Starting phenix.real_space_refine on Wed Feb 14 15:24:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwr_16295/02_2024/8bwr_16295_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwr_16295/02_2024/8bwr_16295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwr_16295/02_2024/8bwr_16295.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwr_16295/02_2024/8bwr_16295.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwr_16295/02_2024/8bwr_16295_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwr_16295/02_2024/8bwr_16295_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 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 6221 2.51 5 N 1602 2.21 5 O 1704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9570 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1195, 9545 Classifications: {'peptide': 1195} Link IDs: {'PTRANS': 37, 'TRANS': 1157} Chain breaks: 3 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'P2E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.64, per 1000 atoms: 0.59 Number of scatterers: 9570 At special positions: 0 Unit cell: (74.048, 108.992, 143.936, 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 1704 8.00 N 1602 7.00 C 6221 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: 4.59 Conformation dependent library (CDL) restraints added in 2.0 seconds 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2266 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 4 sheets defined 66.7% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 12 through 14 No H-bonds generated for 'chain 'A' and resid 12 through 14' Processing helix chain 'A' and resid 20 through 23 No H-bonds generated for 'chain 'A' and resid 20 through 23' Processing helix chain 'A' and resid 29 through 36 removed outlier: 3.682A pdb=" N LYS A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 53 through 73 removed outlier: 3.627A pdb=" N PHE A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 121 removed outlier: 5.131A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 3.604A pdb=" N PHE A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 149 removed outlier: 3.600A pdb=" N LEU A 148 " --> pdb=" O CYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 179 removed outlier: 3.856A pdb=" N TYR A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 191 through 199 Processing helix chain 'A' and resid 203 through 289 removed outlier: 3.766A pdb=" N VAL A 208 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL A 210 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N HIS A 213 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 217 " --> pdb=" O PHE A 214 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLY A 218 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Proline residue: A 219 - end of helix removed outlier: 4.107A pdb=" N ILE A 233 " --> pdb=" O TRP A 230 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLY A 234 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ILE A 235 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET A 241 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 242 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 247 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.780A pdb=" N PHE A 258 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR A 267 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP A 270 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 272 " --> pdb=" O THR A 269 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 274 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 283 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ARG A 284 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 287 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 341 removed outlier: 3.784A pdb=" N LYS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASN A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 366 removed outlier: 4.151A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 391 removed outlier: 3.552A pdb=" N VAL A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 458 Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 513 through 520 removed outlier: 4.557A pdb=" N LEU A 519 " --> pdb=" O LYS A 515 " (cutoff:3.500A) 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 removed outlier: 3.652A pdb=" N LEU A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 565 No H-bonds generated for 'chain 'A' and resid 563 through 565' Processing helix chain 'A' and resid 568 through 573 Processing helix chain 'A' and resid 594 through 599 removed outlier: 5.015A pdb=" N ALA A 599 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 698 through 706 Processing helix chain 'A' and resid 713 through 744 removed outlier: 3.771A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 807 removed outlier: 4.006A pdb=" N GLY A 766 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 787 " --> pdb=" O SER A 783 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 806 " --> pdb=" O PHE A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 815 Processing helix chain 'A' and resid 818 through 826 removed outlier: 3.934A pdb=" N ARG A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 834 removed outlier: 3.806A pdb=" N LEU A 832 " --> pdb=" O ASP A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 860 removed outlier: 3.693A pdb=" N GLN A 849 " --> pdb=" O GLN A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 909 Proline residue: A 867 - end of helix Proline residue: A 870 - end of helix removed outlier: 3.893A pdb=" N ILE A 874 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 882 " --> pdb=" O ARG A 879 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU A 884 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG A 887 " --> pdb=" O GLU A 884 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG A 897 " --> pdb=" O SER A 894 " (cutoff:3.500A) Proline residue: A 899 - end of helix Processing helix chain 'A' and resid 911 through 916 Processing helix chain 'A' and resid 920 through 969 removed outlier: 4.722A pdb=" N ILE A 955 " --> pdb=" O ARG A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 1018 removed outlier: 3.687A pdb=" N GLY A 980 " --> pdb=" O ALA A 976 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 988 " --> pdb=" O SER A 984 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET A 990 " --> pdb=" O ALA A 986 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLY A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLN A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TRP A 995 " --> pdb=" O GLY A 991 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 997 " --> pdb=" O PHE A 993 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A1017 " --> pdb=" O VAL A1013 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP A1018 " --> pdb=" O ILE A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1037 No H-bonds generated for 'chain 'A' and resid 1035 through 1037' Processing helix chain 'A' and resid 1077 through 1088 removed outlier: 5.175A pdb=" N SER A1082 " --> pdb=" O GLY A1078 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N SER A1083 " --> pdb=" O ALA A1079 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A1084 " --> pdb=" O GLY A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1107 No H-bonds generated for 'chain 'A' and resid 1105 through 1107' Processing helix chain 'A' and resid 1110 through 1116 removed outlier: 4.561A pdb=" N LYS A1116 " --> pdb=" O ASP A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1136 Processing helix chain 'A' and resid 1143 through 1152 Processing helix chain 'A' and resid 1155 through 1159 Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' 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 1203 through 1206 removed outlier: 4.248A pdb=" N ASN A1206 " --> pdb=" O ALA A1203 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1203 through 1206' Processing helix chain 'A' and resid 1209 through 1222 Processing helix chain 'A' and resid 1235 through 1237 No H-bonds generated for 'chain 'A' and resid 1235 through 1237' Processing helix chain 'A' and resid 1248 through 1250 No H-bonds generated for 'chain 'A' and resid 1248 through 1250' Processing helix chain 'A' and resid 1258 through 1263 Processing helix chain 'A' and resid 1268 through 1276 removed outlier: 3.873A pdb=" N LEU A1276 " --> pdb=" O MET A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1293 removed outlier: 3.525A pdb=" N GLU A1286 " --> pdb=" O ALA A1283 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A1290 " --> pdb=" O THR A1287 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 433 through 435 removed outlier: 3.539A pdb=" N VAL A 410 " --> pdb=" O VAL A 435 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 610 through 615 removed outlier: 7.051A pdb=" N ILE A 605 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS A 614 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE A 603 " --> pdb=" O LYS A 614 " (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 1254 through 1256 removed outlier: 3.717A pdb=" N LYS A1243 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL A1228 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE A1073 " --> pdb=" O VAL A1228 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N THR A1230 " --> pdb=" O ILE A1073 " (cutoff:3.500A) 561 hydrogen bonds defined for protein. 1335 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: 3.33 Time building geometry restraints manager: 4.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1550 1.32 - 1.44: 2579 1.44 - 1.56: 5575 1.56 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 9774 Sorted by residual: bond pdb=" C7 P2E A1401 " pdb=" C8 P2E A1401 " ideal model delta sigma weight residual 1.529 1.480 0.049 2.00e-02 2.50e+03 6.03e+00 bond pdb=" CB PHE A 843 " pdb=" CG PHE A 843 " ideal model delta sigma weight residual 1.502 1.451 0.051 2.30e-02 1.89e+03 4.86e+00 bond pdb=" CB PHE A 336 " pdb=" CG PHE A 336 " ideal model delta sigma weight residual 1.502 1.452 0.050 2.30e-02 1.89e+03 4.82e+00 bond pdb=" CB TRP A 291 " pdb=" CG TRP A 291 " ideal model delta sigma weight residual 1.498 1.430 0.068 3.10e-02 1.04e+03 4.76e+00 bond pdb=" CB PHE A 802 " pdb=" CG PHE A 802 " ideal model delta sigma weight residual 1.502 1.453 0.049 2.30e-02 1.89e+03 4.56e+00 ... (remaining 9769 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.46: 158 105.46 - 112.64: 5345 112.64 - 119.81: 3473 119.81 - 126.98: 4144 126.98 - 134.15: 124 Bond angle restraints: 13244 Sorted by residual: angle pdb=" N ASN A 28 " pdb=" CA ASN A 28 " pdb=" C ASN A 28 " ideal model delta sigma weight residual 109.81 117.75 -7.94 2.21e+00 2.05e-01 1.29e+01 angle pdb=" C LEU A 27 " pdb=" N ASN A 28 " pdb=" CA ASN A 28 " ideal model delta sigma weight residual 121.80 129.95 -8.15 2.44e+00 1.68e-01 1.11e+01 angle pdb=" N PHE A 205 " pdb=" CA PHE A 205 " pdb=" C PHE A 205 " ideal model delta sigma weight residual 111.82 115.57 -3.75 1.16e+00 7.43e-01 1.04e+01 angle pdb=" CA LEU A 357 " pdb=" CB LEU A 357 " pdb=" CG LEU A 357 " ideal model delta sigma weight residual 116.30 106.15 10.15 3.50e+00 8.16e-02 8.41e+00 angle pdb=" CA TYR A 881 " pdb=" CB TYR A 881 " pdb=" CG TYR A 881 " ideal model delta sigma weight residual 113.90 118.81 -4.91 1.80e+00 3.09e-01 7.43e+00 ... (remaining 13239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 5355 17.56 - 35.12: 394 35.12 - 52.68: 77 52.68 - 70.24: 19 70.24 - 87.80: 8 Dihedral angle restraints: 5853 sinusoidal: 2359 harmonic: 3494 Sorted by residual: dihedral pdb=" CA ASP A 834 " pdb=" C ASP A 834 " pdb=" N LEU A 835 " pdb=" CA LEU A 835 " ideal model delta harmonic sigma weight residual -180.00 -150.64 -29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA VAL A1057 " pdb=" C VAL A1057 " pdb=" N LEU A1058 " pdb=" CA LEU A1058 " ideal model delta harmonic sigma weight residual 180.00 151.98 28.02 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA ARG A 37 " pdb=" C ARG A 37 " pdb=" N ARG A 38 " pdb=" CA ARG A 38 " ideal model delta harmonic sigma weight residual 180.00 152.85 27.15 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 5850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 936 0.044 - 0.088: 448 0.088 - 0.131: 131 0.131 - 0.175: 19 0.175 - 0.219: 7 Chirality restraints: 1541 Sorted by residual: chirality pdb=" C15 P2E A1401 " pdb=" C14 P2E A1401 " pdb=" C16 P2E A1401 " pdb=" O5 P2E A1401 " both_signs ideal model delta sigma weight residual False 2.23 2.44 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA HIS A 158 " pdb=" N HIS A 158 " pdb=" C HIS A 158 " pdb=" CB HIS A 158 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA PRO A 110 " pdb=" N PRO A 110 " pdb=" C PRO A 110 " pdb=" CB PRO A 110 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.28e-01 ... (remaining 1538 not shown) Planarity restraints: 1644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 358 " 0.006 2.00e-02 2.50e+03 2.16e-02 9.29e+00 pdb=" CG TYR A 358 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 358 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR A 358 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 358 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR A 358 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 358 " 0.031 2.00e-02 2.50e+03 pdb=" OH TYR A 358 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 547 " 0.217 9.50e-02 1.11e+02 9.76e-02 6.79e+00 pdb=" NE ARG A 547 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 547 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A 547 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 547 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 782 " -0.226 9.50e-02 1.11e+02 1.02e-01 6.42e+00 pdb=" NE ARG A 782 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 782 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 782 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 782 " -0.006 2.00e-02 2.50e+03 ... (remaining 1641 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1398 2.74 - 3.28: 10857 3.28 - 3.82: 16003 3.82 - 4.36: 19667 4.36 - 4.90: 31619 Nonbonded interactions: 79544 Sorted by model distance: nonbonded pdb=" O LYS A 498 " pdb=" OH TYR A 550 " model vdw 2.203 2.440 nonbonded pdb=" O ILE A 223 " pdb=" OG1 THR A 226 " model vdw 2.268 2.440 nonbonded pdb=" NH1 ARG A1076 " pdb=" OD1 ASP A1248 " model vdw 2.274 2.520 nonbonded pdb=" O ARG A1234 " pdb=" OG1 THR A1237 " model vdw 2.291 2.440 nonbonded pdb=" O ALA A 379 " pdb=" OG SER A 382 " model vdw 2.291 2.440 ... (remaining 79539 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=0.00 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: 3.030 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: 12.250 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 31.960 Find NCS groups from input model: 0.280 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 : 0.010 0.068 9774 Z= 0.618 Angle : 0.933 10.148 13244 Z= 0.499 Chirality : 0.053 0.219 1541 Planarity : 0.008 0.102 1644 Dihedral : 13.672 87.802 3587 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.96 % Allowed : 3.74 % Favored : 95.30 % 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: -1.63 (0.22), residues: 1187 helix: -1.43 (0.15), residues: 723 sheet: 0.25 (0.49), residues: 80 loop : -0.18 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A1025 HIS 0.015 0.002 HIS A 798 PHE 0.034 0.004 PHE A 336 TYR 0.032 0.004 TYR A 358 ARG 0.018 0.003 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 237 time to evaluate : 1.388 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: symmetry clash revert: symmetry clash REVERT: A 26 TRP cc_start: 0.5585 (OUTLIER) cc_final: 0.5009 (t-100) REVERT: A 44 MET cc_start: 0.8220 (ptp) cc_final: 0.7446 (ptp) REVERT: A 143 PHE cc_start: 0.8136 (m-10) cc_final: 0.7274 (t80) REVERT: A 146 LEU cc_start: 0.7612 (mm) cc_final: 0.7381 (mm) REVERT: A 167 ARG cc_start: 0.8572 (ttp80) cc_final: 0.8322 (ttt-90) REVERT: A 201 ASP cc_start: 0.8801 (t0) cc_final: 0.8545 (t0) REVERT: A 221 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7959 (tp-100) REVERT: A 258 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7915 (p90) REVERT: A 278 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7923 (mm-30) REVERT: A 309 LYS cc_start: 0.9206 (mttp) cc_final: 0.8895 (mttp) REVERT: A 312 ARG cc_start: 0.8548 (ttp-110) cc_final: 0.8078 (tpt170) REVERT: A 336 PHE cc_start: 0.8580 (m-80) cc_final: 0.8266 (m-80) REVERT: A 352 PHE cc_start: 0.7713 (m-80) cc_final: 0.7401 (m-80) REVERT: A 363 LEU cc_start: 0.8541 (mm) cc_final: 0.8261 (mt) REVERT: A 368 PHE cc_start: 0.8882 (m-10) cc_final: 0.8636 (m-80) REVERT: A 387 GLN cc_start: 0.9159 (tt0) cc_final: 0.8753 (tt0) REVERT: A 505 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8218 (pt0) REVERT: A 711 TRP cc_start: 0.7228 (p-90) cc_final: 0.6979 (t-100) REVERT: A 712 ILE cc_start: 0.7954 (mm) cc_final: 0.7450 (mm) REVERT: A 741 LYS cc_start: 0.8634 (mmmt) cc_final: 0.8394 (tppt) REVERT: A 744 MET cc_start: 0.8871 (mpm) cc_final: 0.8648 (mpp) REVERT: A 908 LEU cc_start: 0.9316 (tp) cc_final: 0.9058 (pp) REVERT: A 925 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8590 (tp30) REVERT: A 970 LEU cc_start: 0.9396 (mt) cc_final: 0.9173 (mp) REVERT: A 1011 GLU cc_start: 0.7973 (tt0) cc_final: 0.7669 (tm-30) REVERT: A 1043 PHE cc_start: 0.9336 (m-80) cc_final: 0.8977 (m-80) REVERT: A 1217 LYS cc_start: 0.9566 (tttt) cc_final: 0.9221 (ttpp) REVERT: A 1238 ILE cc_start: 0.9483 (pt) cc_final: 0.9236 (pt) REVERT: A 1245 MET cc_start: 0.9281 (mtp) cc_final: 0.8893 (mtt) outliers start: 10 outliers final: 3 residues processed: 244 average time/residue: 0.3045 time to fit residues: 99.0067 Evaluate side-chains 158 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 152 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1248 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 0.0770 chunk 48 optimal weight: 8.9990 chunk 93 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 20.0000 chunk 69 optimal weight: 0.3980 chunk 108 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 203 ASN A 703 ASN A 710 HIS A 903 HIS A 909 GLN ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9774 Z= 0.194 Angle : 0.614 7.393 13244 Z= 0.328 Chirality : 0.041 0.223 1541 Planarity : 0.004 0.047 1644 Dihedral : 7.034 57.984 1332 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.30 % Allowed : 9.88 % Favored : 87.81 % 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: 0.14 (0.24), residues: 1187 helix: 0.20 (0.18), residues: 739 sheet: 0.79 (0.52), residues: 82 loop : 0.03 (0.36), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 89 HIS 0.005 0.001 HIS A 153 PHE 0.013 0.001 PHE A1048 TYR 0.014 0.001 TYR A 92 ARG 0.004 0.000 ARG A 706 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 200 time to evaluate : 1.150 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 26 TRP cc_start: 0.5304 (OUTLIER) cc_final: 0.4488 (t-100) REVERT: A 143 PHE cc_start: 0.7753 (m-10) cc_final: 0.6910 (t80) REVERT: A 186 MET cc_start: 0.9158 (tpt) cc_final: 0.8900 (tpt) REVERT: A 201 ASP cc_start: 0.8789 (t0) cc_final: 0.8418 (t0) REVERT: A 309 LYS cc_start: 0.9037 (mttp) cc_final: 0.8783 (mttp) REVERT: A 312 ARG cc_start: 0.8558 (ttp-110) cc_final: 0.8074 (tpt170) REVERT: A 368 PHE cc_start: 0.8726 (m-10) cc_final: 0.8481 (m-80) REVERT: A 712 ILE cc_start: 0.7888 (mm) cc_final: 0.7414 (mm) REVERT: A 835 LEU cc_start: 0.8343 (tp) cc_final: 0.8009 (tp) REVERT: A 873 ILE cc_start: 0.9306 (mm) cc_final: 0.9102 (mt) REVERT: A 925 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8555 (tp30) REVERT: A 1011 GLU cc_start: 0.7884 (tt0) cc_final: 0.7527 (tm-30) REVERT: A 1020 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8134 (tm-30) REVERT: A 1107 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8943 (pt0) REVERT: A 1108 ILE cc_start: 0.8945 (mm) cc_final: 0.8627 (tp) REVERT: A 1233 HIS cc_start: 0.7121 (p90) cc_final: 0.5683 (p-80) REVERT: A 1270 TYR cc_start: 0.8435 (t80) cc_final: 0.7909 (t80) outliers start: 24 outliers final: 13 residues processed: 215 average time/residue: 0.2332 time to fit residues: 68.8183 Evaluate side-chains 161 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 909 GLN Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1197 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9774 Z= 0.264 Angle : 0.629 8.948 13244 Z= 0.328 Chirality : 0.042 0.318 1541 Planarity : 0.004 0.051 1644 Dihedral : 6.532 54.892 1324 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.03 % Allowed : 12.67 % Favored : 83.30 % 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: 0.22 (0.24), residues: 1187 helix: 0.23 (0.18), residues: 755 sheet: 0.97 (0.56), residues: 79 loop : 0.12 (0.36), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1147 HIS 0.008 0.001 HIS A1233 PHE 0.040 0.002 PHE A 352 TYR 0.012 0.002 TYR A1292 ARG 0.007 0.000 ARG A 503 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 162 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TRP cc_start: 0.5303 (OUTLIER) cc_final: 0.4491 (t-100) REVERT: A 44 MET cc_start: 0.8091 (ptp) cc_final: 0.7884 (ptp) REVERT: A 143 PHE cc_start: 0.7893 (m-10) cc_final: 0.6927 (t80) REVERT: A 173 MET cc_start: 0.8993 (ttm) cc_final: 0.8582 (mtt) REVERT: A 201 ASP cc_start: 0.8725 (t0) cc_final: 0.8458 (t0) REVERT: A 221 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7832 (tm-30) REVERT: A 312 ARG cc_start: 0.8630 (ttp-110) cc_final: 0.8217 (tpt170) REVERT: A 352 PHE cc_start: 0.7939 (m-80) cc_final: 0.7636 (m-80) REVERT: A 492 ASN cc_start: 0.7328 (OUTLIER) cc_final: 0.7033 (m110) REVERT: A 744 MET cc_start: 0.9107 (mmt) cc_final: 0.8774 (mpp) REVERT: A 835 LEU cc_start: 0.8251 (tp) cc_final: 0.7895 (tp) REVERT: A 908 LEU cc_start: 0.9306 (tp) cc_final: 0.9006 (pp) REVERT: A 925 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8600 (tp30) REVERT: A 1011 GLU cc_start: 0.7848 (tt0) cc_final: 0.7503 (tm-30) REVERT: A 1020 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8038 (tm-30) REVERT: A 1107 GLU cc_start: 0.9211 (mt-10) cc_final: 0.9010 (pt0) REVERT: A 1134 ASN cc_start: 0.8275 (OUTLIER) cc_final: 0.7953 (t0) outliers start: 42 outliers final: 27 residues processed: 190 average time/residue: 0.2233 time to fit residues: 60.0407 Evaluate side-chains 175 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 144 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1134 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.7980 chunk 81 optimal weight: 0.0970 chunk 56 optimal weight: 20.0000 chunk 11 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 102 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN A 710 HIS ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1216 GLN A1274 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9774 Z= 0.167 Angle : 0.567 10.895 13244 Z= 0.291 Chirality : 0.040 0.353 1541 Planarity : 0.004 0.046 1644 Dihedral : 6.213 59.839 1324 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.55 % Allowed : 14.78 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.25), residues: 1187 helix: 0.47 (0.19), residues: 751 sheet: 0.95 (0.55), residues: 83 loop : 0.35 (0.37), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 89 HIS 0.003 0.001 HIS A 798 PHE 0.028 0.001 PHE A 352 TYR 0.019 0.001 TYR A1270 ARG 0.002 0.000 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 164 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TRP cc_start: 0.5129 (OUTLIER) cc_final: 0.4162 (t-100) REVERT: A 44 MET cc_start: 0.7737 (ptp) cc_final: 0.7501 (ptp) REVERT: A 143 PHE cc_start: 0.7888 (m-10) cc_final: 0.6858 (t80) REVERT: A 161 CYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7235 (t) REVERT: A 173 MET cc_start: 0.8909 (ttm) cc_final: 0.8661 (mtt) REVERT: A 201 ASP cc_start: 0.8625 (t0) cc_final: 0.8361 (t0) REVERT: A 221 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8052 (tm-30) REVERT: A 309 LYS cc_start: 0.8996 (mttt) cc_final: 0.8576 (ptpp) REVERT: A 312 ARG cc_start: 0.8592 (ttp-110) cc_final: 0.8190 (tpt170) REVERT: A 352 PHE cc_start: 0.7882 (m-80) cc_final: 0.7606 (m-80) REVERT: A 492 ASN cc_start: 0.7246 (OUTLIER) cc_final: 0.6989 (m110) REVERT: A 744 MET cc_start: 0.9099 (mmt) cc_final: 0.8641 (mpp) REVERT: A 908 LEU cc_start: 0.9277 (tp) cc_final: 0.9016 (pp) REVERT: A 921 GLU cc_start: 0.8761 (pm20) cc_final: 0.8414 (pm20) REVERT: A 1011 GLU cc_start: 0.7812 (tt0) cc_final: 0.7491 (tm-30) REVERT: A 1020 GLU cc_start: 0.8517 (mt-10) cc_final: 0.7959 (tm-30) REVERT: A 1166 MET cc_start: 0.7324 (mtm) cc_final: 0.6692 (pmm) outliers start: 37 outliers final: 23 residues processed: 190 average time/residue: 0.2210 time to fit residues: 59.5454 Evaluate side-chains 169 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 142 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1027 TYR Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1280 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9774 Z= 0.212 Angle : 0.587 11.212 13244 Z= 0.300 Chirality : 0.041 0.385 1541 Planarity : 0.004 0.049 1644 Dihedral : 6.104 57.248 1324 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.74 % Allowed : 16.89 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1187 helix: 0.47 (0.19), residues: 747 sheet: 1.26 (0.56), residues: 78 loop : 0.23 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 89 HIS 0.005 0.001 HIS A 798 PHE 0.029 0.002 PHE A 352 TYR 0.016 0.001 TYR A1270 ARG 0.002 0.000 ARG A 503 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 152 time to evaluate : 1.005 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 13 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8138 (tt) REVERT: A 26 TRP cc_start: 0.5097 (OUTLIER) cc_final: 0.4149 (t-100) REVERT: A 143 PHE cc_start: 0.7956 (m-10) cc_final: 0.6888 (t80) REVERT: A 161 CYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7275 (t) REVERT: A 173 MET cc_start: 0.8863 (ttm) cc_final: 0.8632 (mtt) REVERT: A 201 ASP cc_start: 0.8554 (t0) cc_final: 0.8322 (t0) REVERT: A 221 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7861 (tm-30) REVERT: A 309 LYS cc_start: 0.8953 (mttt) cc_final: 0.8581 (mtmt) REVERT: A 312 ARG cc_start: 0.8622 (ttp-110) cc_final: 0.8270 (tpt170) REVERT: A 352 PHE cc_start: 0.7798 (m-80) cc_final: 0.7546 (m-80) REVERT: A 744 MET cc_start: 0.9101 (mmt) cc_final: 0.8587 (mpp) REVERT: A 835 LEU cc_start: 0.8291 (tp) cc_final: 0.7843 (tp) REVERT: A 908 LEU cc_start: 0.9259 (tp) cc_final: 0.9030 (pp) REVERT: A 1011 GLU cc_start: 0.7824 (tt0) cc_final: 0.7475 (tm-30) REVERT: A 1020 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8053 (tm-30) REVERT: A 1134 ASN cc_start: 0.7980 (OUTLIER) cc_final: 0.7672 (t0) outliers start: 39 outliers final: 26 residues processed: 181 average time/residue: 0.2147 time to fit residues: 54.5177 Evaluate side-chains 168 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1027 TYR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain A residue 1280 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.7644 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9774 Z= 0.200 Angle : 0.578 10.819 13244 Z= 0.293 Chirality : 0.040 0.374 1541 Planarity : 0.004 0.049 1644 Dihedral : 6.010 58.057 1324 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.93 % Allowed : 17.75 % Favored : 78.31 % 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: 0.56 (0.25), residues: 1187 helix: 0.46 (0.19), residues: 752 sheet: 1.44 (0.57), residues: 78 loop : 0.24 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 89 HIS 0.004 0.001 HIS A 798 PHE 0.025 0.001 PHE A 352 TYR 0.015 0.001 TYR A 917 ARG 0.005 0.000 ARG A1234 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 145 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8221 (tt) REVERT: A 26 TRP cc_start: 0.5113 (OUTLIER) cc_final: 0.4176 (t-100) REVERT: A 143 PHE cc_start: 0.7951 (m-10) cc_final: 0.6842 (t80) REVERT: A 161 CYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7259 (t) REVERT: A 235 ILE cc_start: 0.6634 (mm) cc_final: 0.6288 (tp) REVERT: A 309 LYS cc_start: 0.8959 (mttt) cc_final: 0.8573 (mtmt) REVERT: A 312 ARG cc_start: 0.8691 (ttp-110) cc_final: 0.8289 (tpt170) REVERT: A 492 ASN cc_start: 0.7240 (OUTLIER) cc_final: 0.6937 (m110) REVERT: A 550 TYR cc_start: 0.8440 (t80) cc_final: 0.8199 (t80) REVERT: A 920 GLU cc_start: 0.9404 (pp20) cc_final: 0.8866 (pm20) REVERT: A 1011 GLU cc_start: 0.7790 (tt0) cc_final: 0.7449 (tm-30) REVERT: A 1020 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7980 (tm-30) REVERT: A 1134 ASN cc_start: 0.7976 (OUTLIER) cc_final: 0.7765 (t0) REVERT: A 1234 ARG cc_start: 0.8441 (mtm110) cc_final: 0.8208 (ptp90) REVERT: A 1266 GLU cc_start: 0.8476 (tp30) cc_final: 0.8190 (tm-30) outliers start: 41 outliers final: 29 residues processed: 175 average time/residue: 0.2155 time to fit residues: 52.9515 Evaluate side-chains 170 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1027 TYR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1280 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 96 optimal weight: 0.0070 chunk 64 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9774 Z= 0.171 Angle : 0.577 12.559 13244 Z= 0.286 Chirality : 0.040 0.378 1541 Planarity : 0.004 0.047 1644 Dihedral : 5.729 58.237 1321 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.74 % Allowed : 18.81 % Favored : 77.45 % 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: 0.73 (0.25), residues: 1187 helix: 0.62 (0.19), residues: 746 sheet: 1.53 (0.56), residues: 78 loop : 0.23 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 89 HIS 0.003 0.001 HIS A 158 PHE 0.039 0.001 PHE A 352 TYR 0.016 0.001 TYR A1292 ARG 0.004 0.000 ARG A 915 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 147 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TRP cc_start: 0.5008 (OUTLIER) cc_final: 0.4136 (t-100) REVERT: A 143 PHE cc_start: 0.7919 (m-10) cc_final: 0.6782 (t80) REVERT: A 161 CYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7090 (t) REVERT: A 235 ILE cc_start: 0.6570 (mm) cc_final: 0.6288 (tp) REVERT: A 309 LYS cc_start: 0.8941 (mttt) cc_final: 0.8383 (ttmt) REVERT: A 312 ARG cc_start: 0.8680 (ttp-110) cc_final: 0.8280 (tpt170) REVERT: A 492 ASN cc_start: 0.7261 (OUTLIER) cc_final: 0.6971 (m110) REVERT: A 550 TYR cc_start: 0.8477 (t80) cc_final: 0.8258 (t80) REVERT: A 744 MET cc_start: 0.9075 (tpp) cc_final: 0.8591 (mpp) REVERT: A 920 GLU cc_start: 0.9466 (pp20) cc_final: 0.8935 (pm20) REVERT: A 1011 GLU cc_start: 0.7769 (tt0) cc_final: 0.7448 (tm-30) REVERT: A 1020 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7977 (tm-30) REVERT: A 1234 ARG cc_start: 0.8436 (mtm110) cc_final: 0.8123 (ptp90) outliers start: 39 outliers final: 29 residues processed: 175 average time/residue: 0.2177 time to fit residues: 53.7166 Evaluate side-chains 170 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 138 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1027 TYR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1280 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7630 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9774 Z= 0.184 Angle : 0.591 11.935 13244 Z= 0.292 Chirality : 0.040 0.387 1541 Planarity : 0.004 0.047 1644 Dihedral : 5.751 57.946 1321 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.13 % Allowed : 19.00 % Favored : 76.87 % 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: 0.67 (0.24), residues: 1187 helix: 0.56 (0.19), residues: 752 sheet: 1.68 (0.56), residues: 78 loop : 0.21 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 89 HIS 0.004 0.001 HIS A 798 PHE 0.016 0.001 PHE A1089 TYR 0.015 0.001 TYR A1292 ARG 0.015 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 133 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TRP cc_start: 0.4982 (OUTLIER) cc_final: 0.4110 (t-100) REVERT: A 161 CYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7112 (t) REVERT: A 235 ILE cc_start: 0.6674 (mm) cc_final: 0.6398 (tp) REVERT: A 309 LYS cc_start: 0.8956 (mttt) cc_final: 0.8396 (ttmt) REVERT: A 312 ARG cc_start: 0.8705 (ttp-110) cc_final: 0.8287 (tpt170) REVERT: A 492 ASN cc_start: 0.7305 (OUTLIER) cc_final: 0.6994 (m110) REVERT: A 550 TYR cc_start: 0.8461 (t80) cc_final: 0.8258 (t80) REVERT: A 911 LEU cc_start: 0.9280 (mt) cc_final: 0.8826 (pp) REVERT: A 925 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8545 (tp30) REVERT: A 1011 GLU cc_start: 0.7772 (tt0) cc_final: 0.7441 (tm-30) REVERT: A 1020 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7991 (tm-30) REVERT: A 1049 MET cc_start: 0.7818 (tpp) cc_final: 0.7325 (tpp) REVERT: A 1280 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8072 (mp0) outliers start: 43 outliers final: 32 residues processed: 163 average time/residue: 0.2165 time to fit residues: 50.0004 Evaluate side-chains 168 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1027 TYR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1280 GLU Chi-restraints excluded: chain A residue 1287 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7638 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9774 Z= 0.195 Angle : 0.602 11.826 13244 Z= 0.296 Chirality : 0.040 0.387 1541 Planarity : 0.004 0.047 1644 Dihedral : 5.819 59.039 1321 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.74 % Allowed : 19.77 % Favored : 76.49 % 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: 0.75 (0.25), residues: 1187 helix: 0.60 (0.19), residues: 754 sheet: 1.66 (0.57), residues: 78 loop : 0.30 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 89 HIS 0.005 0.001 HIS A 583 PHE 0.014 0.001 PHE A1043 TYR 0.019 0.001 TYR A1292 ARG 0.012 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 133 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TRP cc_start: 0.4969 (OUTLIER) cc_final: 0.4096 (t-100) REVERT: A 161 CYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7141 (t) REVERT: A 235 ILE cc_start: 0.6685 (mm) cc_final: 0.6411 (tp) REVERT: A 312 ARG cc_start: 0.8706 (ttp-110) cc_final: 0.8250 (tpt170) REVERT: A 492 ASN cc_start: 0.7294 (OUTLIER) cc_final: 0.6983 (m110) REVERT: A 550 TYR cc_start: 0.8483 (t80) cc_final: 0.8273 (t80) REVERT: A 711 TRP cc_start: 0.6836 (t-100) cc_final: 0.6412 (m100) REVERT: A 911 LEU cc_start: 0.9440 (mt) cc_final: 0.8915 (pp) REVERT: A 925 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8537 (tp30) REVERT: A 1011 GLU cc_start: 0.7778 (tt0) cc_final: 0.7422 (tm-30) REVERT: A 1020 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7983 (tm-30) REVERT: A 1049 MET cc_start: 0.7890 (tpp) cc_final: 0.7442 (tpp) REVERT: A 1234 ARG cc_start: 0.8457 (mtm110) cc_final: 0.8120 (ptp90) REVERT: A 1280 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8052 (mp0) outliers start: 39 outliers final: 33 residues processed: 158 average time/residue: 0.2127 time to fit residues: 47.1715 Evaluate side-chains 169 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 132 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1027 TYR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1280 GLU Chi-restraints excluded: chain A residue 1287 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 30.0000 chunk 74 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7641 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9774 Z= 0.198 Angle : 0.602 12.030 13244 Z= 0.297 Chirality : 0.040 0.383 1541 Planarity : 0.004 0.047 1644 Dihedral : 5.824 59.537 1321 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.84 % Allowed : 19.67 % Favored : 76.49 % 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: 0.76 (0.25), residues: 1187 helix: 0.60 (0.19), residues: 753 sheet: 1.62 (0.57), residues: 78 loop : 0.33 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 89 HIS 0.004 0.001 HIS A 798 PHE 0.014 0.001 PHE A1043 TYR 0.016 0.001 TYR A 917 ARG 0.011 0.000 ARG A 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 134 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TRP cc_start: 0.4979 (OUTLIER) cc_final: 0.4070 (t-100) REVERT: A 143 PHE cc_start: 0.7947 (m-10) cc_final: 0.6808 (t80) REVERT: A 161 CYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7148 (t) REVERT: A 235 ILE cc_start: 0.6689 (mm) cc_final: 0.6424 (tp) REVERT: A 312 ARG cc_start: 0.8694 (ttp-110) cc_final: 0.8273 (tpt170) REVERT: A 492 ASN cc_start: 0.7263 (OUTLIER) cc_final: 0.6909 (m110) REVERT: A 911 LEU cc_start: 0.9371 (mt) cc_final: 0.8860 (pp) REVERT: A 925 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8520 (tp30) REVERT: A 1011 GLU cc_start: 0.7771 (tt0) cc_final: 0.7410 (tm-30) REVERT: A 1020 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7944 (tm-30) REVERT: A 1021 LYS cc_start: 0.8587 (mttt) cc_final: 0.7958 (ttpp) REVERT: A 1049 MET cc_start: 0.7959 (tpp) cc_final: 0.7481 (tpp) REVERT: A 1234 ARG cc_start: 0.8446 (mtm110) cc_final: 0.8101 (ptp90) REVERT: A 1280 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8064 (mp0) outliers start: 40 outliers final: 32 residues processed: 160 average time/residue: 0.2257 time to fit residues: 51.0244 Evaluate side-chains 164 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TRP Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1027 TYR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1280 GLU Chi-restraints excluded: chain A residue 1287 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 83 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.147841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.112122 restraints weight = 21770.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.109913 restraints weight = 14918.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.110870 restraints weight = 14977.867| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9774 Z= 0.277 Angle : 0.650 11.231 13244 Z= 0.322 Chirality : 0.042 0.403 1541 Planarity : 0.004 0.048 1644 Dihedral : 5.979 57.024 1321 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.93 % Allowed : 20.25 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.25), residues: 1187 helix: 0.52 (0.19), residues: 745 sheet: 1.58 (0.57), residues: 78 loop : 0.33 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 89 HIS 0.006 0.001 HIS A 798 PHE 0.015 0.002 PHE A 336 TYR 0.020 0.002 TYR A1292 ARG 0.011 0.000 ARG A 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2410.89 seconds wall clock time: 45 minutes 18.07 seconds (2718.07 seconds total)