350 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.07 % Allowed : 15.82 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.22 (0.25), residues: 1212 helix: 1.23 (0.19), residues: 790 sheet: 0.43 (0.63), residues: 71 loop : 0.12 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 89 HIS 0.012 0.001 HIS A1060 PHE 0.012 0.001 PHE A 336 TYR 0.018 0.001 TYR A1016 ARG 0.003 0.000 ARG A 915 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2225.38 seconds wall clock time: 40 minutes 49.39 seconds (2449.39 seconds total)