Starting phenix.real_space_refine on Thu Mar 14 20:49:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4b_35168/03_2024/8i4b_35168.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4b_35168/03_2024/8i4b_35168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4b_35168/03_2024/8i4b_35168.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4b_35168/03_2024/8i4b_35168.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4b_35168/03_2024/8i4b_35168.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4b_35168/03_2024/8i4b_35168.pdb" } resolution = 3.13 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= 0.063 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 6316 2.51 5 N 1637 2.21 5 O 1731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 42": "OD1" <-> "OD2" Residue "A ASP 51": "OD1" <-> "OD2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 306": "OE1" <-> "OE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A ASP 393": "OD1" <-> "OD2" 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 TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 803": "OE1" <-> "OE2" Residue "A PHE 825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 875": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 884": "OE1" <-> "OE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1002": "OE1" <-> "OE2" Residue "A GLU 1020": "OE1" <-> "OE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "A GLU 1152": "OE1" <-> "OE2" Residue "A GLU 1172": "OE1" <-> "OE2" Residue "A GLU 1213": "OE1" <-> "OE2" Residue "A GLU 1266": "OE1" <-> "OE2" Residue "A TYR 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 9727 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1218, 9727 Classifications: {'peptide': 1218} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 1178} Chain breaks: 2 Time building chain proxies: 5.62, per 1000 atoms: 0.58 Number of scatterers: 9727 At special positions: 0 Unit cell: (77.04, 114.49, 149.8, 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 1731 8.00 N 1637 7.00 C 6316 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: 3.80 Conformation dependent library (CDL) restraints added in 1.8 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... Secondary structure from input PDB file: 57 helices and 5 sheets defined 66.7% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 18 through 23 removed outlier: 3.797A pdb=" N PHE A 23 " --> pdb=" O CYS A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 27 through 37 removed outlier: 3.676A pdb=" N PHE A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 75 Processing helix chain 'A' and resid 79 through 93 removed outlier: 5.379A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 121 Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 128 through 150 Processing helix chain 'A' and resid 151 through 179 removed outlier: 3.640A pdb=" N GLY A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 189 removed outlier: 3.676A pdb=" N LYS A 188 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 removed outlier: 4.476A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N HIS A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.586A pdb=" N ALA A 222 " --> pdb=" O GLY A 218 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 246 removed outlier: 3.536A pdb=" N GLY A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 248 No H-bonds generated for 'chain 'A' and resid 247 through 248' Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 265 through 282 removed outlier: 4.415A pdb=" N ALA A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 291 through 342 removed outlier: 4.154A pdb=" N LYS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 367 removed outlier: 3.550A pdb=" N VAL A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 390 Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 500 through 512 removed outlier: 3.552A pdb=" N VAL A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 520 removed outlier: 4.493A pdb=" N ASP A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 520 " --> pdb=" O ASP A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 552 removed outlier: 3.734A pdb=" N ASP A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 577 removed outlier: 3.567A pdb=" N SER A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.868A pdb=" N GLU A 584 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 600 removed outlier: 3.573A pdb=" N TYR A 596 " --> pdb=" O GLN A 593 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS A 598 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 623 Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 698 through 709 removed outlier: 3.759A pdb=" N ALA A 707 " --> pdb=" O ASN A 703 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 709 " --> pdb=" O PHE A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 744 removed outlier: 3.917A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 806 removed outlier: 3.500A pdb=" N TYR A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 816 removed outlier: 3.839A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 816 " --> pdb=" O PHE A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 823 Processing helix chain 'A' and resid 827 through 835 removed outlier: 3.662A pdb=" N ASP A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 861 removed outlier: 3.573A pdb=" N ILE A 844 " --> pdb=" O PHE A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 866 Processing helix chain 'A' and resid 869 through 884 removed outlier: 3.632A pdb=" N ILE A 874 " --> pdb=" O PRO A 870 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHE A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 876 " --> pdb=" O GLY A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.880A pdb=" N PHE A 901 " --> pdb=" O ARG A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 917 removed outlier: 3.630A pdb=" N TYR A 917 " --> pdb=" O THR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 932 Processing helix chain 'A' and resid 936 through 967 removed outlier: 3.855A pdb=" N LEU A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER A 945 " --> pdb=" O PHE A 941 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG A 951 " --> pdb=" O TRP A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 1017 removed outlier: 4.254A pdb=" N MET A 990 " --> pdb=" O ALA A 986 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLY A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLN A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1089 removed outlier: 4.054A pdb=" N SER A1086 " --> pdb=" O SER A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1108 Processing helix chain 'A' and resid 1109 through 1113 Processing helix chain 'A' and resid 1130 through 1136 removed outlier: 3.563A pdb=" N LEU A1135 " --> pdb=" O MET A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1153 Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'A' and resid 1178 through 1194 Processing helix chain 'A' and resid 1208 through 1223 removed outlier: 3.681A pdb=" N PHE A1223 " --> pdb=" O ILE A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1264 removed outlier: 3.727A pdb=" N ASN A1264 " --> pdb=" O VAL A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1277 removed outlier: 3.720A pdb=" N LEU A1276 " --> pdb=" O MET A1272 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY A1277 " --> pdb=" O VAL A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1297 Processing sheet with id=AA1, first strand: chain 'A' and resid 434 through 435 removed outlier: 3.905A pdb=" N PHE A 415 " --> pdb=" O HIS A 466 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N HIS A 466 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.447A pdb=" N THR A 587 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N VAL A 443 " --> pdb=" O THR A 587 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU A 589 " --> pdb=" O VAL A 443 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN A 602 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 606 " --> pdb=" O VAL A 444 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN A 613 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LYS A 607 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N MET A 611 " --> pdb=" O LYS A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488 removed outlier: 3.651A pdb=" N GLY A 487 " --> pdb=" O ILE A 528 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1058 through 1065 removed outlier: 6.921A pdb=" N LYS A1059 " --> pdb=" O ASN A1047 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ASN A1047 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LEU A1061 " --> pdb=" O ASN A1045 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N PHE A1043 " --> pdb=" O TRP A1099 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N TRP A1099 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASN A1045 " --> pdb=" O LYS A1097 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS A1097 " --> pdb=" O ASN A1045 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1118 through 1120 removed outlier: 6.490A pdb=" N VAL A1071 " --> pdb=" O THR A1230 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LYS A1070 " --> pdb=" O LYS A1243 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N MET A1245 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLY A1072 " --> pdb=" O MET A1245 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LEU A1247 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL A1074 " --> pdb=" O LEU A1247 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR A1255 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A1246 " --> pdb=" O LYS A1253 " (cutoff:3.500A) 571 hydrogen bonds defined for protein. 1653 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: 3.43 Time building geometry restraints manager: 4.12 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: 1654 1.32 - 1.44: 2578 1.44 - 1.56: 5633 1.56 - 1.69: 1 1.69 - 1.81: 70 Bond restraints: 9936 Sorted by residual: bond pdb=" CB ARG A 782 " pdb=" CG ARG A 782 " ideal model delta sigma weight residual 1.520 1.409 0.111 3.00e-02 1.11e+03 1.38e+01 bond pdb=" CB GLN A 845 " pdb=" CG GLN A 845 " ideal model delta sigma weight residual 1.520 1.422 0.098 3.00e-02 1.11e+03 1.06e+01 bond pdb=" CB VAL A 159 " pdb=" CG1 VAL A 159 " ideal model delta sigma weight residual 1.521 1.415 0.106 3.30e-02 9.18e+02 1.03e+01 bond pdb=" CB ILE A 331 " pdb=" CG2 ILE A 331 " ideal model delta sigma weight residual 1.521 1.418 0.103 3.30e-02 9.18e+02 9.82e+00 bond pdb=" CB THR A 99 " pdb=" CG2 THR A 99 " ideal model delta sigma weight residual 1.521 1.420 0.101 3.30e-02 9.18e+02 9.33e+00 ... (remaining 9931 not shown) Histogram of bond angle deviations from ideal: 97.12 - 104.55: 132 104.55 - 111.97: 4951 111.97 - 119.40: 3536 119.40 - 126.83: 4715 126.83 - 134.26: 129 Bond angle restraints: 13463 Sorted by residual: angle pdb=" CB MET A 990 " pdb=" CG MET A 990 " pdb=" SD MET A 990 " ideal model delta sigma weight residual 112.70 126.55 -13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" CG1 ILE A 147 " pdb=" CB ILE A 147 " pdb=" CG2 ILE A 147 " ideal model delta sigma weight residual 110.70 97.12 13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C ARG A1220 " pdb=" N GLU A1221 " pdb=" CA GLU A1221 " ideal model delta sigma weight residual 122.56 115.53 7.03 1.72e+00 3.38e-01 1.67e+01 angle pdb=" CG1 ILE A 805 " pdb=" CB ILE A 805 " pdb=" CG2 ILE A 805 " ideal model delta sigma weight residual 110.70 99.33 11.37 3.00e+00 1.11e-01 1.44e+01 angle pdb=" C ASP A 43 " pdb=" N MET A 44 " pdb=" CA MET A 44 " ideal model delta sigma weight residual 120.87 127.24 -6.37 1.69e+00 3.50e-01 1.42e+01 ... (remaining 13458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 5346 17.76 - 35.53: 499 35.53 - 53.29: 79 53.29 - 71.06: 11 71.06 - 88.82: 6 Dihedral angle restraints: 5941 sinusoidal: 2382 harmonic: 3559 Sorted by residual: dihedral pdb=" CA ASP A 975 " pdb=" C ASP A 975 " pdb=" N ALA A 976 " pdb=" CA ALA A 976 " ideal model delta harmonic sigma weight residual -180.00 -157.62 -22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA SER A 252 " pdb=" C SER A 252 " pdb=" N CYS A 253 " pdb=" CA CYS A 253 " ideal model delta harmonic sigma weight residual 180.00 157.83 22.17 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA ILE A 194 " pdb=" C ILE A 194 " pdb=" N VAL A 195 " pdb=" CA VAL A 195 " ideal model delta harmonic sigma weight residual 180.00 159.49 20.51 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 5938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1316 0.086 - 0.171: 230 0.171 - 0.257: 12 0.257 - 0.343: 2 0.343 - 0.428: 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 -2.20 -0.43 2.00e-01 2.50e+01 4.58e+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 -2.33 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CB ILE A 346 " pdb=" CA ILE A 346 " pdb=" CG1 ILE A 346 " pdb=" CG2 ILE A 346 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 1558 not shown) Planarity restraints: 1673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 218 " 0.052 5.00e-02 4.00e+02 7.87e-02 9.92e+00 pdb=" N PRO A 219 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 219 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 219 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 109 " 0.049 5.00e-02 4.00e+02 7.44e-02 8.85e+00 pdb=" N PRO A 110 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 110 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 110 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 840 " -0.027 2.00e-02 2.50e+03 2.11e-02 7.77e+00 pdb=" CG PHE A 840 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 840 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 840 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 840 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 840 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 840 " -0.014 2.00e-02 2.50e+03 ... (remaining 1670 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 745 2.71 - 3.26: 9858 3.26 - 3.80: 15696 3.80 - 4.35: 19666 4.35 - 4.90: 33704 Nonbonded interactions: 79669 Sorted by model distance: nonbonded pdb=" OD1 ASP A 953 " pdb=" NE2 GLN A 994 " model vdw 2.161 2.520 nonbonded pdb=" O THR A 488 " pdb=" OG SER A 491 " model vdw 2.179 2.440 nonbonded pdb=" OG SER A 479 " pdb=" O GLN A 481 " model vdw 2.195 2.440 nonbonded pdb=" O ARG A 706 " pdb=" NH1 ARG A 706 " model vdw 2.213 2.520 nonbonded pdb=" OE2 GLU A1221 " pdb=" NZ LYS A1222 " model vdw 2.218 2.520 ... (remaining 79664 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.000 Extract box with map and model: 3.570 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.460 Find NCS groups from input model: 0.370 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 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 : 0.017 0.117 9936 Z= 1.053 Angle : 1.070 13.849 13463 Z= 0.581 Chirality : 0.063 0.428 1561 Planarity : 0.007 0.079 1673 Dihedral : 14.068 88.819 3635 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: -2.17 (0.22), residues: 1212 helix: -1.25 (0.17), residues: 795 sheet: -0.48 (0.54), residues: 72 loop : -1.68 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 64 HIS 0.014 0.002 HIS A 153 PHE 0.046 0.004 PHE A 840 TYR 0.031 0.003 TYR A1016 ARG 0.012 0.001 ARG A 824 *********************** 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 121 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.045 Fit side-chains REVERT: A 206 ASP cc_start: 0.8006 (m-30) cc_final: 0.7619 (m-30) REVERT: A 319 MET cc_start: 0.8159 (tpp) cc_final: 0.7638 (mmt) REVERT: A 345 VAL cc_start: 0.8308 (p) cc_final: 0.8074 (m) REVERT: A 887 ARG cc_start: 0.6917 (mtm110) cc_final: 0.6534 (mtt180) REVERT: A 1135 LEU cc_start: 0.8577 (mp) cc_final: 0.7922 (tt) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2432 time to fit residues: 40.6862 Evaluate side-chains 91 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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: 1.9990 chunk 91 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 109 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1068 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9936 Z= 0.207 Angle : 0.554 7.623 13463 Z= 0.291 Chirality : 0.040 0.143 1561 Planarity : 0.004 0.052 1673 Dihedral : 4.635 17.347 1314 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.85 % Allowed : 4.71 % Favored : 94.44 % 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: -0.20 (0.24), residues: 1212 helix: 0.31 (0.19), residues: 810 sheet: 0.15 (0.53), residues: 74 loop : -1.07 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 733 HIS 0.004 0.001 HIS A 35 PHE 0.024 0.002 PHE A 941 TYR 0.020 0.001 TYR A1016 ARG 0.004 0.000 ARG A 384 *********************** 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 107 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 1.049 Fit side-chains REVERT: A 33 ILE cc_start: 0.7998 (mm) cc_final: 0.7791 (mt) REVERT: A 122 ASN cc_start: 0.8575 (m-40) cc_final: 0.8343 (m-40) REVERT: A 345 VAL cc_start: 0.8414 (p) cc_final: 0.8195 (m) REVERT: A 887 ARG cc_start: 0.7256 (mtm110) cc_final: 0.6874 (mtt180) REVERT: A 933 LEU cc_start: 0.8234 (tp) cc_final: 0.8003 (tp) REVERT: A 1018 ASP cc_start: 0.6431 (t70) cc_final: 0.6192 (t70) REVERT: A 1068 GLN cc_start: 0.6980 (OUTLIER) cc_final: 0.6682 (mm-40) outliers start: 9 outliers final: 5 residues processed: 102 average time/residue: 0.2304 time to fit residues: 33.3170 Evaluate side-chains 92 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1068 GLN Chi-restraints excluded: chain A residue 1167 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 20.0000 chunk 34 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 109 optimal weight: 0.0000 chunk 37 optimal weight: 0.8980 chunk 88 optimal weight: 0.3980 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 35 HIS A 492 ASN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1068 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9936 Z= 0.181 Angle : 0.501 6.838 13463 Z= 0.262 Chirality : 0.039 0.142 1561 Planarity : 0.004 0.054 1673 Dihedral : 4.192 16.207 1314 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.75 % Allowed : 7.06 % Favored : 92.18 % 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: 0.67 (0.25), residues: 1212 helix: 0.90 (0.19), residues: 806 sheet: 0.32 (0.55), residues: 79 loop : -0.44 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 733 HIS 0.003 0.001 HIS A 798 PHE 0.018 0.001 PHE A 336 TYR 0.013 0.001 TYR A 157 ARG 0.008 0.000 ARG A 922 *********************** 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 101 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 89 TRP cc_start: 0.7648 (p-90) cc_final: 0.7383 (p-90) REVERT: A 345 VAL cc_start: 0.8540 (p) cc_final: 0.8262 (m) REVERT: A 391 LEU cc_start: 0.8066 (mt) cc_final: 0.7794 (mt) REVERT: A 926 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8329 (tt) REVERT: A 992 MET cc_start: 0.7960 (ttm) cc_final: 0.7749 (ttm) REVERT: A 1018 ASP cc_start: 0.6475 (t70) cc_final: 0.6273 (t70) REVERT: A 1135 LEU cc_start: 0.8473 (mp) cc_final: 0.8259 (mp) outliers start: 8 outliers final: 6 residues processed: 98 average time/residue: 0.2526 time to fit residues: 34.3639 Evaluate side-chains 90 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1068 GLN Chi-restraints excluded: chain A residue 1167 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.0000 chunk 82 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 50.0000 chunk 73 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 GLN A 725 GLN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1068 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9936 Z= 0.282 Angle : 0.527 5.811 13463 Z= 0.278 Chirality : 0.041 0.157 1561 Planarity : 0.004 0.057 1673 Dihedral : 4.208 17.498 1314 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.51 % Allowed : 8.19 % Favored : 90.30 % 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: 0.72 (0.24), residues: 1212 helix: 0.88 (0.19), residues: 797 sheet: 0.53 (0.55), residues: 79 loop : -0.27 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 734 HIS 0.005 0.001 HIS A 153 PHE 0.023 0.002 PHE A 336 TYR 0.013 0.001 TYR A 157 ARG 0.003 0.000 ARG A 384 *********************** 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 106 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 1.163 Fit side-chains REVERT: A 74 ASP cc_start: 0.7551 (t0) cc_final: 0.6897 (t70) REVERT: A 123 TYR cc_start: 0.8517 (t80) cc_final: 0.8035 (t80) REVERT: A 197 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7305 (pt) REVERT: A 288 MET cc_start: 0.7335 (mtp) cc_final: 0.6993 (mmt) REVERT: A 345 VAL cc_start: 0.8553 (p) cc_final: 0.8268 (m) REVERT: A 887 ARG cc_start: 0.7705 (mtt90) cc_final: 0.7439 (mtt180) REVERT: A 897 ARG cc_start: 0.6757 (ttm-80) cc_final: 0.6505 (ttt-90) REVERT: A 926 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8288 (tt) REVERT: A 1018 ASP cc_start: 0.6721 (t70) cc_final: 0.6503 (t70) REVERT: A 1155 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6387 (tt) outliers start: 16 outliers final: 9 residues processed: 103 average time/residue: 0.2366 time to fit residues: 34.5398 Evaluate side-chains 94 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1167 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 30.0000 chunk 104 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9936 Z= 0.179 Angle : 0.468 5.965 13463 Z= 0.246 Chirality : 0.039 0.153 1561 Planarity : 0.003 0.047 1673 Dihedral : 3.945 15.842 1314 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.51 % Allowed : 9.51 % Favored : 88.98 % 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: 801 sheet: 0.68 (0.55), residues: 79 loop : -0.06 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 733 HIS 0.004 0.001 HIS A 153 PHE 0.019 0.001 PHE A 336 TYR 0.012 0.001 TYR A 157 ARG 0.006 0.000 ARG A 922 *********************** 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 108 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 1.087 Fit side-chains REVERT: A 345 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8226 (m) REVERT: A 763 TRP cc_start: 0.8568 (t60) cc_final: 0.8283 (t-100) REVERT: A 887 ARG cc_start: 0.7688 (mtt90) cc_final: 0.7431 (mtt180) REVERT: A 926 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8135 (tt) REVERT: A 1155 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6356 (tt) outliers start: 16 outliers final: 8 residues processed: 103 average time/residue: 0.2407 time to fit residues: 35.0896 Evaluate side-chains 92 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1167 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 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 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9936 Z= 0.279 Angle : 0.526 9.425 13463 Z= 0.274 Chirality : 0.041 0.164 1561 Planarity : 0.004 0.050 1673 Dihedral : 4.039 16.924 1314 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.69 % Allowed : 9.98 % Favored : 88.32 % 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: 1.07 (0.24), residues: 1212 helix: 1.09 (0.19), residues: 796 sheet: 0.74 (0.54), residues: 80 loop : 0.02 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 734 HIS 0.005 0.001 HIS A 153 PHE 0.023 0.002 PHE A 336 TYR 0.012 0.001 TYR A 737 ARG 0.009 0.000 ARG A 922 *********************** 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 100 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 1.092 Fit side-chains REVERT: A 41 GLU cc_start: 0.7462 (mp0) cc_final: 0.7138 (mt-10) REVERT: A 288 MET cc_start: 0.7435 (mtp) cc_final: 0.7206 (mmt) REVERT: A 345 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8275 (m) REVERT: A 805 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7809 (tt) REVERT: A 926 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8130 (tt) REVERT: A 1155 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6598 (tt) outliers start: 18 outliers final: 11 residues processed: 95 average time/residue: 0.2196 time to fit residues: 31.2304 Evaluate side-chains 93 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1167 ASP Chi-restraints excluded: chain A residue 1187 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 116 optimal weight: 5.9990 chunk 72 optimal weight: 0.1980 chunk 71 optimal weight: 0.5980 chunk 53 optimal weight: 40.0000 chunk 46 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9936 Z= 0.159 Angle : 0.455 8.850 13463 Z= 0.239 Chirality : 0.038 0.142 1561 Planarity : 0.003 0.044 1673 Dihedral : 3.788 14.955 1314 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.51 % Allowed : 10.55 % Favored : 87.95 % 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: 1.40 (0.19), residues: 802 sheet: 0.76 (0.55), residues: 80 loop : 0.15 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 733 HIS 0.003 0.000 HIS A 153 PHE 0.018 0.001 PHE A 389 TYR 0.011 0.001 TYR A 157 ARG 0.003 0.000 ARG A 897 *********************** 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 101 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 1.030 Fit side-chains REVERT: A 41 GLU cc_start: 0.7361 (mp0) cc_final: 0.7056 (mt-10) REVERT: A 288 MET cc_start: 0.7293 (mtp) cc_final: 0.7086 (mmt) REVERT: A 763 TRP cc_start: 0.8556 (t60) cc_final: 0.8309 (t-100) REVERT: A 926 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8134 (tt) REVERT: A 1155 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6468 (tt) outliers start: 16 outliers final: 9 residues processed: 97 average time/residue: 0.2157 time to fit residues: 30.3238 Evaluate side-chains 91 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1167 ASP Chi-restraints excluded: chain A residue 1187 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 0.0570 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 0.1980 chunk 57 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 91 optimal weight: 0.1980 chunk 106 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9936 Z= 0.176 Angle : 0.465 8.116 13463 Z= 0.245 Chirality : 0.039 0.143 1561 Planarity : 0.003 0.045 1673 Dihedral : 3.766 19.709 1314 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.22 % Allowed : 10.73 % Favored : 88.04 % 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: 1.53 (0.24), residues: 1212 helix: 1.43 (0.19), residues: 807 sheet: 0.80 (0.54), residues: 80 loop : 0.19 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 733 HIS 0.004 0.001 HIS A 153 PHE 0.018 0.001 PHE A 336 TYR 0.012 0.001 TYR A 157 ARG 0.004 0.000 ARG A 922 *********************** 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 96 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 1.056 Fit side-chains REVERT: A 41 GLU cc_start: 0.7368 (mp0) cc_final: 0.7094 (mt-10) REVERT: A 74 ASP cc_start: 0.7409 (t0) cc_final: 0.6857 (t0) REVERT: A 288 MET cc_start: 0.7380 (mtp) cc_final: 0.7069 (mmt) REVERT: A 805 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7815 (tt) REVERT: A 926 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8175 (tt) REVERT: A 1155 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6591 (tt) outliers start: 13 outliers final: 8 residues processed: 91 average time/residue: 0.1938 time to fit residues: 26.4829 Evaluate side-chains 92 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1167 ASP Chi-restraints excluded: chain A residue 1187 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 108 optimal weight: 0.0370 chunk 71 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.0064 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9936 Z= 0.221 Angle : 0.483 7.801 13463 Z= 0.255 Chirality : 0.040 0.155 1561 Planarity : 0.003 0.046 1673 Dihedral : 3.841 21.345 1314 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.22 % Allowed : 10.92 % Favored : 87.85 % 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: 1.49 (0.24), residues: 1212 helix: 1.43 (0.19), residues: 793 sheet: 0.85 (0.54), residues: 80 loop : 0.15 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 734 HIS 0.005 0.001 HIS A 153 PHE 0.021 0.001 PHE A 336 TYR 0.013 0.001 TYR A 157 ARG 0.003 0.000 ARG A 262 *********************** 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 89 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 1.173 Fit side-chains REVERT: A 288 MET cc_start: 0.7483 (mtp) cc_final: 0.7168 (mmt) REVERT: A 805 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7859 (tt) REVERT: A 926 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8166 (tt) REVERT: A 1155 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6630 (tt) outliers start: 13 outliers final: 8 residues processed: 87 average time/residue: 0.1925 time to fit residues: 25.1548 Evaluate side-chains 87 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1167 ASP Chi-restraints excluded: chain A residue 1187 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.8980 chunk 79 optimal weight: 0.0470 chunk 120 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 chunk 95 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9936 Z= 0.157 Angle : 0.449 7.652 13463 Z= 0.237 Chirality : 0.038 0.140 1561 Planarity : 0.003 0.045 1673 Dihedral : 3.698 20.994 1314 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.85 % Allowed : 11.58 % Favored : 87.57 % 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: 1.69 (0.24), residues: 1212 helix: 1.56 (0.19), residues: 801 sheet: 0.88 (0.54), residues: 80 loop : 0.26 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 733 HIS 0.004 0.001 HIS A 153 PHE 0.017 0.001 PHE A 336 TYR 0.011 0.001 TYR A 157 ARG 0.008 0.000 ARG A 262 ********************** 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 87 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 1.179 Fit side-chains REVERT: A 262 ARG cc_start: 0.7111 (ttp80) cc_final: 0.6883 (ttp-170) REVERT: A 763 TRP cc_start: 0.8539 (t60) cc_final: 0.8300 (t-100) REVERT: A 890 LYS cc_start: 0.7931 (ttmm) cc_final: 0.7553 (mptt) REVERT: A 926 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8084 (tt) REVERT: A 1155 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6589 (tt) REVERT: A 1183 GLN cc_start: 0.8745 (mm-40) cc_final: 0.8340 (mm-40) outliers start: 9 outliers final: 6 residues processed: 86 average time/residue: 0.1984 time to fit residues: 25.3317 Evaluate side-chains 88 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1187 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 96 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.240298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.173804 restraints weight = 9769.805| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 1.79 r_work: 0.3433 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9936 Z= 0.235 Angle : 0.493 7.390 13463 Z= 0.258 Chirality : 0.040 0.150 1561 Planarity : 0.003 0.046 1673 Dihedral : 3.818 23.325 1314 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.94 % Allowed : 11.49 % Favored : 87.57 % 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: 1.56 (0.24), residues: 1212 helix: 1.46 (0.19), residues: 797 sheet: 0.91 (0.54), residues: 80 loop : 0.22 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.005 0.001 HIS A 153 PHE 0.021 0.001 PHE A 336 TYR 0.012 0.001 TYR A 157 ARG 0.008 0.000 ARG A 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2152.98 seconds wall clock time: 39 minutes 41.12 seconds (2381.12 seconds total)