Starting phenix.real_space_refine on Thu Sep 26 02:31:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v1s_42889/09_2024/8v1s_42889_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v1s_42889/09_2024/8v1s_42889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v1s_42889/09_2024/8v1s_42889.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v1s_42889/09_2024/8v1s_42889.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v1s_42889/09_2024/8v1s_42889_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v1s_42889/09_2024/8v1s_42889_neut.cif" } resolution = 3.26 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= 0.002 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: 6 Type Number sf(0) Gaussians P 59 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 7398 2.51 5 N 2106 2.21 5 O 2277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11889 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8602 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1091, 8582 Classifications: {'peptide': 1091} Link IDs: {'PTRANS': 54, 'TRANS': 1036} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 1091, 8582 Classifications: {'peptide': 1091} Link IDs: {'PTRANS': 54, 'TRANS': 1036} Chain breaks: 3 bond proxies already assigned to first conformer: 8759 Chain: "B" Number of atoms: 2079 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2070 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 14, 'TRANS': 254} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2070 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 14, 'TRANS': 254} Chain breaks: 1 bond proxies already assigned to first conformer: 2098 Chain: "P" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 536 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "T" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 671 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG A 700 " occ=0.44 ... (20 atoms not shown) pdb=" NH2BARG A 700 " occ=0.56 residue: pdb=" N ALYS A1182 " occ=0.52 ... (16 atoms not shown) pdb=" NZ BLYS A1182 " occ=0.48 residue: pdb=" N ALYS B 105 " occ=0.43 ... (16 atoms not shown) pdb=" NZ BLYS B 105 " occ=0.57 Time building chain proxies: 11.97, per 1000 atoms: 1.01 Number of scatterers: 11889 At special positions: 0 Unit cell: (154.275, 115.5, 89.925, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 59 15.00 Mg 1 11.99 O 2277 8.00 N 2106 7.00 C 7398 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 - 3.00 Amino acid : True - 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: 3.34 Conformation dependent library (CDL) restraints added in 2.8 seconds 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2532 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 16 sheets defined 38.7% alpha, 19.1% beta 12 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 4.37 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 168 through 175 removed outlier: 4.399A pdb=" N MET A 172 " --> pdb=" O HIS A 168 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 175 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.702A pdb=" N ARG A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 removed outlier: 3.611A pdb=" N PHE A 335 " --> pdb=" O PRO A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.621A pdb=" N LEU A 350 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 430 Processing helix chain 'A' and resid 442 through 457 Processing helix chain 'A' and resid 470 through 482 Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.705A pdb=" N ASP A 531 " --> pdb=" O GLY A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 548 Processing helix chain 'A' and resid 559 through 567 removed outlier: 4.186A pdb=" N GLY A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 593 Processing helix chain 'A' and resid 593 through 606 removed outlier: 3.789A pdb=" N GLU A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 617 through 632 removed outlier: 4.293A pdb=" N VAL A 621 " --> pdb=" O GLN A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 703 removed outlier: 3.843A pdb=" N ASP A 703 " --> pdb=" O AARG A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 739 through 744 Processing helix chain 'A' and resid 772 through 790 Processing helix chain 'A' and resid 796 through 816 Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 830 through 855 Processing helix chain 'A' and resid 858 through 866 Processing helix chain 'A' and resid 867 through 870 Processing helix chain 'A' and resid 901 through 917 removed outlier: 3.790A pdb=" N LYS A 908 " --> pdb=" O ALA A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 980 Processing helix chain 'A' and resid 983 through 990 Processing helix chain 'A' and resid 996 through 1001 removed outlier: 4.268A pdb=" N ALA A1000 " --> pdb=" O GLU A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1006 No H-bonds generated for 'chain 'A' and resid 1004 through 1006' Processing helix chain 'A' and resid 1007 through 1023 removed outlier: 3.755A pdb=" N VAL A1013 " --> pdb=" O ALA A1009 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A1014 " --> pdb=" O PHE A1010 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP A1016 " --> pdb=" O ALA A1012 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE A1021 " --> pdb=" O ALA A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1059 Processing helix chain 'A' and resid 1082 through 1094 Processing helix chain 'A' and resid 1138 through 1142 Processing helix chain 'A' and resid 1145 through 1152 removed outlier: 3.646A pdb=" N HIS A1152 " --> pdb=" O TYR A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1174 removed outlier: 3.872A pdb=" N TYR A1161 " --> pdb=" O ASN A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1178 removed outlier: 3.559A pdb=" N GLY A1178 " --> pdb=" O ALA A1175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1175 through 1178' Processing helix chain 'A' and resid 1180 through 1189 Processing helix chain 'A' and resid 1190 through 1192 No H-bonds generated for 'chain 'A' and resid 1190 through 1192' Processing helix chain 'A' and resid 1199 through 1209 removed outlier: 4.487A pdb=" N ARG A1205 " --> pdb=" O ASP A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1235 removed outlier: 3.735A pdb=" N THR A1223 " --> pdb=" O THR A1219 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG A1224 " --> pdb=" O ALA A1220 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG A1225 " --> pdb=" O GLU A1221 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 45 Processing helix chain 'B' and resid 101 through 105 removed outlier: 3.614A pdb=" N ALYS B 105 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 removed outlier: 4.003A pdb=" N ARG B 113 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 133 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 181 through 192 Processing helix chain 'B' and resid 273 through 281 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 113 removed outlier: 9.046A pdb=" N VAL A 436 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 409 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU A 438 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A 411 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE A 440 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER A 413 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU A 406 " --> pdb=" O ASP A 400 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP A 400 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE A 392 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N VAL A 391 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LYS A 372 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 113 removed outlier: 9.046A pdb=" N VAL A 436 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 409 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU A 438 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A 411 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE A 440 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER A 413 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU A 406 " --> pdb=" O ASP A 400 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP A 400 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE A 392 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 156 Processing sheet with id=AA6, first strand: chain 'A' and resid 203 through 208 Processing sheet with id=AA7, first strand: chain 'A' and resid 316 through 317 Processing sheet with id=AA8, first strand: chain 'A' and resid 499 through 502 Processing sheet with id=AA9, first strand: chain 'A' and resid 708 through 709 removed outlier: 3.821A pdb=" N LYS A 928 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR A 884 " --> pdb=" O PHE A 891 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU A 893 " --> pdb=" O ILE A 882 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE A 882 " --> pdb=" O LEU A 893 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 708 through 709 removed outlier: 6.580A pdb=" N VAL A 944 " --> pdb=" O THR A 931 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU A 933 " --> pdb=" O ILE A 942 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 942 " --> pdb=" O LEU A 933 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS A 949 " --> pdb=" O ILE A 945 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 754 through 755 Processing sheet with id=AB3, first strand: chain 'A' and resid 1212 through 1215 Processing sheet with id=AB4, first strand: chain 'B' and resid 88 through 90 removed outlier: 6.879A pdb=" N TRP B 141 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL B 123 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG B 139 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU B 125 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 137 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE B 127 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N THR B 135 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 88 through 90 removed outlier: 6.879A pdb=" N TRP B 141 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL B 123 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG B 139 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU B 125 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 137 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE B 127 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N THR B 135 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.598A pdb=" N GLN B 76 " --> pdb=" O VAL B 312 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 255 through 257 removed outlier: 8.485A pdb=" N VAL B 256 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA B 222 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR B 200 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE B 265 " --> pdb=" O LEU B 204 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1305 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 5.36 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.07: 1 1.07 - 1.27: 1789 1.27 - 1.46: 5232 1.46 - 1.66: 5179 1.66 - 1.86: 73 Bond restraints: 12274 Sorted by residual: bond pdb=" N PRO B 132 " pdb=" CD PRO B 132 " ideal model delta sigma weight residual 1.473 1.863 -0.390 1.40e-02 5.10e+03 7.77e+02 bond pdb=" CG PRO B 132 " pdb=" CD PRO B 132 " ideal model delta sigma weight residual 1.503 0.867 0.636 3.40e-02 8.65e+02 3.50e+02 bond pdb=" CB ASN A 518 " pdb=" CG ASN A 518 " ideal model delta sigma weight residual 1.516 1.364 0.152 2.50e-02 1.60e+03 3.70e+01 bond pdb=" CG LEU B 109 " pdb=" CD1 LEU B 109 " ideal model delta sigma weight residual 1.521 1.331 0.190 3.30e-02 9.18e+02 3.30e+01 bond pdb=" CB PRO B 132 " pdb=" CG PRO B 132 " ideal model delta sigma weight residual 1.492 1.241 0.251 5.00e-02 4.00e+02 2.52e+01 ... (remaining 12269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.77: 16893 14.77 - 29.54: 3 29.54 - 44.30: 1 44.30 - 59.07: 0 59.07 - 73.84: 1 Bond angle restraints: 16898 Sorted by residual: angle pdb=" CB PRO B 132 " pdb=" CG PRO B 132 " pdb=" CD PRO B 132 " ideal model delta sigma weight residual 106.10 179.94 -73.84 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO B 132 " pdb=" CD PRO B 132 " pdb=" CG PRO B 132 " ideal model delta sigma weight residual 103.20 72.74 30.46 1.50e+00 4.44e-01 4.12e+02 angle pdb=" CA PRO B 132 " pdb=" N PRO B 132 " pdb=" CD PRO B 132 " ideal model delta sigma weight residual 112.00 86.76 25.24 1.40e+00 5.10e-01 3.25e+02 angle pdb=" CA PRO B 132 " pdb=" CB PRO B 132 " pdb=" CG PRO B 132 " ideal model delta sigma weight residual 104.50 77.70 26.80 1.90e+00 2.77e-01 1.99e+02 angle pdb=" N PRO B 132 " pdb=" CA PRO B 132 " pdb=" C PRO B 132 " ideal model delta sigma weight residual 113.86 124.08 -10.22 1.25e+00 6.40e-01 6.68e+01 ... (remaining 16893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 6616 34.54 - 69.07: 531 69.07 - 103.61: 26 103.61 - 138.15: 1 138.15 - 172.68: 6 Dihedral angle restraints: 7180 sinusoidal: 3240 harmonic: 3940 Sorted by residual: dihedral pdb=" CA ALA A 220 " pdb=" C ALA A 220 " pdb=" N PRO A 221 " pdb=" CA PRO A 221 " ideal model delta harmonic sigma weight residual 180.00 -123.91 -56.09 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA GLY B 305 " pdb=" C GLY B 305 " pdb=" N PRO B 306 " pdb=" CA PRO B 306 " ideal model delta harmonic sigma weight residual -180.00 -125.50 -54.50 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA SER A1038 " pdb=" C SER A1038 " pdb=" N ARG A1039 " pdb=" CA ARG A1039 " ideal model delta harmonic sigma weight residual -180.00 -126.53 -53.47 0 5.00e+00 4.00e-02 1.14e+02 ... (remaining 7177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1165 0.062 - 0.125: 531 0.125 - 0.187: 165 0.187 - 0.249: 33 0.249 - 0.311: 11 Chirality restraints: 1905 Sorted by residual: chirality pdb=" CB VAL B 212 " pdb=" CA VAL B 212 " pdb=" CG1 VAL B 212 " pdb=" CG2 VAL B 212 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CB VAL A 253 " pdb=" CA VAL A 253 " pdb=" CG1 VAL A 253 " pdb=" CG2 VAL A 253 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ASP B 146 " pdb=" N ASP B 146 " pdb=" C ASP B 146 " pdb=" CB ASP B 146 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 1902 not shown) Planarity restraints: 1975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 131 " 0.180 5.00e-02 4.00e+02 2.15e-01 7.42e+01 pdb=" N PRO B 132 " -0.368 5.00e-02 4.00e+02 pdb=" CA PRO B 132 " 0.091 5.00e-02 4.00e+02 pdb=" CD PRO B 132 " 0.098 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 48 " -0.079 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO B 49 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO B 49 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO B 49 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 716 " -0.023 2.00e-02 2.50e+03 4.61e-02 2.13e+01 pdb=" C PHE A 716 " 0.080 2.00e-02 2.50e+03 pdb=" O PHE A 716 " -0.029 2.00e-02 2.50e+03 pdb=" N ASP A 717 " -0.027 2.00e-02 2.50e+03 ... (remaining 1972 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 88 2.45 - 3.06: 8441 3.06 - 3.68: 19079 3.68 - 4.29: 27983 4.29 - 4.90: 46522 Nonbonded interactions: 102113 Sorted by model distance: nonbonded pdb=" O LEU A 583 " pdb=" OE1 GLN A 587 " model vdw 1.841 3.040 nonbonded pdb=" OG1 THR A 312 " pdb=" O ALA A 602 " model vdw 1.933 3.040 nonbonded pdb=" OD2 ASP A 471 " pdb="MG MG A1301 " model vdw 1.970 2.170 nonbonded pdb=" OD1 ASP A 471 " pdb="MG MG A1301 " model vdw 1.973 2.170 nonbonded pdb=" OG SER A 127 " pdb=" O LEU A 129 " model vdw 1.974 3.040 ... (remaining 102108 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=0.43 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: 1.700 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: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 39.250 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.080 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 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 : 0.018 0.636 12274 Z= 1.164 Angle : 1.640 73.840 16898 Z= 0.892 Chirality : 0.078 0.311 1905 Planarity : 0.015 0.215 1975 Dihedral : 22.660 172.682 4648 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 0.30 % Favored : 99.55 % Rotamer: Outliers : 0.18 % Allowed : 31.32 % Favored : 68.50 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.93 % 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: -4.48 (0.19), residues: 1357 helix: -2.28 (0.20), residues: 440 sheet: -2.69 (0.31), residues: 224 loop : -3.62 (0.19), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP A 502 HIS 0.025 0.004 HIS A 192 PHE 0.043 0.005 PHE A 733 TYR 0.034 0.005 TYR A 490 ARG 0.025 0.001 ARG A 302 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 281 TYR cc_start: 0.6443 (t80) cc_final: 0.6147 (t80) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.2678 time to fit residues: 41.2799 Evaluate side-chains 99 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 58 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 12274 Z= 0.313 Angle : 0.878 16.857 16898 Z= 0.471 Chirality : 0.051 0.236 1905 Planarity : 0.007 0.073 1975 Dihedral : 22.628 178.800 2150 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.90 % Favored : 92.73 % Rotamer: Outliers : 3.73 % Allowed : 27.42 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -2.99 (0.21), residues: 1357 helix: -0.98 (0.22), residues: 453 sheet: -2.29 (0.32), residues: 223 loop : -2.60 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 781 HIS 0.009 0.002 HIS A 192 PHE 0.022 0.003 PHE A 240 TYR 0.021 0.002 TYR A1148 ARG 0.008 0.001 ARG A 558 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 147 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 TYR cc_start: 0.6261 (t80) cc_final: 0.5864 (t80) REVERT: A 510 GLN cc_start: 0.5678 (OUTLIER) cc_final: 0.4555 (mt0) REVERT: A 756 GLU cc_start: 0.5521 (OUTLIER) cc_final: 0.5014 (mt-10) REVERT: A 1224 ARG cc_start: 0.6050 (ttm110) cc_final: 0.5792 (mtm-85) REVERT: B 61 MET cc_start: 0.7629 (mtt) cc_final: 0.7192 (mtp) outliers start: 40 outliers final: 16 residues processed: 173 average time/residue: 0.2504 time to fit residues: 62.4021 Evaluate side-chains 128 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1185 GLU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.1980 chunk 39 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 113 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.6512 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12274 Z= 0.277 Angle : 0.785 8.572 16898 Z= 0.419 Chirality : 0.049 0.272 1905 Planarity : 0.006 0.066 1975 Dihedral : 22.465 178.809 2150 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.23 % Favored : 93.62 % Rotamer: Outliers : 3.11 % Allowed : 27.33 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.31 % 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: -2.42 (0.21), residues: 1357 helix: -0.59 (0.23), residues: 455 sheet: -1.88 (0.30), residues: 235 loop : -2.23 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 781 HIS 0.007 0.001 HIS A 709 PHE 0.024 0.002 PHE A 313 TYR 0.017 0.002 TYR A1148 ARG 0.007 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 281 TYR cc_start: 0.6292 (t80) cc_final: 0.5929 (t80) REVERT: A 510 GLN cc_start: 0.5280 (OUTLIER) cc_final: 0.4490 (mt0) REVERT: A 756 GLU cc_start: 0.5284 (OUTLIER) cc_final: 0.4817 (mt-10) REVERT: A 950 MET cc_start: 0.7443 (tpp) cc_final: 0.6814 (tpp) REVERT: A 1054 VAL cc_start: 0.5989 (OUTLIER) cc_final: 0.5613 (m) REVERT: A 1224 ARG cc_start: 0.6100 (ttm110) cc_final: 0.5899 (mtm-85) REVERT: A 1226 MET cc_start: 0.7413 (tpp) cc_final: 0.7194 (tpp) REVERT: B 51 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7549 (mtt-85) outliers start: 33 outliers final: 17 residues processed: 162 average time/residue: 0.2605 time to fit residues: 59.4550 Evaluate side-chains 137 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 ASN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 12274 Z= 0.329 Angle : 0.787 9.318 16898 Z= 0.416 Chirality : 0.049 0.258 1905 Planarity : 0.006 0.065 1975 Dihedral : 22.311 178.278 2150 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.05 % Favored : 92.88 % Rotamer: Outliers : 4.61 % Allowed : 26.09 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -2.21 (0.22), residues: 1357 helix: -0.55 (0.23), residues: 463 sheet: -1.73 (0.30), residues: 236 loop : -2.02 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 856 HIS 0.005 0.001 HIS A 192 PHE 0.021 0.002 PHE A 733 TYR 0.021 0.002 TYR A 399 ARG 0.007 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 134 time to evaluate : 1.243 Fit side-chains revert: symmetry clash REVERT: A 155 ASN cc_start: 0.7795 (OUTLIER) cc_final: 0.7499 (p0) REVERT: A 281 TYR cc_start: 0.6401 (t80) cc_final: 0.5829 (t80) REVERT: A 510 GLN cc_start: 0.5489 (OUTLIER) cc_final: 0.4636 (mt0) REVERT: A 703 ASP cc_start: 0.7253 (p0) cc_final: 0.7030 (p0) REVERT: A 756 GLU cc_start: 0.5364 (OUTLIER) cc_final: 0.4846 (mt-10) REVERT: A 934 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7073 (tp) REVERT: A 950 MET cc_start: 0.7479 (tpp) cc_final: 0.7026 (tpp) REVERT: A 981 ASP cc_start: 0.5598 (m-30) cc_final: 0.5079 (p0) REVERT: A 1054 VAL cc_start: 0.5966 (OUTLIER) cc_final: 0.5682 (m) REVERT: A 1224 ARG cc_start: 0.6052 (ttm110) cc_final: 0.5726 (mtm-85) REVERT: B 51 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7683 (mtt-85) REVERT: B 309 VAL cc_start: 0.6686 (OUTLIER) cc_final: 0.5689 (p) outliers start: 50 outliers final: 30 residues processed: 169 average time/residue: 0.2575 time to fit residues: 63.0487 Evaluate side-chains 158 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 121 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1185 GLU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 93 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 121 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A 323 ASN A 806 GLN A1157 ASN A1164 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12274 Z= 0.230 Angle : 0.730 9.389 16898 Z= 0.388 Chirality : 0.047 0.214 1905 Planarity : 0.005 0.063 1975 Dihedral : 22.022 170.123 2150 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.08 % Favored : 93.84 % Rotamer: Outliers : 3.11 % Allowed : 28.39 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.23 % 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: -1.84 (0.22), residues: 1357 helix: -0.25 (0.23), residues: 460 sheet: -1.43 (0.31), residues: 228 loop : -1.83 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 856 HIS 0.006 0.001 HIS A 709 PHE 0.045 0.002 PHE A 313 TYR 0.018 0.002 TYR A 399 ARG 0.006 0.001 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 133 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: A 155 ASN cc_start: 0.7660 (OUTLIER) cc_final: 0.7303 (p0) REVERT: A 281 TYR cc_start: 0.6178 (t80) cc_final: 0.5744 (t80) REVERT: A 510 GLN cc_start: 0.4969 (OUTLIER) cc_final: 0.4535 (mt0) REVERT: A 703 ASP cc_start: 0.7113 (p0) cc_final: 0.6812 (p0) REVERT: A 756 GLU cc_start: 0.5235 (OUTLIER) cc_final: 0.4760 (mt-10) REVERT: A 981 ASP cc_start: 0.5107 (m-30) cc_final: 0.4839 (p0) REVERT: A 1224 ARG cc_start: 0.6147 (ttm110) cc_final: 0.5789 (mtm-85) REVERT: B 51 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7465 (mtt-85) REVERT: B 309 VAL cc_start: 0.6300 (OUTLIER) cc_final: 0.5419 (p) outliers start: 33 outliers final: 20 residues processed: 157 average time/residue: 0.2666 time to fit residues: 59.2679 Evaluate side-chains 141 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 79 optimal weight: 0.0770 chunk 33 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 overall best weight: 3.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 729 HIS A1152 HIS A1157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 12274 Z= 0.433 Angle : 0.832 10.748 16898 Z= 0.438 Chirality : 0.051 0.236 1905 Planarity : 0.006 0.064 1975 Dihedral : 22.106 171.409 2150 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.42 % Favored : 92.51 % Rotamer: Outliers : 4.17 % Allowed : 27.60 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -2.00 (0.22), residues: 1357 helix: -0.45 (0.23), residues: 455 sheet: -1.36 (0.31), residues: 231 loop : -1.92 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 856 HIS 0.006 0.001 HIS A 192 PHE 0.042 0.003 PHE A 313 TYR 0.028 0.003 TYR A 818 ARG 0.019 0.001 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 117 time to evaluate : 1.276 Fit side-chains revert: symmetry clash REVERT: A 155 ASN cc_start: 0.7787 (OUTLIER) cc_final: 0.7458 (p0) REVERT: A 281 TYR cc_start: 0.6444 (t80) cc_final: 0.5924 (t80) REVERT: A 348 ASP cc_start: 0.6842 (p0) cc_final: 0.6592 (p0) REVERT: A 510 GLN cc_start: 0.5256 (OUTLIER) cc_final: 0.4699 (mt0) REVERT: A 756 GLU cc_start: 0.5473 (OUTLIER) cc_final: 0.4928 (mt-10) REVERT: A 872 MET cc_start: 0.6879 (ttm) cc_final: 0.6644 (ttm) REVERT: A 934 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7323 (tp) REVERT: A 965 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7765 (t80) REVERT: A 981 ASP cc_start: 0.5718 (m-30) cc_final: 0.5321 (p0) REVERT: A 1054 VAL cc_start: 0.5927 (OUTLIER) cc_final: 0.5678 (m) REVERT: A 1197 HIS cc_start: 0.6546 (OUTLIER) cc_final: 0.6234 (p90) REVERT: A 1224 ARG cc_start: 0.6122 (ttm110) cc_final: 0.5798 (mtm-85) REVERT: A 1234 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6584 (mp) REVERT: B 51 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7591 (mtt-85) outliers start: 45 outliers final: 31 residues processed: 147 average time/residue: 0.2470 time to fit residues: 52.9720 Evaluate side-chains 147 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 107 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1197 HIS Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 98 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 83 optimal weight: 0.0770 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12274 Z= 0.235 Angle : 0.722 9.580 16898 Z= 0.383 Chirality : 0.046 0.205 1905 Planarity : 0.005 0.063 1975 Dihedral : 21.886 171.063 2150 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.23 % Favored : 93.69 % Rotamer: Outliers : 4.17 % Allowed : 27.60 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.15 % 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: -1.73 (0.22), residues: 1357 helix: -0.16 (0.24), residues: 460 sheet: -1.38 (0.32), residues: 231 loop : -1.76 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 781 HIS 0.006 0.001 HIS A 709 PHE 0.029 0.002 PHE A 313 TYR 0.023 0.002 TYR A 490 ARG 0.012 0.001 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 122 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 155 ASN cc_start: 0.7584 (OUTLIER) cc_final: 0.7243 (p0) REVERT: A 281 TYR cc_start: 0.6260 (t80) cc_final: 0.5759 (t80) REVERT: A 322 ARG cc_start: 0.5619 (ptp-170) cc_final: 0.5252 (ptp-170) REVERT: A 510 GLN cc_start: 0.4890 (OUTLIER) cc_final: 0.4647 (mt0) REVERT: A 560 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7375 (mm) REVERT: A 703 ASP cc_start: 0.7217 (p0) cc_final: 0.6921 (p0) REVERT: A 756 GLU cc_start: 0.5395 (OUTLIER) cc_final: 0.4896 (mt-10) REVERT: A 1138 LEU cc_start: 0.5709 (OUTLIER) cc_final: 0.5460 (tt) REVERT: A 1224 ARG cc_start: 0.6152 (ttm110) cc_final: 0.5810 (mtm-85) REVERT: B 51 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7508 (mtt-85) REVERT: B 265 PHE cc_start: 0.5658 (p90) cc_final: 0.5410 (p90) REVERT: B 309 VAL cc_start: 0.6336 (OUTLIER) cc_final: 0.5518 (p) outliers start: 45 outliers final: 29 residues processed: 158 average time/residue: 0.2593 time to fit residues: 59.1210 Evaluate side-chains 147 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 111 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12274 Z= 0.289 Angle : 0.740 10.020 16898 Z= 0.390 Chirality : 0.047 0.193 1905 Planarity : 0.005 0.063 1975 Dihedral : 21.850 172.593 2150 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.97 % Favored : 92.95 % Rotamer: Outliers : 4.35 % Allowed : 27.68 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.72 (0.22), residues: 1357 helix: -0.17 (0.24), residues: 460 sheet: -1.34 (0.32), residues: 230 loop : -1.75 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 856 HIS 0.004 0.001 HIS A 192 PHE 0.025 0.002 PHE A 313 TYR 0.025 0.002 TYR A1148 ARG 0.014 0.001 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 116 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: A 155 ASN cc_start: 0.7640 (OUTLIER) cc_final: 0.7275 (p0) REVERT: A 281 TYR cc_start: 0.6358 (t80) cc_final: 0.5798 (t80) REVERT: A 510 GLN cc_start: 0.4874 (OUTLIER) cc_final: 0.4615 (mt0) REVERT: A 703 ASP cc_start: 0.7289 (p0) cc_final: 0.6904 (p0) REVERT: A 756 GLU cc_start: 0.5389 (OUTLIER) cc_final: 0.4865 (mt-10) REVERT: A 934 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7110 (tp) REVERT: A 965 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7801 (t80) REVERT: A 1138 LEU cc_start: 0.5806 (OUTLIER) cc_final: 0.5535 (tt) REVERT: A 1197 HIS cc_start: 0.6641 (OUTLIER) cc_final: 0.6271 (p90) REVERT: A 1224 ARG cc_start: 0.6182 (ttm110) cc_final: 0.5876 (mtm-85) REVERT: B 51 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7625 (mtt-85) REVERT: B 265 PHE cc_start: 0.5796 (p90) cc_final: 0.5526 (p90) REVERT: B 309 VAL cc_start: 0.6557 (OUTLIER) cc_final: 0.5782 (p) outliers start: 47 outliers final: 36 residues processed: 153 average time/residue: 0.2496 time to fit residues: 55.6186 Evaluate side-chains 151 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 106 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1197 HIS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 chunk 75 optimal weight: 8.9990 chunk 54 optimal weight: 0.5980 chunk 98 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 82 optimal weight: 0.0970 chunk 132 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12274 Z= 0.227 Angle : 0.702 8.996 16898 Z= 0.372 Chirality : 0.046 0.191 1905 Planarity : 0.006 0.097 1975 Dihedral : 21.705 177.995 2150 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.38 % Favored : 93.55 % Rotamer: Outliers : 4.17 % Allowed : 27.68 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.55 (0.23), residues: 1357 helix: -0.01 (0.24), residues: 464 sheet: -1.28 (0.32), residues: 229 loop : -1.66 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 856 HIS 0.004 0.001 HIS A 709 PHE 0.022 0.002 PHE A 965 TYR 0.023 0.002 TYR A1148 ARG 0.020 0.001 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 121 time to evaluate : 1.309 Fit side-chains REVERT: A 155 ASN cc_start: 0.7576 (OUTLIER) cc_final: 0.7228 (p0) REVERT: A 222 ARG cc_start: 0.4856 (tpt90) cc_final: 0.4039 (tpt-90) REVERT: A 281 TYR cc_start: 0.6239 (t80) cc_final: 0.5798 (t80) REVERT: A 703 ASP cc_start: 0.7222 (p0) cc_final: 0.6823 (p0) REVERT: A 756 GLU cc_start: 0.5362 (OUTLIER) cc_final: 0.4863 (mt-10) REVERT: A 1138 LEU cc_start: 0.5627 (OUTLIER) cc_final: 0.5414 (tt) REVERT: A 1197 HIS cc_start: 0.6655 (OUTLIER) cc_final: 0.6291 (p90) REVERT: A 1224 ARG cc_start: 0.6074 (ttm110) cc_final: 0.5799 (mtm-85) REVERT: B 51 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7698 (mtt-85) REVERT: B 265 PHE cc_start: 0.5721 (p90) cc_final: 0.5476 (p90) REVERT: B 309 VAL cc_start: 0.6137 (OUTLIER) cc_final: 0.5700 (p) outliers start: 45 outliers final: 35 residues processed: 157 average time/residue: 0.2638 time to fit residues: 59.5818 Evaluate side-chains 152 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 111 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1197 HIS Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 2.9990 chunk 63 optimal weight: 0.0060 chunk 92 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 128 optimal weight: 0.0020 chunk 111 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.9408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A 912 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12274 Z= 0.238 Angle : 0.706 9.071 16898 Z= 0.373 Chirality : 0.046 0.187 1905 Planarity : 0.005 0.063 1975 Dihedral : 21.644 174.997 2150 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.68 % Favored : 93.25 % Rotamer: Outliers : 3.82 % Allowed : 28.22 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.47 (0.23), residues: 1357 helix: 0.08 (0.24), residues: 463 sheet: -1.23 (0.32), residues: 229 loop : -1.62 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 856 HIS 0.022 0.001 HIS A 215 PHE 0.031 0.002 PHE A 965 TYR 0.024 0.002 TYR A1148 ARG 0.010 0.001 ARG A 222 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 115 time to evaluate : 1.219 Fit side-chains REVERT: A 155 ASN cc_start: 0.7643 (OUTLIER) cc_final: 0.7303 (p0) REVERT: A 222 ARG cc_start: 0.4856 (tpt90) cc_final: 0.3859 (tpt-90) REVERT: A 281 TYR cc_start: 0.6282 (t80) cc_final: 0.5814 (t80) REVERT: A 703 ASP cc_start: 0.7205 (p0) cc_final: 0.6792 (p0) REVERT: A 756 GLU cc_start: 0.5379 (OUTLIER) cc_final: 0.4877 (mt-10) REVERT: A 1138 LEU cc_start: 0.5637 (OUTLIER) cc_final: 0.5384 (tt) REVERT: A 1197 HIS cc_start: 0.6631 (OUTLIER) cc_final: 0.6266 (p90) REVERT: A 1224 ARG cc_start: 0.6056 (ttm110) cc_final: 0.5777 (mtm-85) REVERT: B 51 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7744 (mtt-85) REVERT: B 265 PHE cc_start: 0.5770 (p90) cc_final: 0.5525 (p90) REVERT: B 309 VAL cc_start: 0.6089 (OUTLIER) cc_final: 0.5679 (p) outliers start: 41 outliers final: 35 residues processed: 148 average time/residue: 0.2558 time to fit residues: 53.8942 Evaluate side-chains 151 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 110 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 825 HIS Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1197 HIS Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 0.0070 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 6 optimal weight: 0.0770 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.179718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.158178 restraints weight = 54372.704| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 4.07 r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4133 r_free = 0.4133 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4132 r_free = 0.4132 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12274 Z= 0.226 Angle : 0.695 8.340 16898 Z= 0.367 Chirality : 0.045 0.181 1905 Planarity : 0.005 0.063 1975 Dihedral : 21.569 173.545 2150 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.90 % Allowed : 28.13 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.23), residues: 1357 helix: 0.12 (0.24), residues: 463 sheet: -1.19 (0.33), residues: 228 loop : -1.62 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 856 HIS 0.015 0.001 HIS A 215 PHE 0.030 0.002 PHE A 965 TYR 0.023 0.002 TYR A1148 ARG 0.012 0.001 ARG A 222 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2493.41 seconds wall clock time: 48 minutes 6.02 seconds (2886.02 seconds total)