Starting phenix.real_space_refine on Sat Aug 3 23:54:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u0w_41790/08_2024/8u0w_41790.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u0w_41790/08_2024/8u0w_41790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u0w_41790/08_2024/8u0w_41790.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u0w_41790/08_2024/8u0w_41790.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u0w_41790/08_2024/8u0w_41790.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u0w_41790/08_2024/8u0w_41790.cif" } resolution = 2.99 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 23 5.16 5 C 5726 2.51 5 N 1565 2.21 5 O 1760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 197": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A ASP 263": "OD1" <-> "OD2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A ARG 298": "NH1" <-> "NH2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 352": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A ARG 511": "NH1" <-> "NH2" Residue "A PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 547": "NH1" <-> "NH2" Residue "A ARG 563": "NH1" <-> "NH2" Residue "A ARG 573": "NH1" <-> "NH2" Residue "A ARG 578": "NH1" <-> "NH2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A ARG 604": "NH1" <-> "NH2" Residue "A ARG 620": "NH1" <-> "NH2" Residue "A PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A ARG 661": "NH1" <-> "NH2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 709": "NH1" <-> "NH2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A ARG 768": "NH1" <-> "NH2" Residue "A ASP 772": "OD1" <-> "OD2" Residue "A ASP 786": "OD1" <-> "OD2" Residue "A ASP 787": "OD1" <-> "OD2" Residue "A GLU 809": "OE1" <-> "OE2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "A ARG 828": "NH1" <-> "NH2" Residue "A ARG 830": "NH1" <-> "NH2" Residue "A ARG 846": "NH1" <-> "NH2" Residue "A ARG 855": "NH1" <-> "NH2" Residue "A ARG 858": "NH1" <-> "NH2" Residue "A ARG 863": "NH1" <-> "NH2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A GLU 881": "OE1" <-> "OE2" Residue "A ARG 883": "NH1" <-> "NH2" Residue "A GLU 891": "OE1" <-> "OE2" Residue "A ARG 910": "NH1" <-> "NH2" Residue "A ARG 913": "NH1" <-> "NH2" Residue "A ARG 914": "NH1" <-> "NH2" Residue "A ARG 921": "NH1" <-> "NH2" Residue "A ARG 936": "NH1" <-> "NH2" Residue "A ARG 954": "NH1" <-> "NH2" Residue "A ARG 959": "NH1" <-> "NH2" Residue "A ARG 969": "NH1" <-> "NH2" Residue "A ARG 972": "NH1" <-> "NH2" Residue "A ARG 984": "NH1" <-> "NH2" Residue "A GLU 997": "OE1" <-> "OE2" Residue "A ASP 1000": "OD1" <-> "OD2" Residue "A ARG 1001": "NH1" <-> "NH2" Residue "A GLU 1011": "OE1" <-> "OE2" Residue "A ARG 1025": "NH1" <-> "NH2" Residue "A ARG 1030": "NH1" <-> "NH2" Residue "A ARG 1083": "NH1" <-> "NH2" Residue "A ARG 1087": "NH1" <-> "NH2" Residue "A TYR 1133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1145": "NH1" <-> "NH2" Residue "A ARG 1177": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9086 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8845 Classifications: {'peptide': 1099} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 1066} Chain breaks: 6 Chain: "C" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 241 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Time building chain proxies: 6.40, per 1000 atoms: 0.70 Number of scatterers: 9086 At special positions: 0 Unit cell: (84.9864, 98.3176, 134.145, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 12 15.00 O 1760 8.00 N 1565 7.00 C 5726 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: 3.84 Conformation dependent library (CDL) restraints added in 1.6 seconds 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 10 sheets defined 56.7% alpha, 9.8% beta 0 base pairs and 9 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 20 through 38 removed outlier: 3.697A pdb=" N VAL A 25 " --> pdb=" O PRO A 21 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 78 removed outlier: 3.686A pdb=" N PHE A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 112 Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.549A pdb=" N GLN A 131 " --> pdb=" O TYR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 146 through 157 Processing helix chain 'A' and resid 158 through 161 removed outlier: 3.825A pdb=" N ALA A 161 " --> pdb=" O ASN A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 158 through 161' Processing helix chain 'A' and resid 162 through 179 removed outlier: 4.227A pdb=" N HIS A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 209 Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 227 through 235 removed outlier: 4.139A pdb=" N LYS A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.588A pdb=" N VAL A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 299 Processing helix chain 'A' and resid 324 through 336 Processing helix chain 'A' and resid 402 through 428 Processing helix chain 'A' and resid 445 through 457 removed outlier: 3.609A pdb=" N LEU A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 462 removed outlier: 3.821A pdb=" N GLN A 462 " --> pdb=" O PHE A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 474 removed outlier: 3.869A pdb=" N SER A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 removed outlier: 3.752A pdb=" N HIS A 496 " --> pdb=" O SER A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 558 through 565 Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'A' and resid 588 through 593 removed outlier: 3.796A pdb=" N ASN A 592 " --> pdb=" O ASN A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 616 removed outlier: 3.673A pdb=" N LEU A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 633 through 656 removed outlier: 4.482A pdb=" N ALA A 638 " --> pdb=" O GLU A 634 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N PHE A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 675 through 694 Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.520A pdb=" N SER A 717 " --> pdb=" O TYR A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 752 removed outlier: 3.696A pdb=" N GLY A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 807 removed outlier: 3.909A pdb=" N LEU A 795 " --> pdb=" O THR A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 824 Processing helix chain 'A' and resid 828 through 836 removed outlier: 3.629A pdb=" N GLN A 833 " --> pdb=" O GLU A 829 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN A 834 " --> pdb=" O ARG A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 853 removed outlier: 3.545A pdb=" N VAL A 853 " --> pdb=" O ILE A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 879 Processing helix chain 'A' and resid 889 through 902 removed outlier: 4.068A pdb=" N ALA A 902 " --> pdb=" O LYS A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 939 removed outlier: 3.924A pdb=" N ARG A 913 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 960 Processing helix chain 'A' and resid 970 through 972 No H-bonds generated for 'chain 'A' and resid 970 through 972' Processing helix chain 'A' and resid 992 through 996 removed outlier: 3.514A pdb=" N SER A 995 " --> pdb=" O ASP A 992 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE A 996 " --> pdb=" O PRO A 993 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 992 through 996' Processing helix chain 'A' and resid 1009 through 1013 Processing helix chain 'A' and resid 1014 through 1019 Processing helix chain 'A' and resid 1023 through 1032 removed outlier: 3.503A pdb=" N TRP A1027 " --> pdb=" O TYR A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1052 Processing helix chain 'A' and resid 1052 through 1068 Processing helix chain 'A' and resid 1077 through 1081 removed outlier: 3.703A pdb=" N TYR A1081 " --> pdb=" O ASN A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1127 Processing helix chain 'A' and resid 1155 through 1159 Processing helix chain 'A' and resid 1176 through 1189 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 44 removed outlier: 5.749A pdb=" N ALA A 43 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLY A 541 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 269 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE A 542 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A 271 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR A 89 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASP A 272 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL A 91 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 252 Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 292 removed outlier: 3.506A pdb=" N VAL A 354 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 595 through 601 removed outlier: 6.009A pdb=" N ILE A 774 " --> pdb=" O PHE A 869 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ASP A 871 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU A 776 " --> pdb=" O ASP A 871 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS A 698 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N PHE A 730 " --> pdb=" O LYS A 698 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE A 700 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N THR A 732 " --> pdb=" O PHE A 700 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 744 through 745 Processing sheet with id=AA7, first strand: chain 'A' and resid 755 through 757 Processing sheet with id=AA8, first strand: chain 'A' and resid 962 through 963 removed outlier: 3.519A pdb=" N ASN A1042 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 983 through 985 Processing sheet with id=AB1, first strand: chain 'A' and resid 1071 through 1074 removed outlier: 3.699A pdb=" N ASN A1086 " --> pdb=" O LEU A1099 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A1088 " --> pdb=" O ILE A1097 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE A1097 " --> pdb=" O VAL A1088 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 9 stacking parallelities Total time for adding SS restraints: 3.47 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2171 1.33 - 1.45: 1939 1.45 - 1.57: 5115 1.57 - 1.69: 23 1.69 - 1.81: 36 Bond restraints: 9284 Sorted by residual: bond pdb=" CA PHE A 999 " pdb=" CB PHE A 999 " ideal model delta sigma weight residual 1.530 1.498 0.032 1.69e-02 3.50e+03 3.65e+00 bond pdb=" CG1 ILE A 771 " pdb=" CD1 ILE A 771 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.34e+00 bond pdb=" CB VAL A 91 " pdb=" CG2 VAL A 91 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.34e+00 bond pdb=" CG LEU A 782 " pdb=" CD1 LEU A 782 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.07e+00 bond pdb=" CB THR A 363 " pdb=" CG2 THR A 363 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.95e+00 ... (remaining 9279 not shown) Histogram of bond angle deviations from ideal: 96.27 - 103.84: 108 103.84 - 111.42: 4059 111.42 - 119.00: 3420 119.00 - 126.58: 4893 126.58 - 134.16: 123 Bond angle restraints: 12603 Sorted by residual: angle pdb=" C SER A 361 " pdb=" N PHE A 362 " pdb=" CA PHE A 362 " ideal model delta sigma weight residual 121.54 129.77 -8.23 1.91e+00 2.74e-01 1.86e+01 angle pdb=" C PHE A 998 " pdb=" N PHE A 999 " pdb=" CA PHE A 999 " ideal model delta sigma weight residual 121.54 128.99 -7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" N PHE A 362 " pdb=" CA PHE A 362 " pdb=" C PHE A 362 " ideal model delta sigma weight residual 110.80 117.18 -6.38 2.13e+00 2.20e-01 8.97e+00 angle pdb=" N PHE A 459 " pdb=" CA PHE A 459 " pdb=" C PHE A 459 " ideal model delta sigma weight residual 111.28 114.53 -3.25 1.09e+00 8.42e-01 8.90e+00 angle pdb=" C GLY A 565 " pdb=" N ASN A 566 " pdb=" CA ASN A 566 " ideal model delta sigma weight residual 122.73 117.99 4.74 1.61e+00 3.86e-01 8.65e+00 ... (remaining 12598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 5013 17.85 - 35.70: 414 35.70 - 53.55: 108 53.55 - 71.40: 13 71.40 - 89.25: 12 Dihedral angle restraints: 5560 sinusoidal: 2330 harmonic: 3230 Sorted by residual: dihedral pdb=" CA GLU A 997 " pdb=" C GLU A 997 " pdb=" N PHE A 998 " pdb=" CA PHE A 998 " ideal model delta harmonic sigma weight residual 180.00 -151.77 -28.23 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA SER A 358 " pdb=" C SER A 358 " pdb=" N ASP A 359 " pdb=" CA ASP A 359 " ideal model delta harmonic sigma weight residual 180.00 151.79 28.21 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA HIS A 238 " pdb=" C HIS A 238 " pdb=" N VAL A 239 " pdb=" CA VAL A 239 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 5557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1077 0.051 - 0.102: 269 0.102 - 0.152: 49 0.152 - 0.203: 6 0.203 - 0.254: 2 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CB THR A 363 " pdb=" CA THR A 363 " pdb=" OG1 THR A 363 " pdb=" CG2 THR A 363 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA PHE A 362 " pdb=" N PHE A 362 " pdb=" C PHE A 362 " pdb=" CB PHE A 362 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB ILE A1047 " pdb=" CA ILE A1047 " pdb=" CG1 ILE A1047 " pdb=" CG2 ILE A1047 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.91e-01 ... (remaining 1400 not shown) Planarity restraints: 1592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 662 " 0.019 2.00e-02 2.50e+03 2.20e-02 9.67e+00 pdb=" CG TYR A 662 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 662 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 662 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 662 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 662 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 662 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 662 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 416 " -0.018 2.00e-02 2.50e+03 1.73e-02 5.26e+00 pdb=" CG PHE A 416 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 416 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 416 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 416 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 416 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 416 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 999 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.81e+00 pdb=" C PHE A 999 " -0.038 2.00e-02 2.50e+03 pdb=" O PHE A 999 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP A1000 " 0.013 2.00e-02 2.50e+03 ... (remaining 1589 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 132 2.65 - 3.21: 8521 3.21 - 3.78: 13652 3.78 - 4.34: 19827 4.34 - 4.90: 32863 Nonbonded interactions: 74995 Sorted by model distance: nonbonded pdb=" O LEU A 488 " pdb=" OG SER A 489 " model vdw 2.091 3.040 nonbonded pdb=" O PHE A 999 " pdb=" N ARG A1001 " model vdw 2.135 3.120 nonbonded pdb=" OE2 GLU A 331 " pdb=" ND2 ASN A 335 " model vdw 2.173 3.120 nonbonded pdb=" OG SER A 754 " pdb=" NH1 ARG A 863 " model vdw 2.203 3.120 nonbonded pdb=" OE1 GLN A 683 " pdb=" OG1 THR A 699 " model vdw 2.212 3.040 ... (remaining 74990 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 31.510 Find NCS groups from input model: 0.090 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:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 9284 Z= 0.449 Angle : 0.761 8.784 12603 Z= 0.437 Chirality : 0.046 0.254 1403 Planarity : 0.004 0.048 1592 Dihedral : 14.845 89.249 3462 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.50 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.58 (0.24), residues: 1085 helix: 0.37 (0.22), residues: 524 sheet: -0.85 (0.42), residues: 147 loop : -1.06 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 643 HIS 0.020 0.002 HIS A 836 PHE 0.040 0.002 PHE A 416 TYR 0.052 0.002 TYR A 662 ARG 0.010 0.001 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8817 (mt) cc_final: 0.8510 (mm) REVERT: A 1097 ILE cc_start: 0.8888 (mt) cc_final: 0.8627 (mm) REVERT: A 1100 ASP cc_start: 0.7137 (t0) cc_final: 0.6675 (p0) REVERT: A 1118 LYS cc_start: 0.8339 (mttt) cc_final: 0.8063 (mttp) REVERT: A 1184 ILE cc_start: 0.9197 (mt) cc_final: 0.8458 (pp) outliers start: 0 outliers final: 1 residues processed: 115 average time/residue: 1.4080 time to fit residues: 172.4057 Evaluate side-chains 68 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** A 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 GLN A 800 GLN A 940 GLN A1022 GLN A1135 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9284 Z= 0.210 Angle : 0.606 10.445 12603 Z= 0.323 Chirality : 0.042 0.208 1403 Planarity : 0.004 0.039 1592 Dihedral : 11.425 86.260 1318 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.04 % Favored : 96.77 % Rotamer: Outliers : 1.65 % Allowed : 7.20 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.42 (0.25), residues: 1085 helix: 1.38 (0.22), residues: 530 sheet: -0.48 (0.46), residues: 131 loop : -0.84 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 643 HIS 0.010 0.001 HIS A 836 PHE 0.030 0.001 PHE A 362 TYR 0.031 0.001 TYR A 662 ARG 0.005 0.001 ARG A1177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7302 (tm) REVERT: A 1078 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.8103 (t0) outliers start: 16 outliers final: 5 residues processed: 100 average time/residue: 1.0033 time to fit residues: 109.3825 Evaluate side-chains 71 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1078 ASN Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1187 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 584 HIS ** A1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9284 Z= 0.414 Angle : 0.637 8.337 12603 Z= 0.335 Chirality : 0.045 0.208 1403 Planarity : 0.004 0.039 1592 Dihedral : 11.311 79.527 1316 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.95 % Favored : 96.87 % Rotamer: Outliers : 2.37 % Allowed : 10.60 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.65 (0.26), residues: 1085 helix: 1.70 (0.22), residues: 531 sheet: -0.56 (0.47), residues: 131 loop : -0.84 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 643 HIS 0.019 0.002 HIS A1188 PHE 0.032 0.002 PHE A 362 TYR 0.027 0.001 TYR A 662 ARG 0.003 0.000 ARG A1087 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 72 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 969 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6983 (ttt90) REVERT: A 1095 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6912 (tp-100) REVERT: A 1118 LYS cc_start: 0.8494 (mttt) cc_final: 0.7970 (mtpp) outliers start: 23 outliers final: 11 residues processed: 85 average time/residue: 1.0103 time to fit residues: 94.0322 Evaluate side-chains 77 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 826 MET Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 969 ARG Chi-restraints excluded: chain A residue 1095 GLN Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1187 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN ** A 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9284 Z= 0.228 Angle : 0.536 8.650 12603 Z= 0.286 Chirality : 0.041 0.192 1403 Planarity : 0.003 0.040 1592 Dihedral : 11.474 80.363 1316 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.76 % Favored : 97.05 % Rotamer: Outliers : 1.95 % Allowed : 11.21 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.26), residues: 1085 helix: 2.07 (0.22), residues: 534 sheet: -0.47 (0.47), residues: 131 loop : -0.67 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 643 HIS 0.007 0.001 HIS A 836 PHE 0.025 0.001 PHE A 362 TYR 0.018 0.001 TYR A 662 ARG 0.004 0.000 ARG A 573 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 72 time to evaluate : 0.990 Fit side-chains REVERT: A 1095 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6824 (tp-100) REVERT: A 1118 LYS cc_start: 0.8508 (mttt) cc_final: 0.8060 (mtpp) outliers start: 19 outliers final: 8 residues processed: 84 average time/residue: 0.9766 time to fit residues: 90.2768 Evaluate side-chains 72 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 968 GLU Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1095 GLN Chi-restraints excluded: chain A residue 1100 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9284 Z= 0.248 Angle : 0.571 8.950 12603 Z= 0.296 Chirality : 0.041 0.195 1403 Planarity : 0.003 0.042 1592 Dihedral : 11.496 84.040 1316 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.76 % Favored : 97.05 % Rotamer: Outliers : 1.95 % Allowed : 12.35 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.28 (0.26), residues: 1085 helix: 2.27 (0.22), residues: 533 sheet: -0.51 (0.46), residues: 134 loop : -0.55 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 643 HIS 0.006 0.001 HIS A 836 PHE 0.025 0.001 PHE A 362 TYR 0.015 0.001 TYR A 662 ARG 0.002 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: A 1118 LYS cc_start: 0.8515 (mttt) cc_final: 0.7976 (mtpp) outliers start: 19 outliers final: 9 residues processed: 80 average time/residue: 0.8843 time to fit residues: 78.4204 Evaluate side-chains 71 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 826 MET Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 968 GLU Chi-restraints excluded: chain A residue 999 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 0.0970 chunk 102 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN A 581 ASN A 966 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9284 Z= 0.201 Angle : 0.545 8.503 12603 Z= 0.285 Chirality : 0.040 0.194 1403 Planarity : 0.003 0.042 1592 Dihedral : 11.461 89.658 1316 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.58 % Favored : 97.24 % Rotamer: Outliers : 1.65 % Allowed : 13.79 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.43 (0.26), residues: 1085 helix: 2.45 (0.22), residues: 534 sheet: -0.57 (0.46), residues: 134 loop : -0.51 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 643 HIS 0.005 0.001 HIS A1188 PHE 0.024 0.001 PHE A 362 TYR 0.013 0.001 TYR A 662 ARG 0.002 0.000 ARG A 573 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 1.102 Fit side-chains REVERT: A 1095 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6818 (tp-100) REVERT: A 1118 LYS cc_start: 0.8541 (mttt) cc_final: 0.8064 (mtpp) outliers start: 16 outliers final: 5 residues processed: 79 average time/residue: 0.7449 time to fit residues: 66.4651 Evaluate side-chains 68 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1095 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.0000 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 0.0770 chunk 89 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 overall best weight: 0.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN A 966 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9284 Z= 0.163 Angle : 0.532 10.091 12603 Z= 0.276 Chirality : 0.040 0.199 1403 Planarity : 0.003 0.041 1592 Dihedral : 11.416 86.510 1316 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.49 % Favored : 97.33 % Rotamer: Outliers : 1.23 % Allowed : 14.40 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.58 (0.26), residues: 1085 helix: 2.61 (0.22), residues: 534 sheet: -0.57 (0.45), residues: 135 loop : -0.46 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 643 HIS 0.005 0.001 HIS A 836 PHE 0.023 0.001 PHE A 362 TYR 0.021 0.001 TYR A 788 ARG 0.004 0.000 ARG A 573 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 1095 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6797 (tp-100) REVERT: A 1118 LYS cc_start: 0.8498 (mttt) cc_final: 0.8031 (mtpp) outliers start: 12 outliers final: 5 residues processed: 83 average time/residue: 0.8509 time to fit residues: 78.5362 Evaluate side-chains 75 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1095 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 0.0870 chunk 101 optimal weight: 0.3980 chunk 92 optimal weight: 0.0000 overall best weight: 0.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 966 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9284 Z= 0.169 Angle : 0.532 9.617 12603 Z= 0.277 Chirality : 0.040 0.203 1403 Planarity : 0.003 0.041 1592 Dihedral : 11.463 89.063 1316 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.30 % Favored : 97.51 % Rotamer: Outliers : 1.34 % Allowed : 14.81 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.26), residues: 1085 helix: 2.70 (0.22), residues: 534 sheet: -0.53 (0.46), residues: 134 loop : -0.40 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 643 HIS 0.005 0.001 HIS A1188 PHE 0.023 0.001 PHE A 362 TYR 0.008 0.001 TYR A1004 ARG 0.004 0.000 ARG A 573 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: A 328 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8084 (mtm-85) REVERT: A 1095 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6737 (tp-100) REVERT: A 1118 LYS cc_start: 0.8488 (mttt) cc_final: 0.8039 (mtpp) outliers start: 13 outliers final: 5 residues processed: 79 average time/residue: 0.9365 time to fit residues: 81.5830 Evaluate side-chains 70 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1095 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 chunk 30 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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: 0.8080 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9284 Z= 0.299 Angle : 0.580 9.536 12603 Z= 0.298 Chirality : 0.042 0.196 1403 Planarity : 0.003 0.040 1592 Dihedral : 11.698 88.522 1316 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.49 % Favored : 97.33 % Rotamer: Outliers : 1.13 % Allowed : 15.12 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.61 (0.26), residues: 1085 helix: 2.62 (0.22), residues: 535 sheet: -0.58 (0.46), residues: 134 loop : -0.42 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 643 HIS 0.006 0.001 HIS A 458 PHE 0.027 0.001 PHE A 362 TYR 0.019 0.001 TYR A 788 ARG 0.002 0.000 ARG A 573 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 1095 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6788 (tp-100) REVERT: A 1118 LYS cc_start: 0.8479 (mttt) cc_final: 0.8071 (mtpp) outliers start: 11 outliers final: 8 residues processed: 72 average time/residue: 0.8637 time to fit residues: 68.9924 Evaluate side-chains 74 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 826 MET Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1095 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.8047 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9284 Z= 0.221 Angle : 0.551 9.659 12603 Z= 0.285 Chirality : 0.041 0.208 1403 Planarity : 0.003 0.040 1592 Dihedral : 11.702 87.901 1316 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.40 % Favored : 97.42 % Rotamer: Outliers : 1.13 % Allowed : 15.43 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.65 (0.26), residues: 1085 helix: 2.64 (0.22), residues: 535 sheet: -0.57 (0.46), residues: 134 loop : -0.39 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 643 HIS 0.005 0.001 HIS A 458 PHE 0.025 0.001 PHE A 362 TYR 0.023 0.001 TYR A 788 ARG 0.002 0.000 ARG A1145 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 1095 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6782 (tp-100) REVERT: A 1118 LYS cc_start: 0.8463 (mttt) cc_final: 0.8063 (mppt) outliers start: 11 outliers final: 7 residues processed: 74 average time/residue: 0.8641 time to fit residues: 71.2198 Evaluate side-chains 72 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 826 MET Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1095 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 63 optimal weight: 0.0040 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.115206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.078361 restraints weight = 17271.849| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.02 r_work: 0.2996 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9284 Z= 0.203 Angle : 0.550 9.774 12603 Z= 0.283 Chirality : 0.041 0.225 1403 Planarity : 0.003 0.040 1592 Dihedral : 11.684 87.547 1316 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.40 % Favored : 97.42 % Rotamer: Outliers : 1.13 % Allowed : 15.64 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.26), residues: 1085 helix: 2.68 (0.22), residues: 535 sheet: -0.60 (0.46), residues: 134 loop : -0.38 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 643 HIS 0.005 0.001 HIS A 458 PHE 0.025 0.001 PHE A 362 TYR 0.022 0.001 TYR A 788 ARG 0.002 0.000 ARG A 972 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2662.58 seconds wall clock time: 48 minutes 23.08 seconds (2903.08 seconds total)