Starting phenix.real_space_refine on Sun Mar 17 05:03:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4y_14510/03_2024/7z4y_14510.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4y_14510/03_2024/7z4y_14510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4y_14510/03_2024/7z4y_14510.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4y_14510/03_2024/7z4y_14510.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4y_14510/03_2024/7z4y_14510.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4y_14510/03_2024/7z4y_14510.pdb" } resolution = 4.5 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= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 10676 2.51 5 N 2863 2.21 5 O 3115 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 164": "OE1" <-> "OE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 697": "OE1" <-> "OE2" Residue "B ASP 772": "OD1" <-> "OD2" Residue "B ASP 899": "OD1" <-> "OD2" Residue "B TYR 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 697": "OE1" <-> "OE2" Residue "D TYR 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16756 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1184 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 7, 'TRANS': 159} Chain breaks: 1 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 110 Chain: "B" Number of atoms: 7198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7198 Classifications: {'peptide': 930} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 40, 'TRANS': 887} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'ASN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 Chain: "C" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1208 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 7, 'TRANS': 162} Chain breaks: 1 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 14, 'ARG:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 118 Chain: "D" Number of atoms: 7166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7166 Classifications: {'peptide': 930} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 888} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 137 Time building chain proxies: 8.42, per 1000 atoms: 0.50 Number of scatterers: 16756 At special positions: 0 Unit cell: (99.554, 120.34, 233.022, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 3115 8.00 N 2863 7.00 C 10676 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: 6.33 Conformation dependent library (CDL) restraints added in 3.2 seconds 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4182 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 9 sheets defined 47.7% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 43 through 74 removed outlier: 4.060A pdb=" N ARG A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 108 through 123 removed outlier: 3.756A pdb=" N ILE A 112 " --> pdb=" O TYR A 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 153 Processing helix chain 'B' and resid 162 through 166 Processing helix chain 'B' and resid 167 through 181 removed outlier: 3.622A pdb=" N TYR B 173 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 205 removed outlier: 3.982A pdb=" N SER B 195 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN B 196 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN B 197 " --> pdb=" O ALA B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 238 Processing helix chain 'B' and resid 242 through 246 removed outlier: 3.627A pdb=" N GLU B 245 " --> pdb=" O VAL B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 264 through 273 removed outlier: 4.141A pdb=" N GLU B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 300 removed outlier: 4.255A pdb=" N PHE B 292 " --> pdb=" O ASN B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 354 removed outlier: 3.727A pdb=" N PHE B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 384 removed outlier: 3.642A pdb=" N GLU B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG B 384 " --> pdb=" O MET B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 406 removed outlier: 3.682A pdb=" N GLU B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 428 Processing helix chain 'B' and resid 433 through 437 Processing helix chain 'B' and resid 438 through 450 removed outlier: 3.601A pdb=" N GLU B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Proline residue: B 446 - end of helix removed outlier: 3.735A pdb=" N ARG B 450 " --> pdb=" O PRO B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 474 removed outlier: 4.646A pdb=" N GLU B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 466 " --> pdb=" O ILE B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 486 removed outlier: 3.687A pdb=" N ALA B 486 " --> pdb=" O GLU B 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 513 through 522 Processing helix chain 'B' and resid 549 through 553 Processing helix chain 'B' and resid 566 through 576 removed outlier: 3.575A pdb=" N VAL B 570 " --> pdb=" O THR B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 removed outlier: 4.131A pdb=" N GLU B 586 " --> pdb=" O GLU B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 595 Processing helix chain 'B' and resid 597 through 615 WARNING: missing atoms! Processing helix chain 'B' and resid 620 through 645 removed outlier: 4.002A pdb=" N VAL B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR B 643 " --> pdb=" O GLU B 639 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS B 645 " --> pdb=" O GLU B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 654 Processing helix chain 'B' and resid 703 through 710 removed outlier: 3.849A pdb=" N ASN B 709 " --> pdb=" O GLU B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 767 Processing helix chain 'B' and resid 789 through 806 Processing helix chain 'B' and resid 807 through 812 removed outlier: 4.303A pdb=" N ASN B 811 " --> pdb=" O HIS B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 840 Processing helix chain 'B' and resid 848 through 862 removed outlier: 3.744A pdb=" N LEU B 858 " --> pdb=" O ARG B 854 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG B 859 " --> pdb=" O LYS B 855 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG B 860 " --> pdb=" O ARG B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 879 removed outlier: 4.179A pdb=" N ALA B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU B 879 " --> pdb=" O ARG B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 894 removed outlier: 3.988A pdb=" N LEU B 888 " --> pdb=" O ASP B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 910 removed outlier: 4.246A pdb=" N ALA B 907 " --> pdb=" O GLU B 903 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B 908 " --> pdb=" O GLN B 904 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 910 " --> pdb=" O THR B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 913 No H-bonds generated for 'chain 'B' and resid 911 through 913' Processing helix chain 'B' and resid 925 through 948 Proline residue: B 931 - end of helix removed outlier: 3.539A pdb=" N CYS B 938 " --> pdb=" O GLN B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 962 removed outlier: 4.242A pdb=" N PHE B 962 " --> pdb=" O TYR B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 974 Processing helix chain 'B' and resid 978 through 983 Processing helix chain 'B' and resid 989 through 1012 removed outlier: 3.678A pdb=" N CYS B 996 " --> pdb=" O SER B 992 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET B 997 " --> pdb=" O ILE B 993 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG B 998 " --> pdb=" O ILE B 994 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B1000 " --> pdb=" O CYS B 996 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN B1009 " --> pdb=" O ARG B1005 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS B1012 " --> pdb=" O CYS B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1029 removed outlier: 3.531A pdb=" N LYS B1029 " --> pdb=" O GLU B1025 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 74 removed outlier: 5.091A pdb=" N LYS C 71 " --> pdb=" O ASN C 67 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG C 72 " --> pdb=" O GLN C 68 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 109 removed outlier: 3.911A pdb=" N GLN C 107 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR C 108 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 126 removed outlier: 4.219A pdb=" N VAL C 120 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS C 121 " --> pdb=" O SER C 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 153 removed outlier: 3.937A pdb=" N ASN D 153 " --> pdb=" O GLN D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 166 removed outlier: 3.797A pdb=" N GLY D 166 " --> pdb=" O THR D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 181 removed outlier: 4.206A pdb=" N ALA D 171 " --> pdb=" O LYS D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 204 removed outlier: 3.669A pdb=" N GLU D 204 " --> pdb=" O ARG D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 238 removed outlier: 4.140A pdb=" N MET D 235 " --> pdb=" O ILE D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 253 through 257 removed outlier: 3.501A pdb=" N MET D 257 " --> pdb=" O ILE D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 273 removed outlier: 3.576A pdb=" N THR D 269 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE D 270 " --> pdb=" O TRP D 266 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE D 271 " --> pdb=" O GLU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 300 removed outlier: 4.166A pdb=" N PHE D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N HIS D 300 " --> pdb=" O ILE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 353 removed outlier: 4.217A pdb=" N PHE D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN D 344 " --> pdb=" O GLU D 340 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR D 345 " --> pdb=" O ASP D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 384 removed outlier: 3.756A pdb=" N ARG D 384 " --> pdb=" O MET D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 407 Processing helix chain 'D' and resid 413 through 430 removed outlier: 3.548A pdb=" N GLU D 421 " --> pdb=" O LYS D 417 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN D 426 " --> pdb=" O GLU D 422 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D 427 " --> pdb=" O VAL D 423 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N CYS D 430 " --> pdb=" O ASN D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 437 removed outlier: 4.056A pdb=" N ASP D 435 " --> pdb=" O LEU D 431 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 451 Proline residue: D 446 - end of helix removed outlier: 3.611A pdb=" N ARG D 450 " --> pdb=" O PRO D 446 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY D 451 " --> pdb=" O LEU D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 474 removed outlier: 3.550A pdb=" N GLU D 473 " --> pdb=" O ILE D 469 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 522 removed outlier: 4.391A pdb=" N GLN D 519 " --> pdb=" O GLY D 515 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET D 520 " --> pdb=" O GLU D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 576 Processing helix chain 'D' and resid 580 through 587 removed outlier: 3.528A pdb=" N MET D 584 " --> pdb=" O ASN D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 596 Processing helix chain 'D' and resid 597 through 616 WARNING: missing atoms! removed outlier: 3.803A pdb=" N ILE D 615 " --> pdb=" O GLN D 611 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 616 " --> pdb=" O TYR D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 641 removed outlier: 4.080A pdb=" N GLU D 641 " --> pdb=" O GLY D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 654 Processing helix chain 'D' and resid 703 through 709 removed outlier: 4.153A pdb=" N ASN D 709 " --> pdb=" O GLU D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 736 No H-bonds generated for 'chain 'D' and resid 734 through 736' Processing helix chain 'D' and resid 755 through 770 removed outlier: 4.229A pdb=" N VAL D 759 " --> pdb=" O ASN D 755 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU D 760 " --> pdb=" O ARG D 756 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS D 768 " --> pdb=" O GLN D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 805 Processing helix chain 'D' and resid 814 through 845 removed outlier: 3.955A pdb=" N VAL D 818 " --> pdb=" O ASN D 814 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA D 842 " --> pdb=" O GLU D 838 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ARG D 843 " --> pdb=" O LEU D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 848 through 862 Processing helix chain 'D' and resid 871 through 878 removed outlier: 4.180A pdb=" N ALA D 877 " --> pdb=" O LYS D 873 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS D 878 " --> pdb=" O GLY D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 895 removed outlier: 3.624A pdb=" N LEU D 888 " --> pdb=" O ASP D 884 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU D 890 " --> pdb=" O LEU D 886 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET D 891 " --> pdb=" O LEU D 887 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 907 removed outlier: 3.707A pdb=" N ALA D 907 " --> pdb=" O GLU D 903 " (cutoff:3.500A) Processing helix chain 'D' and resid 909 through 913 Processing helix chain 'D' and resid 925 through 948 Proline residue: D 931 - end of helix removed outlier: 3.561A pdb=" N GLN D 936 " --> pdb=" O LEU D 932 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL D 945 " --> pdb=" O ARG D 941 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 962 removed outlier: 3.522A pdb=" N SER D 960 " --> pdb=" O GLU D 956 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE D 962 " --> pdb=" O TYR D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 974 Processing helix chain 'D' and resid 978 through 983 Processing helix chain 'D' and resid 989 through 1012 removed outlier: 3.779A pdb=" N ILE D 993 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS D 996 " --> pdb=" O SER D 992 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET D 997 " --> pdb=" O ILE D 993 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG D 998 " --> pdb=" O ILE D 994 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU D1003 " --> pdb=" O ARG D 999 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG D1005 " --> pdb=" O GLU D1001 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN D1006 " --> pdb=" O GLU D1002 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS D1012 " --> pdb=" O CYS D1008 " (cutoff:3.500A) Processing helix chain 'D' and resid 1019 through 1029 removed outlier: 3.730A pdb=" N LYS D1029 " --> pdb=" O GLU D1025 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 182 removed outlier: 3.773A pdb=" N VAL A 172 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE C 97 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TYR A 174 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU C 95 " --> pdb=" O TYR A 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 100 through 101 removed outlier: 7.001A pdb=" N SER B 156 " --> pdb=" O HIS B 305 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ILE B 307 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU B 158 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 157 " --> pdb=" O PHE B 281 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N SER B 283 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL B 159 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE B 186 " --> pdb=" O TRP B 248 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 250 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLY B 210 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 329 through 330 removed outlier: 3.587A pdb=" N VAL B 539 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL B 496 " --> pdb=" O ILE B 536 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N MET B 538 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N PHE B 498 " --> pdb=" O MET B 538 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL B 389 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ALA B 481 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE B 391 " --> pdb=" O ALA B 481 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 502 through 504 Processing sheet with id=AA5, first strand: chain 'B' and resid 725 through 732 removed outlier: 5.975A pdb=" N LEU B 699 " --> pdb=" O VAL B 674 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL B 674 " --> pdb=" O LEU B 699 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N ARG B 701 " --> pdb=" O GLY B 672 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N GLY B 672 " --> pdb=" O ARG B 701 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 738 " --> pdb=" O LYS B 661 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 99 through 101 removed outlier: 6.967A pdb=" N SER D 156 " --> pdb=" O HIS D 305 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ILE D 307 " --> pdb=" O SER D 156 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU D 158 " --> pdb=" O ILE D 307 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL D 157 " --> pdb=" O TYR D 279 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ARG D 184 " --> pdb=" O TRP D 248 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N ILE D 250 " --> pdb=" O ARG D 184 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE D 186 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL D 185 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET D 227 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N PHE D 187 " --> pdb=" O MET D 227 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 316 through 322 removed outlier: 3.515A pdb=" N VAL D 539 " --> pdb=" O PHE D 321 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET D 538 " --> pdb=" O PHE D 498 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 502 through 504 Processing sheet with id=AA9, first strand: chain 'D' and resid 727 through 732 removed outlier: 3.796A pdb=" N VAL D 673 " --> pdb=" O LEU D 699 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ASP D 668 " --> pdb=" O ASN D 664 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ASN D 664 " --> pdb=" O ASP D 668 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY D 670 " --> pdb=" O VAL D 662 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL D 662 " --> pdb=" O GLY D 670 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ARG D 658 " --> pdb=" O VAL D 674 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LEU D 659 " --> pdb=" O SER D 740 " (cutoff:3.500A) 696 hydrogen bonds defined for protein. 1995 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.11 Time building geometry restraints manager: 6.83 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: 3651 1.33 - 1.45: 3485 1.45 - 1.57: 9772 1.57 - 1.69: 0 1.69 - 1.81: 166 Bond restraints: 17074 Sorted by residual: bond pdb=" N VAL D 845 " pdb=" CA VAL D 845 " ideal model delta sigma weight residual 1.459 1.507 -0.048 1.12e-02 7.97e+03 1.82e+01 bond pdb=" C THR D 844 " pdb=" N VAL D 845 " ideal model delta sigma weight residual 1.332 1.350 -0.018 5.60e-03 3.19e+04 1.03e+01 bond pdb=" N LYS D 841 " pdb=" CA LYS D 841 " ideal model delta sigma weight residual 1.459 1.492 -0.034 1.16e-02 7.43e+03 8.49e+00 bond pdb=" N ILE B 547 " pdb=" CA ILE B 547 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.21e-02 6.83e+03 7.94e+00 bond pdb=" N VAL B 845 " pdb=" CA VAL B 845 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.94e+00 ... (remaining 17069 not shown) Histogram of bond angle deviations from ideal: 97.77 - 105.03: 332 105.03 - 112.29: 8423 112.29 - 119.54: 5988 119.54 - 126.80: 8241 126.80 - 134.06: 171 Bond angle restraints: 23155 Sorted by residual: angle pdb=" C VAL D 845 " pdb=" CA VAL D 845 " pdb=" CB VAL D 845 " ideal model delta sigma weight residual 111.74 106.47 5.27 9.40e-01 1.13e+00 3.14e+01 angle pdb=" C VAL D 845 " pdb=" N LEU D 846 " pdb=" CA LEU D 846 " ideal model delta sigma weight residual 121.76 129.80 -8.04 1.51e+00 4.39e-01 2.84e+01 angle pdb=" N GLU B 765 " pdb=" CA GLU B 765 " pdb=" CB GLU B 765 " ideal model delta sigma weight residual 110.28 117.29 -7.01 1.55e+00 4.16e-01 2.04e+01 angle pdb=" N GLU B 201 " pdb=" CA GLU B 201 " pdb=" CB GLU B 201 " ideal model delta sigma weight residual 110.01 116.25 -6.24 1.45e+00 4.76e-01 1.85e+01 angle pdb=" N LYS D 182 " pdb=" CA LYS D 182 " pdb=" C LYS D 182 " ideal model delta sigma weight residual 111.28 116.61 -5.33 1.35e+00 5.49e-01 1.56e+01 ... (remaining 23150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 9418 17.85 - 35.70: 801 35.70 - 53.56: 141 53.56 - 71.41: 29 71.41 - 89.26: 16 Dihedral angle restraints: 10405 sinusoidal: 3972 harmonic: 6433 Sorted by residual: dihedral pdb=" CA HIS D 300 " pdb=" C HIS D 300 " pdb=" N LYS D 301 " pdb=" CA LYS D 301 " ideal model delta harmonic sigma weight residual 180.00 153.17 26.83 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA GLN D1006 " pdb=" C GLN D1006 " pdb=" N MET D1007 " pdb=" CA MET D1007 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ARG C 79 " pdb=" C ARG C 79 " pdb=" N PRO C 80 " pdb=" CA PRO C 80 " ideal model delta harmonic sigma weight residual -180.00 -154.70 -25.30 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 10402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2574 0.111 - 0.221: 89 0.221 - 0.331: 5 0.331 - 0.442: 0 0.442 - 0.552: 1 Chirality restraints: 2669 Sorted by residual: chirality pdb=" CB VAL D 845 " pdb=" CA VAL D 845 " pdb=" CG1 VAL D 845 " pdb=" CG2 VAL D 845 " both_signs ideal model delta sigma weight residual False -2.63 -2.08 -0.55 2.00e-01 2.50e+01 7.63e+00 chirality pdb=" CA ARG B 751 " pdb=" N ARG B 751 " pdb=" C ARG B 751 " pdb=" CB ARG B 751 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA ILE B 547 " pdb=" N ILE B 547 " pdb=" C ILE B 547 " pdb=" CB ILE B 547 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2666 not shown) Planarity restraints: 3004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 778 " 0.061 5.00e-02 4.00e+02 9.30e-02 1.38e+01 pdb=" N PRO B 779 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO B 779 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 779 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 126 " -0.060 5.00e-02 4.00e+02 9.09e-02 1.32e+01 pdb=" N PRO B 127 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO B 127 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 127 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 118 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.20e+00 pdb=" C ASN A 118 " -0.046 2.00e-02 2.50e+03 pdb=" O ASN A 118 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU A 119 " 0.016 2.00e-02 2.50e+03 ... (remaining 3001 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 533 2.70 - 3.25: 17764 3.25 - 3.80: 25897 3.80 - 4.35: 32819 4.35 - 4.90: 52006 Nonbonded interactions: 129019 Sorted by model distance: nonbonded pdb=" OD1 ASN B 676 " pdb=" N PHE B 677 " model vdw 2.154 2.520 nonbonded pdb=" O PRO D 808 " pdb=" O LEU D 809 " model vdw 2.163 3.040 nonbonded pdb=" O HIS B 802 " pdb=" OG SER B 806 " model vdw 2.205 2.440 nonbonded pdb=" O LEU D 404 " pdb=" OG1 THR D 407 " model vdw 2.218 2.440 nonbonded pdb=" O THR D 972 " pdb=" OG1 THR D 975 " model vdw 2.227 2.440 ... (remaining 129014 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 43 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 through 89 or (resid 90 through 91 and (na \ me N or name CA or name C or name O or name CB )) or resid 92 through 100 or (re \ sid 101 through 103 and (name N or name CA or name C or name O or name CB )) or \ resid 104 through 120 or (resid 121 and (name N or name CA or name C or name O o \ r name CB )) or resid 122 through 123 or (resid 124 through 125 and (name N or n \ ame CA or name C or name O or name CB )) or resid 126 through 131 or (resid 132 \ through 136 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 7 through 148 or (resid 149 through 165 and (name N or name CA or name C or name \ O or name CB )) or resid 166 through 195 or (resid 196 and (name N or name CA o \ r name C or name O or name CB )) or resid 197 through 198 or (resid 199 and (nam \ e N or name CA or name C or name O or name CB )) or resid 200 through 218)) selection = (chain 'C' and ((resid 43 through 66 and (name N or name CA or name C or name O \ or name CB )) or resid 67 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 84 or (resid 85 through 91 and (n \ ame N or name CA or name C or name O or name CB )) or resid 92 through 130 or (r \ esid 131 through 136 and (name N or name CA or name C or name O or name CB )) or \ resid 137 through 147 or (resid 148 through 165 and (name N or name CA or name \ C or name O or name CB )) or resid 166 through 168 or (resid 169 and (name N or \ name CA or name C or name O or name CB )) or resid 170 through 211 or (resid 212 \ through 214 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 15 through 218)) } ncs_group { reference = (chain 'B' and (resid 96 through 619 or (resid 620 through 621 and (name N or na \ me CA or name C or name O or name CB )) or resid 622 through 637 or (resid 638 t \ hrough 639 and (name N or name CA or name C or name O or name CB )) or resid 640 \ through 703 or (resid 704 and (name N or name CA or name C or name O or name CB \ )) or resid 705 through 724 or (resid 725 through 726 and (name N or name CA or \ name C or name O or name CB )) or resid 727 through 744 or (resid 745 and (name \ N or name CA or name C or name O or name CB )) or resid 746 through 773 or (res \ id 774 and (name N or name CA or name C or name O or name CB )) or resid 775 thr \ ough 792 or (resid 793 through 794 and (name N or name CA or name C or name O or \ name CB )) or resid 795 or (resid 796 through 801 and (name N or name CA or nam \ e C or name O or name CB )) or resid 802 or (resid 803 through 805 and (name N o \ r name CA or name C or name O or name CB )) or resid 806 through 1042)) selection = (chain 'D' and (resid 96 through 629 or (resid 630 through 636 and (name N or na \ me CA or name C or name O or name CB )) or resid 637 through 641 or (resid 642 a \ nd (name N or name CA or name C or name O or name CB )) or resid 643 through 663 \ or (resid 664 through 665 and (name N or name CA or name C or name O or name CB \ )) or resid 666 or (resid 667 and (name N or name CA or name C or name O or nam \ e CB )) or resid 668 through 677 or (resid 678 through 684 and (name N or name C \ A or name C or name O or name CB )) or resid 685 through 718 or (resid 719 and ( \ name N or name CA or name C or name O or name CB )) or resid 720 or (resid 721 t \ hrough 723 and (name N or name CA or name C or name O or name CB )) or resid 724 \ through 730 or (resid 731 and (name N or name CA or name C or name O or name CB \ )) or resid 732 through 763 or (resid 764 and (name N or name CA or name C or n \ ame O or name CB )) or resid 765 through 779 or (resid 780 and (name N or name C \ A or name C or name O or name CB )) or resid 781 through 1042)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.020 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 44.430 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.070 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 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 : 0.003 0.059 17074 Z= 0.217 Angle : 0.741 10.093 23155 Z= 0.416 Chirality : 0.050 0.552 2669 Planarity : 0.005 0.093 3004 Dihedral : 14.192 89.259 6223 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.60 % Allowed : 1.88 % Favored : 97.52 % Rotamer: Outliers : 0.46 % Allowed : 0.58 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.17), residues: 2181 helix: 0.04 (0.17), residues: 895 sheet: 0.39 (0.39), residues: 170 loop : -2.89 (0.16), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 266 HIS 0.007 0.001 HIS B 318 PHE 0.023 0.002 PHE A 115 TYR 0.028 0.001 TYR A 108 ARG 0.006 0.000 ARG B 933 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 436 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASN cc_start: 0.8288 (m110) cc_final: 0.7965 (m-40) REVERT: B 140 LEU cc_start: 0.8880 (mm) cc_final: 0.8551 (mm) REVERT: B 146 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8568 (mt-10) REVERT: B 257 MET cc_start: 0.7481 (mmm) cc_final: 0.5736 (mmm) REVERT: B 279 TYR cc_start: 0.8480 (m-80) cc_final: 0.8162 (m-80) REVERT: B 347 MET cc_start: 0.8997 (ptp) cc_final: 0.8550 (mtm) REVERT: B 390 ILE cc_start: 0.9542 (tp) cc_final: 0.9338 (tp) REVERT: B 456 HIS cc_start: 0.8256 (p90) cc_final: 0.7749 (p-80) REVERT: B 482 THR cc_start: 0.6658 (m) cc_final: 0.6360 (m) REVERT: B 495 THR cc_start: 0.8944 (t) cc_final: 0.8637 (m) REVERT: B 538 MET cc_start: 0.8538 (ppp) cc_final: 0.7804 (ppp) REVERT: B 650 CYS cc_start: 0.7930 (p) cc_final: 0.7646 (p) REVERT: B 750 LEU cc_start: 0.7007 (mp) cc_final: 0.6334 (tp) REVERT: B 809 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.5962 (mt) REVERT: C 74 LEU cc_start: 0.8443 (mt) cc_final: 0.8161 (mt) REVERT: C 100 MET cc_start: 0.8568 (mmm) cc_final: 0.8282 (mmm) REVERT: D 122 TYR cc_start: 0.8639 (p90) cc_final: 0.8315 (t80) REVERT: D 202 MET cc_start: 0.7902 (ptp) cc_final: 0.7346 (ptp) REVERT: D 203 TYR cc_start: 0.8334 (t80) cc_final: 0.7575 (t80) REVERT: D 212 MET cc_start: 0.1027 (tpt) cc_final: -0.1036 (mmt) REVERT: D 281 PHE cc_start: 0.7716 (m-10) cc_final: 0.7291 (m-10) REVERT: D 299 LEU cc_start: 0.8030 (mt) cc_final: 0.7432 (mt) REVERT: D 308 TYR cc_start: 0.7701 (t80) cc_final: 0.7427 (t80) REVERT: D 382 MET cc_start: 0.7822 (mmp) cc_final: 0.7603 (mmp) REVERT: D 487 MET cc_start: 0.4312 (tpt) cc_final: 0.4093 (tpt) REVERT: D 676 ASN cc_start: 0.8478 (t0) cc_final: 0.7907 (t0) REVERT: D 1031 LYS cc_start: 0.8574 (pttm) cc_final: 0.7998 (tptt) outliers start: 8 outliers final: 2 residues processed: 441 average time/residue: 0.2712 time to fit residues: 184.5464 Evaluate side-chains 372 residues out of total 1955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 369 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 184 optimal weight: 0.8980 chunk 165 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 88 optimal weight: 0.0970 chunk 171 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 HIS B 904 GLN B1006 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 HIS D 300 HIS ** D 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 ASN D 904 GLN ** D 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17074 Z= 0.184 Angle : 0.597 8.537 23155 Z= 0.315 Chirality : 0.043 0.168 2669 Planarity : 0.005 0.064 3004 Dihedral : 4.687 20.805 2346 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.67 % Favored : 91.06 % Rotamer: Outliers : 0.06 % Allowed : 5.84 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.18), residues: 2181 helix: 0.63 (0.17), residues: 952 sheet: 0.47 (0.39), residues: 184 loop : -2.83 (0.17), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 266 HIS 0.011 0.001 HIS C 209 PHE 0.017 0.001 PHE A 166 TYR 0.013 0.001 TYR C 174 ARG 0.007 0.001 ARG B 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 445 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.9052 (mmtm) cc_final: 0.8670 (mmtm) REVERT: A 75 ASN cc_start: 0.9009 (m-40) cc_final: 0.8802 (m-40) REVERT: A 179 CYS cc_start: 0.7779 (m) cc_final: 0.7334 (m) REVERT: B 140 LEU cc_start: 0.8888 (mm) cc_final: 0.8567 (mm) REVERT: B 253 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7153 (tm-30) REVERT: B 257 MET cc_start: 0.7339 (mmm) cc_final: 0.6598 (mmt) REVERT: B 347 MET cc_start: 0.8895 (ptp) cc_final: 0.8587 (ptt) REVERT: B 456 HIS cc_start: 0.8350 (p90) cc_final: 0.7771 (p-80) REVERT: B 495 THR cc_start: 0.9109 (t) cc_final: 0.8876 (m) REVERT: B 538 MET cc_start: 0.8630 (ppp) cc_final: 0.7866 (ppp) REVERT: B 700 LEU cc_start: 0.9446 (mm) cc_final: 0.9121 (mm) REVERT: B 979 PHE cc_start: 0.8703 (t80) cc_final: 0.8055 (t80) REVERT: C 169 VAL cc_start: 0.8528 (t) cc_final: 0.8198 (p) REVERT: C 203 TYR cc_start: 0.7743 (p90) cc_final: 0.7169 (p90) REVERT: D 122 TYR cc_start: 0.8605 (p90) cc_final: 0.8285 (t80) REVERT: D 212 MET cc_start: 0.0594 (tpt) cc_final: -0.1074 (mmt) REVERT: D 281 PHE cc_start: 0.7642 (m-10) cc_final: 0.7246 (m-10) REVERT: D 296 ILE cc_start: 0.9314 (mm) cc_final: 0.9114 (mm) REVERT: D 299 LEU cc_start: 0.7852 (mt) cc_final: 0.7588 (mt) REVERT: D 308 TYR cc_start: 0.7645 (t80) cc_final: 0.7416 (t80) REVERT: D 487 MET cc_start: 0.4516 (tpt) cc_final: 0.4275 (tpt) REVERT: D 587 LYS cc_start: 0.8108 (mmtt) cc_final: 0.7873 (mtpt) REVERT: D 676 ASN cc_start: 0.8386 (t0) cc_final: 0.8111 (t0) REVERT: D 872 MET cc_start: 0.5698 (pmm) cc_final: 0.5468 (pmm) REVERT: D 940 LYS cc_start: 0.9273 (pptt) cc_final: 0.9067 (tptt) REVERT: D 995 ARG cc_start: 0.8562 (ppt170) cc_final: 0.8209 (ppt170) REVERT: D 996 CYS cc_start: 0.8606 (p) cc_final: 0.7018 (p) REVERT: D 997 MET cc_start: 0.8675 (ppp) cc_final: 0.8391 (ppp) REVERT: D 1031 LYS cc_start: 0.8519 (pttm) cc_final: 0.7947 (tptt) outliers start: 1 outliers final: 0 residues processed: 446 average time/residue: 0.2689 time to fit residues: 183.0443 Evaluate side-chains 362 residues out of total 1955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 110 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 135 optimal weight: 20.0000 chunk 54 optimal weight: 0.0370 chunk 199 optimal weight: 0.7980 chunk 215 optimal weight: 0.7980 chunk 177 optimal weight: 0.9980 chunk 197 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 159 optimal weight: 0.6980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 GLN B1006 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 568 ASN ** D 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 ASN D 904 GLN ** D 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17074 Z= 0.165 Angle : 0.572 8.415 23155 Z= 0.303 Chirality : 0.042 0.148 2669 Planarity : 0.004 0.072 3004 Dihedral : 4.616 22.540 2346 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.12 % Favored : 91.70 % Rotamer: Outliers : 0.12 % Allowed : 3.82 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.18), residues: 2181 helix: 0.75 (0.17), residues: 952 sheet: 0.43 (0.39), residues: 188 loop : -2.66 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 266 HIS 0.008 0.001 HIS D 594 PHE 0.035 0.001 PHE B1023 TYR 0.011 0.001 TYR B 256 ARG 0.005 0.000 ARG B 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 445 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.9012 (mmtm) cc_final: 0.8766 (mmtm) REVERT: A 199 GLU cc_start: 0.7283 (tm-30) cc_final: 0.7039 (tm-30) REVERT: B 140 LEU cc_start: 0.8951 (mm) cc_final: 0.8636 (mm) REVERT: B 251 PHE cc_start: 0.7771 (m-80) cc_final: 0.7560 (m-80) REVERT: B 257 MET cc_start: 0.7407 (mmm) cc_final: 0.7143 (mmt) REVERT: B 347 MET cc_start: 0.8872 (ptp) cc_final: 0.8570 (ptt) REVERT: B 456 HIS cc_start: 0.8465 (p90) cc_final: 0.7897 (p-80) REVERT: B 460 LEU cc_start: 0.9313 (mt) cc_final: 0.8978 (mt) REVERT: B 538 MET cc_start: 0.8640 (ppp) cc_final: 0.7821 (ppp) REVERT: B 650 CYS cc_start: 0.7979 (p) cc_final: 0.7746 (p) REVERT: B 944 LYS cc_start: 0.9421 (mmpt) cc_final: 0.9098 (mmmt) REVERT: C 203 TYR cc_start: 0.7633 (p90) cc_final: 0.7401 (p90) REVERT: D 122 TYR cc_start: 0.8421 (p90) cc_final: 0.8120 (t80) REVERT: D 212 MET cc_start: 0.0465 (tpt) cc_final: -0.1534 (mmt) REVERT: D 243 MET cc_start: 0.7988 (ppp) cc_final: 0.7512 (pmm) REVERT: D 281 PHE cc_start: 0.7656 (m-10) cc_final: 0.7194 (m-10) REVERT: D 308 TYR cc_start: 0.7629 (t80) cc_final: 0.7399 (t80) REVERT: D 511 TRP cc_start: 0.8303 (m100) cc_final: 0.7619 (m100) REVERT: D 940 LYS cc_start: 0.9319 (pptt) cc_final: 0.9084 (tptt) REVERT: D 994 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7539 (mt) REVERT: D 995 ARG cc_start: 0.8630 (ppt170) cc_final: 0.8223 (ppt170) REVERT: D 996 CYS cc_start: 0.8692 (p) cc_final: 0.7141 (p) outliers start: 2 outliers final: 0 residues processed: 446 average time/residue: 0.2686 time to fit residues: 182.9430 Evaluate side-chains 373 residues out of total 1955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 372 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 196 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 199 optimal weight: 8.9990 chunk 211 optimal weight: 0.4980 chunk 104 optimal weight: 0.0060 chunk 189 optimal weight: 0.0370 chunk 57 optimal weight: 7.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS B 440 GLN B 904 GLN B1006 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 GLN D 655 GLN D 904 GLN ** D 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 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 : 0.002 0.048 17074 Z= 0.158 Angle : 0.557 7.979 23155 Z= 0.291 Chirality : 0.042 0.149 2669 Planarity : 0.004 0.077 3004 Dihedral : 4.466 21.794 2346 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.80 % Favored : 91.01 % Rotamer: Outliers : 0.06 % Allowed : 3.70 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.18), residues: 2181 helix: 0.90 (0.18), residues: 950 sheet: 0.28 (0.39), residues: 198 loop : -2.58 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 266 HIS 0.010 0.001 HIS A 204 PHE 0.015 0.001 PHE C 115 TYR 0.013 0.001 TYR A 108 ARG 0.006 0.000 ARG B 933 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 444 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.9100 (mmtm) cc_final: 0.8825 (mmtm) REVERT: A 110 GLN cc_start: 0.8288 (mm-40) cc_final: 0.8076 (mm-40) REVERT: A 179 CYS cc_start: 0.8036 (m) cc_final: 0.7616 (m) REVERT: A 199 GLU cc_start: 0.7296 (tm-30) cc_final: 0.6862 (tm-30) REVERT: B 140 LEU cc_start: 0.8891 (mm) cc_final: 0.8553 (mm) REVERT: B 251 PHE cc_start: 0.7923 (m-80) cc_final: 0.7331 (m-80) REVERT: B 347 MET cc_start: 0.8831 (ptp) cc_final: 0.8601 (ptt) REVERT: B 456 HIS cc_start: 0.8447 (p90) cc_final: 0.7940 (p-80) REVERT: B 460 LEU cc_start: 0.9301 (mt) cc_final: 0.8961 (mt) REVERT: B 520 MET cc_start: 0.8390 (mmt) cc_final: 0.8106 (mmt) REVERT: B 538 MET cc_start: 0.8670 (ppp) cc_final: 0.7865 (ppp) REVERT: B 743 ARG cc_start: 0.7622 (ttm-80) cc_final: 0.7414 (ttm-80) REVERT: B 944 LYS cc_start: 0.9445 (mmpt) cc_final: 0.9138 (mmmt) REVERT: B 985 MET cc_start: 0.7239 (pmm) cc_final: 0.7025 (pmm) REVERT: B 995 ARG cc_start: 0.9174 (pmt-80) cc_final: 0.8739 (pmt-80) REVERT: B 1007 MET cc_start: 0.8979 (tpt) cc_final: 0.8636 (tpt) REVERT: B 1023 PHE cc_start: 0.8983 (m-80) cc_final: 0.8720 (m-80) REVERT: C 73 LYS cc_start: 0.9002 (mppt) cc_final: 0.8695 (mptt) REVERT: C 203 TYR cc_start: 0.7621 (p90) cc_final: 0.7342 (p90) REVERT: D 122 TYR cc_start: 0.8424 (p90) cc_final: 0.8111 (t80) REVERT: D 212 MET cc_start: 0.0405 (tpt) cc_final: -0.1269 (mmt) REVERT: D 243 MET cc_start: 0.8029 (ppp) cc_final: 0.7585 (pmm) REVERT: D 281 PHE cc_start: 0.7572 (m-10) cc_final: 0.7172 (m-10) REVERT: D 973 TRP cc_start: 0.8338 (t-100) cc_final: 0.7822 (t-100) REVERT: D 996 CYS cc_start: 0.8724 (p) cc_final: 0.8309 (p) outliers start: 1 outliers final: 0 residues processed: 444 average time/residue: 0.2645 time to fit residues: 179.8777 Evaluate side-chains 369 residues out of total 1955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 176 optimal weight: 0.7980 chunk 120 optimal weight: 0.0060 chunk 3 optimal weight: 0.0470 chunk 157 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 180 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 108 optimal weight: 0.2980 chunk 190 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 GLN B 767 GLN B 904 GLN B1006 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 GLN D 676 ASN D 904 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 17074 Z= 0.152 Angle : 0.565 7.993 23155 Z= 0.293 Chirality : 0.042 0.156 2669 Planarity : 0.004 0.079 3004 Dihedral : 4.428 22.099 2346 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.84 % Favored : 91.93 % Rotamer: Outliers : 0.12 % Allowed : 2.78 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.18), residues: 2181 helix: 0.95 (0.18), residues: 950 sheet: 0.29 (0.39), residues: 198 loop : -2.55 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 266 HIS 0.008 0.001 HIS D 594 PHE 0.013 0.001 PHE A 115 TYR 0.014 0.001 TYR B 256 ARG 0.004 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 448 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.9134 (mmtm) cc_final: 0.8833 (mmtm) REVERT: A 96 GLN cc_start: 0.8973 (tm-30) cc_final: 0.8613 (tm-30) REVERT: A 100 MET cc_start: 0.8843 (mmm) cc_final: 0.8630 (mmm) REVERT: A 179 CYS cc_start: 0.7973 (m) cc_final: 0.7470 (m) REVERT: A 190 GLU cc_start: 0.7815 (pt0) cc_final: 0.7591 (tt0) REVERT: A 199 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6880 (tm-30) REVERT: B 140 LEU cc_start: 0.8882 (mm) cc_final: 0.8556 (mm) REVERT: B 347 MET cc_start: 0.8928 (ptp) cc_final: 0.8633 (ptt) REVERT: B 455 HIS cc_start: 0.7648 (t-90) cc_final: 0.6976 (t-170) REVERT: B 456 HIS cc_start: 0.8486 (p90) cc_final: 0.8096 (p-80) REVERT: B 460 LEU cc_start: 0.9291 (mt) cc_final: 0.8955 (mt) REVERT: B 485 PHE cc_start: 0.8009 (t80) cc_final: 0.7720 (t80) REVERT: B 538 MET cc_start: 0.8610 (ppp) cc_final: 0.7867 (ppp) REVERT: B 743 ARG cc_start: 0.7540 (ttm-80) cc_final: 0.7299 (ttm-80) REVERT: B 944 LYS cc_start: 0.9430 (mmpt) cc_final: 0.9081 (mmmt) REVERT: B 1007 MET cc_start: 0.8966 (tpt) cc_final: 0.8565 (tpt) REVERT: B 1023 PHE cc_start: 0.9002 (m-80) cc_final: 0.8710 (m-80) REVERT: C 73 LYS cc_start: 0.8963 (mppt) cc_final: 0.8566 (mptt) REVERT: C 111 GLU cc_start: 0.8906 (pm20) cc_final: 0.8642 (pm20) REVERT: C 174 TYR cc_start: 0.8733 (m-80) cc_final: 0.8505 (m-80) REVERT: C 203 TYR cc_start: 0.7646 (p90) cc_final: 0.7036 (p90) REVERT: C 205 GLN cc_start: 0.8770 (tm-30) cc_final: 0.7836 (pm20) REVERT: D 122 TYR cc_start: 0.8421 (p90) cc_final: 0.8111 (t80) REVERT: D 212 MET cc_start: 0.0250 (tpt) cc_final: -0.1436 (mmt) REVERT: D 243 MET cc_start: 0.8034 (ppp) cc_final: 0.7549 (pmm) REVERT: D 281 PHE cc_start: 0.7603 (m-10) cc_final: 0.7100 (m-10) REVERT: D 308 TYR cc_start: 0.7634 (t80) cc_final: 0.7409 (t80) REVERT: D 471 PHE cc_start: 0.9180 (t80) cc_final: 0.8775 (t80) REVERT: D 538 MET cc_start: 0.6755 (mmp) cc_final: 0.6417 (mmp) REVERT: D 572 ASN cc_start: 0.7139 (m110) cc_final: 0.6890 (p0) REVERT: D 676 ASN cc_start: 0.8429 (t160) cc_final: 0.8196 (t0) REVERT: D 777 LEU cc_start: 0.9326 (mt) cc_final: 0.9100 (mt) REVERT: D 973 TRP cc_start: 0.8328 (t-100) cc_final: 0.7846 (t-100) REVERT: D 996 CYS cc_start: 0.8644 (p) cc_final: 0.8243 (p) outliers start: 2 outliers final: 0 residues processed: 448 average time/residue: 0.2625 time to fit residues: 179.4907 Evaluate side-chains 377 residues out of total 1955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 71 optimal weight: 0.0470 chunk 190 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 318 HIS B 440 GLN B 904 GLN B1006 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 GLN D 676 ASN D 904 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17074 Z= 0.173 Angle : 0.576 7.582 23155 Z= 0.304 Chirality : 0.043 0.197 2669 Planarity : 0.004 0.081 3004 Dihedral : 4.419 21.524 2346 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.67 % Favored : 91.10 % Rotamer: Outliers : 0.06 % Allowed : 2.49 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.18), residues: 2181 helix: 0.84 (0.18), residues: 964 sheet: 0.26 (0.39), residues: 198 loop : -2.50 (0.18), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 266 HIS 0.009 0.001 HIS D 594 PHE 0.015 0.001 PHE A 115 TYR 0.013 0.001 TYR B 256 ARG 0.007 0.000 ARG B 933 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 443 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.9116 (mmtm) cc_final: 0.8833 (mmtm) REVERT: A 96 GLN cc_start: 0.8973 (tm-30) cc_final: 0.8588 (tm-30) REVERT: A 110 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7868 (mm-40) REVERT: A 179 CYS cc_start: 0.8050 (m) cc_final: 0.7610 (m) REVERT: A 199 GLU cc_start: 0.7417 (tm-30) cc_final: 0.6985 (tm-30) REVERT: B 140 LEU cc_start: 0.8905 (mm) cc_final: 0.8594 (mm) REVERT: B 251 PHE cc_start: 0.7810 (m-80) cc_final: 0.7437 (m-80) REVERT: B 257 MET cc_start: 0.6915 (mmp) cc_final: 0.5685 (mmp) REVERT: B 347 MET cc_start: 0.8896 (ptp) cc_final: 0.8586 (ptt) REVERT: B 456 HIS cc_start: 0.8514 (p90) cc_final: 0.8162 (p-80) REVERT: B 460 LEU cc_start: 0.9294 (mt) cc_final: 0.8962 (mt) REVERT: B 538 MET cc_start: 0.8634 (ppp) cc_final: 0.7828 (ppp) REVERT: B 743 ARG cc_start: 0.7727 (ttm-80) cc_final: 0.7512 (ttm-80) REVERT: B 944 LYS cc_start: 0.9424 (mmpt) cc_final: 0.9068 (mmmt) REVERT: B 979 PHE cc_start: 0.8772 (t80) cc_final: 0.8173 (t80) REVERT: B 1007 MET cc_start: 0.9003 (tpt) cc_final: 0.8641 (tpt) REVERT: B 1023 PHE cc_start: 0.8994 (m-80) cc_final: 0.8743 (m-80) REVERT: C 114 GLU cc_start: 0.9048 (pm20) cc_final: 0.8840 (mp0) REVERT: C 136 PHE cc_start: 0.8531 (m-10) cc_final: 0.8265 (t80) REVERT: C 203 TYR cc_start: 0.7754 (p90) cc_final: 0.7537 (p90) REVERT: D 122 TYR cc_start: 0.8420 (p90) cc_final: 0.8102 (t80) REVERT: D 202 MET cc_start: 0.8132 (ptp) cc_final: 0.7618 (ptp) REVERT: D 212 MET cc_start: 0.0382 (tpt) cc_final: -0.1383 (mmt) REVERT: D 281 PHE cc_start: 0.7604 (m-10) cc_final: 0.7040 (m-10) REVERT: D 299 LEU cc_start: 0.8277 (mt) cc_final: 0.8067 (mt) REVERT: D 308 TYR cc_start: 0.7601 (t80) cc_final: 0.7393 (t80) REVERT: D 471 PHE cc_start: 0.9168 (t80) cc_final: 0.8733 (t80) REVERT: D 538 MET cc_start: 0.6806 (mmp) cc_final: 0.6497 (mmp) REVERT: D 777 LEU cc_start: 0.9343 (mt) cc_final: 0.9107 (mt) REVERT: D 973 TRP cc_start: 0.8281 (t-100) cc_final: 0.7810 (t-100) REVERT: D 996 CYS cc_start: 0.8681 (p) cc_final: 0.7078 (p) outliers start: 1 outliers final: 0 residues processed: 443 average time/residue: 0.2615 time to fit residues: 176.0398 Evaluate side-chains 362 residues out of total 1955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 204 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 120 optimal weight: 0.3980 chunk 154 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 chunk 128 optimal weight: 0.0770 chunk 97 optimal weight: 1.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 GLN B 904 GLN B1006 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17074 Z= 0.171 Angle : 0.578 7.823 23155 Z= 0.303 Chirality : 0.043 0.177 2669 Planarity : 0.004 0.081 3004 Dihedral : 4.413 21.976 2346 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.34 % Favored : 91.43 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % 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: -0.96 (0.18), residues: 2181 helix: 0.97 (0.18), residues: 954 sheet: 0.22 (0.38), residues: 199 loop : -2.51 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 266 HIS 0.008 0.001 HIS D 594 PHE 0.014 0.001 PHE A 115 TYR 0.016 0.001 TYR A 108 ARG 0.005 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 448 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.9118 (mmtm) cc_final: 0.8844 (mmtm) REVERT: A 96 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8519 (tm-30) REVERT: A 109 HIS cc_start: 0.7581 (t-90) cc_final: 0.7230 (t-90) REVERT: A 179 CYS cc_start: 0.8005 (m) cc_final: 0.7630 (m) REVERT: A 199 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7077 (tm-30) REVERT: B 140 LEU cc_start: 0.8412 (mm) cc_final: 0.8050 (mm) REVERT: B 257 MET cc_start: 0.6882 (mmp) cc_final: 0.5591 (mmp) REVERT: B 294 GLU cc_start: 0.8809 (pt0) cc_final: 0.8557 (pt0) REVERT: B 347 MET cc_start: 0.8896 (ptp) cc_final: 0.8582 (ptt) REVERT: B 456 HIS cc_start: 0.8481 (p90) cc_final: 0.8156 (p-80) REVERT: B 460 LEU cc_start: 0.9310 (mt) cc_final: 0.8974 (mt) REVERT: B 538 MET cc_start: 0.8653 (ppp) cc_final: 0.7861 (ppp) REVERT: B 743 ARG cc_start: 0.7679 (ttm-80) cc_final: 0.7409 (ttm-80) REVERT: B 944 LYS cc_start: 0.9442 (mmpt) cc_final: 0.9087 (mmmt) REVERT: B 995 ARG cc_start: 0.9136 (pmt-80) cc_final: 0.8712 (pmt-80) REVERT: B 1007 MET cc_start: 0.9037 (tpt) cc_final: 0.8754 (tpt) REVERT: B 1023 PHE cc_start: 0.9083 (m-80) cc_final: 0.8791 (m-80) REVERT: C 74 LEU cc_start: 0.8530 (mt) cc_final: 0.8270 (mt) REVERT: C 136 PHE cc_start: 0.8577 (m-10) cc_final: 0.8243 (t80) REVERT: C 203 TYR cc_start: 0.7758 (p90) cc_final: 0.7322 (p90) REVERT: C 205 GLN cc_start: 0.8634 (tm-30) cc_final: 0.7757 (pm20) REVERT: D 122 TYR cc_start: 0.8368 (p90) cc_final: 0.8048 (t80) REVERT: D 202 MET cc_start: 0.8055 (ptp) cc_final: 0.7521 (ptp) REVERT: D 212 MET cc_start: 0.0301 (tpt) cc_final: -0.1488 (mmt) REVERT: D 216 VAL cc_start: 0.6325 (t) cc_final: 0.6078 (t) REVERT: D 266 TRP cc_start: 0.7094 (t60) cc_final: 0.6817 (t60) REVERT: D 281 PHE cc_start: 0.7717 (m-10) cc_final: 0.7103 (m-10) REVERT: D 299 LEU cc_start: 0.8212 (mt) cc_final: 0.8010 (mt) REVERT: D 308 TYR cc_start: 0.7586 (t80) cc_final: 0.7373 (t80) REVERT: D 471 PHE cc_start: 0.9179 (t80) cc_final: 0.8741 (t80) REVERT: D 676 ASN cc_start: 0.8379 (t0) cc_final: 0.8133 (t0) REVERT: D 743 ARG cc_start: 0.8515 (mtp85) cc_final: 0.8258 (mtm110) REVERT: D 940 LYS cc_start: 0.9225 (pptt) cc_final: 0.9003 (tptt) REVERT: D 973 TRP cc_start: 0.8300 (t-100) cc_final: 0.7859 (t-100) REVERT: D 985 MET cc_start: 0.7824 (mpp) cc_final: 0.6938 (pmm) outliers start: 0 outliers final: 0 residues processed: 448 average time/residue: 0.2798 time to fit residues: 192.1179 Evaluate side-chains 365 residues out of total 1955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 130 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 126 optimal weight: 0.0970 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 19 optimal weight: 0.0770 chunk 165 optimal weight: 4.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 440 GLN B 519 GLN B 904 GLN B1006 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 GLN D 568 ASN D 904 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 17074 Z= 0.159 Angle : 0.589 8.617 23155 Z= 0.309 Chirality : 0.043 0.167 2669 Planarity : 0.004 0.081 3004 Dihedral : 4.392 21.024 2346 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.57 % Favored : 91.20 % Rotamer: Outliers : 0.12 % Allowed : 1.10 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % 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: -0.94 (0.19), residues: 2181 helix: 0.95 (0.18), residues: 957 sheet: 0.18 (0.38), residues: 204 loop : -2.46 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 266 HIS 0.008 0.001 HIS D 594 PHE 0.021 0.001 PHE D 343 TYR 0.012 0.001 TYR B 256 ARG 0.005 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 447 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.9120 (mmtm) cc_final: 0.8361 (mmtm) REVERT: A 75 ASN cc_start: 0.9038 (m-40) cc_final: 0.8701 (m-40) REVERT: A 96 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8432 (tm-30) REVERT: A 100 MET cc_start: 0.8800 (mmm) cc_final: 0.8527 (mmm) REVERT: A 179 CYS cc_start: 0.7994 (m) cc_final: 0.7619 (m) REVERT: A 199 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7133 (tm-30) REVERT: B 140 LEU cc_start: 0.8428 (mm) cc_final: 0.8106 (mm) REVERT: B 257 MET cc_start: 0.7033 (mmp) cc_final: 0.5829 (mmp) REVERT: B 294 GLU cc_start: 0.8787 (pt0) cc_final: 0.8556 (pt0) REVERT: B 347 MET cc_start: 0.8904 (ptp) cc_final: 0.8608 (ptt) REVERT: B 456 HIS cc_start: 0.8467 (p90) cc_final: 0.8129 (p-80) REVERT: B 460 LEU cc_start: 0.9272 (mt) cc_final: 0.8948 (mt) REVERT: B 538 MET cc_start: 0.8628 (ppp) cc_final: 0.7906 (ppp) REVERT: B 743 ARG cc_start: 0.7574 (ttm-80) cc_final: 0.7329 (ttm-80) REVERT: B 944 LYS cc_start: 0.9445 (mmpt) cc_final: 0.9104 (mmmt) REVERT: B 995 ARG cc_start: 0.9122 (pmt-80) cc_final: 0.8777 (pmt-80) REVERT: B 1007 MET cc_start: 0.9026 (tpt) cc_final: 0.8753 (tpt) REVERT: B 1023 PHE cc_start: 0.9078 (m-80) cc_final: 0.8799 (m-80) REVERT: C 136 PHE cc_start: 0.8635 (m-10) cc_final: 0.8227 (t80) REVERT: C 203 TYR cc_start: 0.7711 (p90) cc_final: 0.7438 (p90) REVERT: C 205 GLN cc_start: 0.8702 (tm-30) cc_final: 0.7874 (pm20) REVERT: D 122 TYR cc_start: 0.8363 (p90) cc_final: 0.8045 (t80) REVERT: D 202 MET cc_start: 0.8140 (ptp) cc_final: 0.7592 (ptp) REVERT: D 212 MET cc_start: 0.0278 (tpt) cc_final: -0.1562 (mmt) REVERT: D 216 VAL cc_start: 0.6268 (t) cc_final: 0.6011 (t) REVERT: D 268 GLU cc_start: 0.8101 (tp30) cc_final: 0.7840 (tp30) REVERT: D 281 PHE cc_start: 0.7757 (m-10) cc_final: 0.7050 (m-10) REVERT: D 299 LEU cc_start: 0.8302 (mt) cc_final: 0.8011 (mt) REVERT: D 308 TYR cc_start: 0.7596 (t80) cc_final: 0.7352 (t80) REVERT: D 471 PHE cc_start: 0.9173 (t80) cc_final: 0.8724 (t80) REVERT: D 743 ARG cc_start: 0.8416 (mtp85) cc_final: 0.8123 (mtm110) REVERT: D 973 TRP cc_start: 0.8239 (t-100) cc_final: 0.7802 (t-100) REVERT: D 985 MET cc_start: 0.7742 (mpp) cc_final: 0.6877 (pmm) REVERT: D 996 CYS cc_start: 0.8694 (p) cc_final: 0.8317 (p) outliers start: 2 outliers final: 0 residues processed: 447 average time/residue: 0.2535 time to fit residues: 173.9233 Evaluate side-chains 372 residues out of total 1955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 192 optimal weight: 0.8980 chunk 202 optimal weight: 0.0970 chunk 184 optimal weight: 0.9980 chunk 196 optimal weight: 0.6980 chunk 118 optimal weight: 7.9990 chunk 85 optimal weight: 0.0980 chunk 154 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 177 optimal weight: 0.0000 chunk 186 optimal weight: 0.4980 chunk 129 optimal weight: 0.0050 overall best weight: 0.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 GLN ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 ASN B 904 GLN B1006 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 HIS D 291 GLN D 904 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 17074 Z= 0.155 Angle : 0.610 10.289 23155 Z= 0.315 Chirality : 0.043 0.172 2669 Planarity : 0.004 0.081 3004 Dihedral : 4.334 20.953 2346 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.16 % Favored : 91.61 % Rotamer: Outliers : 0.12 % Allowed : 0.64 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % 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: -0.90 (0.19), residues: 2181 helix: 0.95 (0.18), residues: 957 sheet: 0.24 (0.38), residues: 205 loop : -2.43 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 266 HIS 0.007 0.001 HIS D 594 PHE 0.019 0.001 PHE D 343 TYR 0.013 0.001 TYR B 256 ARG 0.004 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 453 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.9104 (mmtm) cc_final: 0.8838 (mmtm) REVERT: A 96 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8505 (tm-30) REVERT: A 179 CYS cc_start: 0.7916 (m) cc_final: 0.7587 (m) REVERT: A 199 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7077 (tm-30) REVERT: B 140 LEU cc_start: 0.8451 (mm) cc_final: 0.7981 (mm) REVERT: B 156 SER cc_start: 0.7232 (m) cc_final: 0.6601 (p) REVERT: B 257 MET cc_start: 0.6896 (mmp) cc_final: 0.4966 (mmp) REVERT: B 347 MET cc_start: 0.8887 (ptp) cc_final: 0.8614 (ptt) REVERT: B 456 HIS cc_start: 0.8397 (p90) cc_final: 0.8094 (p-80) REVERT: B 460 LEU cc_start: 0.9265 (mt) cc_final: 0.8968 (mt) REVERT: B 482 THR cc_start: 0.6734 (m) cc_final: 0.6529 (m) REVERT: B 538 MET cc_start: 0.8627 (ppp) cc_final: 0.7926 (ppp) REVERT: B 944 LYS cc_start: 0.9441 (mmpt) cc_final: 0.9134 (mmmt) REVERT: B 999 ARG cc_start: 0.8862 (mpp-170) cc_final: 0.8498 (mpp-170) REVERT: B 1007 MET cc_start: 0.9013 (tpt) cc_final: 0.8772 (tpt) REVERT: B 1023 PHE cc_start: 0.9074 (m-80) cc_final: 0.8843 (m-80) REVERT: C 110 GLN cc_start: 0.9116 (mp10) cc_final: 0.8768 (mp10) REVERT: C 136 PHE cc_start: 0.8610 (m-10) cc_final: 0.8091 (t80) REVERT: D 122 TYR cc_start: 0.8362 (p90) cc_final: 0.8038 (t80) REVERT: D 202 MET cc_start: 0.8121 (ptp) cc_final: 0.7560 (ptp) REVERT: D 212 MET cc_start: 0.0066 (tpt) cc_final: -0.1688 (mmt) REVERT: D 216 VAL cc_start: 0.6332 (t) cc_final: 0.6074 (t) REVERT: D 281 PHE cc_start: 0.7749 (m-10) cc_final: 0.7100 (m-10) REVERT: D 299 LEU cc_start: 0.8323 (mt) cc_final: 0.8007 (mt) REVERT: D 308 TYR cc_start: 0.7660 (t80) cc_final: 0.7450 (t80) REVERT: D 471 PHE cc_start: 0.9165 (t80) cc_final: 0.8722 (t80) REVERT: D 538 MET cc_start: 0.6752 (mmp) cc_final: 0.6421 (mmp) REVERT: D 733 VAL cc_start: 0.8903 (m) cc_final: 0.8690 (m) REVERT: D 743 ARG cc_start: 0.8331 (mtp85) cc_final: 0.8051 (mtm110) REVERT: D 863 PHE cc_start: 0.6006 (m-80) cc_final: 0.5561 (m-80) REVERT: D 973 TRP cc_start: 0.8309 (t-100) cc_final: 0.7838 (t-100) REVERT: D 985 MET cc_start: 0.7739 (mpp) cc_final: 0.6820 (pmm) outliers start: 2 outliers final: 0 residues processed: 454 average time/residue: 0.2660 time to fit residues: 183.4170 Evaluate side-chains 374 residues out of total 1955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 207 optimal weight: 7.9990 chunk 126 optimal weight: 0.1980 chunk 98 optimal weight: 0.8980 chunk 144 optimal weight: 0.2980 chunk 218 optimal weight: 9.9990 chunk 200 optimal weight: 0.7980 chunk 173 optimal weight: 0.0000 chunk 18 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 138 optimal weight: 10.0000 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 GLN ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 GLN B1006 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 HIS D 291 GLN D 904 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17074 Z= 0.170 Angle : 0.617 10.224 23155 Z= 0.320 Chirality : 0.043 0.227 2669 Planarity : 0.004 0.084 3004 Dihedral : 4.354 21.320 2346 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.71 % Favored : 91.06 % Rotamer: Outliers : 0.06 % Allowed : 0.35 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % 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: -0.85 (0.19), residues: 2181 helix: 0.97 (0.18), residues: 955 sheet: 0.49 (0.40), residues: 191 loop : -2.38 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 266 HIS 0.011 0.001 HIS B 300 PHE 0.014 0.001 PHE A 166 TYR 0.012 0.001 TYR B 203 ARG 0.004 0.000 ARG B 743 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 441 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.9084 (mmtm) cc_final: 0.8788 (mmtm) REVERT: A 96 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8584 (tm-30) REVERT: A 179 CYS cc_start: 0.8017 (m) cc_final: 0.7658 (m) REVERT: A 199 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7091 (tm-30) REVERT: B 140 LEU cc_start: 0.8462 (mm) cc_final: 0.8007 (mm) REVERT: B 156 SER cc_start: 0.7262 (m) cc_final: 0.6600 (p) REVERT: B 257 MET cc_start: 0.6948 (mmp) cc_final: 0.5005 (mmp) REVERT: B 347 MET cc_start: 0.8878 (ptp) cc_final: 0.8584 (ptt) REVERT: B 456 HIS cc_start: 0.8414 (p90) cc_final: 0.8156 (p-80) REVERT: B 460 LEU cc_start: 0.9254 (mt) cc_final: 0.8982 (mt) REVERT: B 538 MET cc_start: 0.8653 (ppp) cc_final: 0.7948 (ppp) REVERT: B 650 CYS cc_start: 0.7936 (p) cc_final: 0.7720 (p) REVERT: B 696 VAL cc_start: 0.9396 (t) cc_final: 0.9101 (p) REVERT: B 944 LYS cc_start: 0.9443 (mmpt) cc_final: 0.9144 (mmmt) REVERT: B 995 ARG cc_start: 0.9120 (pmt-80) cc_final: 0.8524 (pmt-80) REVERT: B 1007 MET cc_start: 0.9021 (tpt) cc_final: 0.8783 (tpt) REVERT: B 1023 PHE cc_start: 0.9067 (m-80) cc_final: 0.8858 (m-80) REVERT: C 110 GLN cc_start: 0.9134 (mp10) cc_final: 0.8868 (mp10) REVERT: C 111 GLU cc_start: 0.8854 (pm20) cc_final: 0.8597 (pm20) REVERT: C 136 PHE cc_start: 0.8630 (m-10) cc_final: 0.8236 (t80) REVERT: D 122 TYR cc_start: 0.8363 (p90) cc_final: 0.8042 (t80) REVERT: D 173 TYR cc_start: 0.7792 (t80) cc_final: 0.7391 (t80) REVERT: D 202 MET cc_start: 0.8025 (ptp) cc_final: 0.7486 (ptp) REVERT: D 212 MET cc_start: 0.0178 (tpt) cc_final: -0.1570 (mmt) REVERT: D 216 VAL cc_start: 0.6178 (t) cc_final: 0.5895 (t) REVERT: D 281 PHE cc_start: 0.7757 (m-10) cc_final: 0.7174 (m-10) REVERT: D 299 LEU cc_start: 0.8319 (mt) cc_final: 0.8028 (mt) REVERT: D 308 TYR cc_start: 0.7659 (t80) cc_final: 0.7454 (t80) REVERT: D 471 PHE cc_start: 0.9154 (t80) cc_final: 0.8711 (t80) REVERT: D 538 MET cc_start: 0.6756 (mmp) cc_final: 0.6446 (mmp) REVERT: D 573 LEU cc_start: 0.7448 (mt) cc_final: 0.7228 (mt) REVERT: D 733 VAL cc_start: 0.8970 (m) cc_final: 0.8716 (m) REVERT: D 743 ARG cc_start: 0.8377 (mtp85) cc_final: 0.8076 (mtm110) REVERT: D 783 MET cc_start: 0.8296 (mpp) cc_final: 0.8031 (mpp) REVERT: D 973 TRP cc_start: 0.8289 (t-100) cc_final: 0.7859 (t-100) REVERT: D 985 MET cc_start: 0.7713 (mpp) cc_final: 0.6773 (pmm) outliers start: 1 outliers final: 0 residues processed: 441 average time/residue: 0.2680 time to fit residues: 180.8383 Evaluate side-chains 371 residues out of total 1955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 185 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 160 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 174 optimal weight: 0.0050 chunk 72 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 22 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 overall best weight: 0.5372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 GLN ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 GLN B1006 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 GLN D 904 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.132767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.093125 restraints weight = 60329.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.095492 restraints weight = 40937.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.097221 restraints weight = 31054.227| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17074 Z= 0.176 Angle : 0.618 10.074 23155 Z= 0.321 Chirality : 0.043 0.213 2669 Planarity : 0.004 0.080 3004 Dihedral : 4.391 21.858 2346 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.57 % Favored : 91.20 % Rotamer: Outliers : 0.06 % Allowed : 0.58 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % 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: -0.84 (0.19), residues: 2181 helix: 1.05 (0.18), residues: 951 sheet: 0.57 (0.41), residues: 176 loop : -2.41 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 266 HIS 0.007 0.001 HIS B 300 PHE 0.015 0.001 PHE D 343 TYR 0.011 0.001 TYR D 256 ARG 0.005 0.000 ARG D 998 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4205.42 seconds wall clock time: 75 minutes 54.82 seconds (4554.82 seconds total)