Starting phenix.real_space_refine on Sat Mar 16 01:01:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isk_35693/03_2024/8isk_35693_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isk_35693/03_2024/8isk_35693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isk_35693/03_2024/8isk_35693.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isk_35693/03_2024/8isk_35693.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isk_35693/03_2024/8isk_35693_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isk_35693/03_2024/8isk_35693_updated.pdb" } resolution = 3.3 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= 0.020 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 95 5.16 5 C 8436 2.51 5 N 2282 2.21 5 O 2460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B GLU 837": "OE1" <-> "OE2" Residue "B GLU 1071": "OE1" <-> "OE2" Residue "B ARG 1082": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13273 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6581 Classifications: {'peptide': 845} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 812} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 6606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 848, 6606 Classifications: {'peptide': 848} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 815} Chain breaks: 5 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.27, per 1000 atoms: 0.55 Number of scatterers: 13273 At special positions: 0 Unit cell: (110.5, 129.2, 153, 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 95 16.00 O 2460 8.00 N 2282 7.00 C 8436 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.36 Conformation dependent library (CDL) restraints added in 2.4 seconds 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3170 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 15 sheets defined 36.0% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 200 through 214 removed outlier: 3.903A pdb=" N ALA A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LYS A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 235 Processing helix chain 'A' and resid 277 through 285 Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 383 through 427 removed outlier: 3.904A pdb=" N ASN A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS A 402 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU A 403 " --> pdb=" O HIS A 399 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 481 Processing helix chain 'A' and resid 573 through 590 removed outlier: 3.720A pdb=" N ILE A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 788 Processing helix chain 'A' and resid 792 through 795 No H-bonds generated for 'chain 'A' and resid 792 through 795' Processing helix chain 'A' and resid 817 through 832 Processing helix chain 'A' and resid 879 through 908 removed outlier: 4.204A pdb=" N GLN A 893 " --> pdb=" O GLN A 889 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N THR A 894 " --> pdb=" O ALA A 890 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 925 removed outlier: 3.692A pdb=" N GLY A 915 " --> pdb=" O LYS A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 950 removed outlier: 3.604A pdb=" N ILE A 949 " --> pdb=" O GLN A 945 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 950 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 992 removed outlier: 3.821A pdb=" N VAL A 985 " --> pdb=" O ALA A 981 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE A 987 " --> pdb=" O SER A 983 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLY A 988 " --> pdb=" O GLN A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1005 No H-bonds generated for 'chain 'A' and resid 1002 through 1005' Processing helix chain 'A' and resid 1014 through 1029 removed outlier: 3.706A pdb=" N PHE A1023 " --> pdb=" O ILE A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1077 Processing helix chain 'A' and resid 1086 through 1100 Processing helix chain 'B' and resid 73 through 77 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 136 through 145 removed outlier: 4.036A pdb=" N ALA B 141 " --> pdb=" O PRO B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 188 through 193 Proline residue: B 192 - end of helix Processing helix chain 'B' and resid 206 through 210 Processing helix chain 'B' and resid 220 through 235 Processing helix chain 'B' and resid 277 through 285 removed outlier: 3.582A pdb=" N LYS B 285 " --> pdb=" O PHE B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 331 Processing helix chain 'B' and resid 383 through 427 removed outlier: 3.958A pdb=" N SER B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE B 415 " --> pdb=" O ARG B 411 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 437 removed outlier: 4.094A pdb=" N VAL B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 432 through 437' Processing helix chain 'B' and resid 468 through 481 removed outlier: 3.740A pdb=" N ARG B 472 " --> pdb=" O GLU B 468 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 496 No H-bonds generated for 'chain 'B' and resid 493 through 496' Processing helix chain 'B' and resid 573 through 590 removed outlier: 3.632A pdb=" N ILE B 579 " --> pdb=" O GLU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 788 Processing helix chain 'B' and resid 792 through 794 No H-bonds generated for 'chain 'B' and resid 792 through 794' Processing helix chain 'B' and resid 817 through 832 Processing helix chain 'B' and resid 879 through 883 Processing helix chain 'B' and resid 891 through 894 No H-bonds generated for 'chain 'B' and resid 891 through 894' Processing helix chain 'B' and resid 903 through 925 removed outlier: 3.843A pdb=" N HIS B 907 " --> pdb=" O SER B 903 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP B 910 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS B 911 " --> pdb=" O HIS B 907 " (cutoff:3.500A) Proline residue: B 912 - end of helix Processing helix chain 'B' and resid 930 through 953 removed outlier: 3.526A pdb=" N GLN B 935 " --> pdb=" O GLU B 931 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP B 952 " --> pdb=" O LYS B 948 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU B 953 " --> pdb=" O ILE B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 959 Processing helix chain 'B' and resid 974 through 992 removed outlier: 3.984A pdb=" N VAL B 985 " --> pdb=" O ALA B 981 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE B 987 " --> pdb=" O SER B 983 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLY B 988 " --> pdb=" O GLN B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1005 No H-bonds generated for 'chain 'B' and resid 1002 through 1005' Processing helix chain 'B' and resid 1013 through 1030 Processing helix chain 'B' and resid 1070 through 1076 Processing helix chain 'B' and resid 1086 through 1101 removed outlier: 3.921A pdb=" N LEU B1100 " --> pdb=" O ASN B1096 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N MET B1101 " --> pdb=" O LEU B1097 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 80 through 82 Processing sheet with id= B, first strand: chain 'A' and resid 85 through 90 Processing sheet with id= C, first strand: chain 'A' and resid 251 through 258 removed outlier: 6.608A pdb=" N ALA A 242 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU A 256 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL A 240 " --> pdb=" O GLU A 256 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP A 368 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL A 342 " --> pdb=" O TRP A 368 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU A 370 " --> pdb=" O MET A 340 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N MET A 340 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N VAL A 372 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU A 338 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N HIS A 374 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA A 336 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 458 through 463 removed outlier: 3.713A pdb=" N ALA A 452 " --> pdb=" O PHE A 523 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 521 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A 514 " --> pdb=" O LEU A 522 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 531 through 535 Processing sheet with id= F, first strand: chain 'A' and resid 777 through 780 removed outlier: 6.071A pdb=" N GLY A 770 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TRP A 780 " --> pdb=" O ILE A 768 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE A 768 " --> pdb=" O TRP A 780 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA A 771 " --> pdb=" O VAL A 870 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LYS A 860 " --> pdb=" O THR A 868 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N VAL A 870 " --> pdb=" O ASN A 858 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN A 858 " --> pdb=" O VAL A 870 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N CYS A 872 " --> pdb=" O SER A 856 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER A 856 " --> pdb=" O CYS A 872 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE A 874 " --> pdb=" O LEU A 854 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A 854 " --> pdb=" O ILE A 874 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 970 through 972 removed outlier: 3.670A pdb=" N PHE A 972 " --> pdb=" O VAL A1009 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A1009 " --> pdb=" O PHE A 972 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 995 through 1000 removed outlier: 3.996A pdb=" N SER A1041 " --> pdb=" O ASN A 999 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER A1036 " --> pdb=" O GLN A1064 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A1064 " --> pdb=" O SER A1036 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 157 through 160 removed outlier: 3.635A pdb=" N ALA B 99 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 251 through 258 removed outlier: 6.851A pdb=" N ALA B 242 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU B 256 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 240 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 372 " --> pdb=" O MET B 241 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP B 368 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL B 342 " --> pdb=" O TRP B 368 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU B 370 " --> pdb=" O MET B 340 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N MET B 340 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL B 372 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU B 338 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 458 through 463 removed outlier: 3.553A pdb=" N ALA B 451 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 531 through 534 removed outlier: 3.773A pdb=" N ALA B 531 " --> pdb=" O VAL B 564 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 564 " --> pdb=" O ALA B 531 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE B 533 " --> pdb=" O GLU B 562 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU B 562 " --> pdb=" O ILE B 533 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'B' and resid 777 through 780 removed outlier: 6.059A pdb=" N GLY B 770 " --> pdb=" O SER B 778 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TRP B 780 " --> pdb=" O ILE B 768 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE B 768 " --> pdb=" O TRP B 780 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 771 " --> pdb=" O VAL B 870 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS B 860 " --> pdb=" O THR B 868 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL B 870 " --> pdb=" O ASN B 858 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASN B 858 " --> pdb=" O VAL B 870 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N CYS B 872 " --> pdb=" O SER B 856 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER B 856 " --> pdb=" O CYS B 872 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE B 874 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU B 854 " --> pdb=" O ILE B 874 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 970 through 973 Processing sheet with id= O, first strand: chain 'B' and resid 995 through 999 removed outlier: 3.956A pdb=" N SER B1041 " --> pdb=" O ASN B 999 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP B1104 " --> pdb=" O THR B1119 " (cutoff:3.500A) 563 hydrogen bonds defined for protein. 1620 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: 4.69 Time building geometry restraints manager: 5.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4221 1.34 - 1.46: 1744 1.46 - 1.57: 7411 1.57 - 1.69: 0 1.69 - 1.81: 148 Bond restraints: 13524 Sorted by residual: bond pdb=" N ILE B 508 " pdb=" CA ILE B 508 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.84e+00 bond pdb=" CAP O6E B1201 " pdb=" CBL O6E B1201 " ideal model delta sigma weight residual 1.448 1.388 0.060 2.00e-02 2.50e+03 8.92e+00 bond pdb=" CAB O6E A1201 " pdb=" CBI O6E A1201 " ideal model delta sigma weight residual 1.449 1.390 0.059 2.00e-02 2.50e+03 8.68e+00 bond pdb=" CAP O6E A1201 " pdb=" CBL O6E A1201 " ideal model delta sigma weight residual 1.448 1.389 0.059 2.00e-02 2.50e+03 8.62e+00 bond pdb=" CAB O6E B1201 " pdb=" CBI O6E B1201 " ideal model delta sigma weight residual 1.449 1.392 0.057 2.00e-02 2.50e+03 8.20e+00 ... (remaining 13519 not shown) Histogram of bond angle deviations from ideal: 98.78 - 106.31: 364 106.31 - 113.84: 7675 113.84 - 121.37: 6779 121.37 - 128.91: 3355 128.91 - 136.44: 99 Bond angle restraints: 18272 Sorted by residual: angle pdb=" CA GLY B 197 " pdb=" C GLY B 197 " pdb=" O GLY B 197 " ideal model delta sigma weight residual 122.56 118.51 4.05 1.03e+00 9.43e-01 1.55e+01 angle pdb=" C HIS B 250 " pdb=" CA HIS B 250 " pdb=" CB HIS B 250 " ideal model delta sigma weight residual 109.37 116.81 -7.44 1.91e+00 2.74e-01 1.52e+01 angle pdb=" N ILE B 442 " pdb=" CA ILE B 442 " pdb=" C ILE B 442 " ideal model delta sigma weight residual 112.29 108.89 3.40 9.40e-01 1.13e+00 1.31e+01 angle pdb=" CA LEU A 764 " pdb=" CB LEU A 764 " pdb=" CG LEU A 764 " ideal model delta sigma weight residual 116.30 128.77 -12.47 3.50e+00 8.16e-02 1.27e+01 angle pdb=" CAV O6E B1201 " pdb=" CAO O6E B1201 " pdb=" CBO O6E B1201 " ideal model delta sigma weight residual 125.76 136.44 -10.68 3.00e+00 1.11e-01 1.27e+01 ... (remaining 18267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 7128 17.91 - 35.83: 870 35.83 - 53.74: 197 53.74 - 71.66: 21 71.66 - 89.57: 20 Dihedral angle restraints: 8236 sinusoidal: 3349 harmonic: 4887 Sorted by residual: dihedral pdb=" CD ARG B1082 " pdb=" NE ARG B1082 " pdb=" CZ ARG B1082 " pdb=" NH1 ARG B1082 " ideal model delta sinusoidal sigma weight residual 0.00 -46.34 46.34 1 1.00e+01 1.00e-02 2.97e+01 dihedral pdb=" CD ARG A1082 " pdb=" NE ARG A1082 " pdb=" CZ ARG A1082 " pdb=" NH1 ARG A1082 " ideal model delta sinusoidal sigma weight residual 0.00 -34.97 34.97 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" CA TYR B 202 " pdb=" C TYR B 202 " pdb=" N LYS B 203 " pdb=" CA LYS B 203 " ideal model delta harmonic sigma weight residual 180.00 160.46 19.54 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 8233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1680 0.054 - 0.109: 320 0.109 - 0.163: 56 0.163 - 0.218: 6 0.218 - 0.272: 1 Chirality restraints: 2063 Sorted by residual: chirality pdb=" CA TYR B 202 " pdb=" N TYR B 202 " pdb=" C TYR B 202 " pdb=" CB TYR B 202 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA LEU A1092 " pdb=" N LEU A1092 " pdb=" C LEU A1092 " pdb=" CB LEU A1092 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA LEU B1020 " pdb=" N LEU B1020 " pdb=" C LEU B1020 " pdb=" CB LEU B1020 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.84e-01 ... (remaining 2060 not shown) Planarity restraints: 2344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAB O6E A1201 " 0.621 2.00e-02 2.50e+03 3.13e-01 2.45e+03 pdb=" CAP O6E A1201 " -0.059 2.00e-02 2.50e+03 pdb=" CAS O6E A1201 " -0.495 2.00e-02 2.50e+03 pdb=" CAW O6E A1201 " 0.020 2.00e-02 2.50e+03 pdb=" CBC O6E A1201 " -0.120 2.00e-02 2.50e+03 pdb=" CBI O6E A1201 " 0.172 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " 0.295 2.00e-02 2.50e+03 pdb=" CBM O6E A1201 " -0.096 2.00e-02 2.50e+03 pdb=" NAJ O6E A1201 " 0.103 2.00e-02 2.50e+03 pdb=" OAK O6E A1201 " -0.440 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAA O6E A1201 " 0.505 2.00e-02 2.50e+03 2.89e-01 2.09e+03 pdb=" CAO O6E A1201 " -0.138 2.00e-02 2.50e+03 pdb=" CAP O6E A1201 " 0.300 2.00e-02 2.50e+03 pdb=" CAR O6E A1201 " -0.584 2.00e-02 2.50e+03 pdb=" CAV O6E A1201 " 0.032 2.00e-02 2.50e+03 pdb=" CBB O6E A1201 " 0.124 2.00e-02 2.50e+03 pdb=" CBH O6E A1201 " -0.163 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " 0.050 2.00e-02 2.50e+03 pdb=" CBO O6E A1201 " -0.258 2.00e-02 2.50e+03 pdb=" NAE O6E A1201 " 0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAB O6E B1201 " 0.364 2.00e-02 2.50e+03 2.16e-01 1.17e+03 pdb=" CAP O6E B1201 " 0.259 2.00e-02 2.50e+03 pdb=" CAS O6E B1201 " -0.303 2.00e-02 2.50e+03 pdb=" CAW O6E B1201 " -0.072 2.00e-02 2.50e+03 pdb=" CBC O6E B1201 " -0.095 2.00e-02 2.50e+03 pdb=" CBI O6E B1201 " 0.088 2.00e-02 2.50e+03 pdb=" CBL O6E B1201 " 0.172 2.00e-02 2.50e+03 pdb=" CBM O6E B1201 " -0.077 2.00e-02 2.50e+03 pdb=" NAJ O6E B1201 " -0.343 2.00e-02 2.50e+03 pdb=" OAK O6E B1201 " 0.007 2.00e-02 2.50e+03 ... (remaining 2341 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 218 2.67 - 3.23: 12304 3.23 - 3.79: 19550 3.79 - 4.34: 25237 4.34 - 4.90: 42782 Nonbonded interactions: 100091 Sorted by model distance: nonbonded pdb=" OD2 ASP A1022 " pdb=" OG SER A1094 " model vdw 2.116 2.440 nonbonded pdb=" OG1 THR B 517 " pdb=" OD1 ASP B 520 " model vdw 2.138 2.440 nonbonded pdb=" O GLU B 106 " pdb=" OG1 THR B 110 " model vdw 2.189 2.440 nonbonded pdb=" OG SER B 101 " pdb=" OD1 ASN B 103 " model vdw 2.204 2.440 nonbonded pdb=" OG SER A 492 " pdb=" OD1 ASP A 495 " model vdw 2.214 2.440 ... (remaining 100086 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 73 through 1045 or resid 1054 through 1125 or resid 1201)) \ selection = (chain 'B' and (resid 73 through 347 or resid 363 through 591 or (resid 745 and \ (name N or name CA or name C or name O or name CB )) or resid 746 through 1125 o \ r resid 1201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 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: 7.530 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 38.130 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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 : 0.004 0.060 13524 Z= 0.228 Angle : 0.689 12.475 18272 Z= 0.373 Chirality : 0.044 0.272 2063 Planarity : 0.015 0.354 2344 Dihedral : 16.319 89.569 5066 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.14 % Allowed : 18.75 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1669 helix: 1.67 (0.22), residues: 624 sheet: 0.50 (0.29), residues: 337 loop : -1.13 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 477 HIS 0.015 0.001 HIS B 325 PHE 0.018 0.001 PHE B 523 TYR 0.017 0.001 TYR A 574 ARG 0.008 0.000 ARG A 937 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 1.527 Fit side-chains revert: symmetry clash REVERT: A 220 MET cc_start: 0.7208 (ttm) cc_final: 0.6943 (tpp) REVERT: A 566 MET cc_start: 0.5745 (mmm) cc_final: 0.5514 (tmm) REVERT: A 900 LYS cc_start: 0.8973 (ttmm) cc_final: 0.8517 (mtpp) REVERT: A 966 ASP cc_start: 0.7478 (t0) cc_final: 0.6981 (p0) REVERT: B 148 PHE cc_start: 0.7846 (p90) cc_final: 0.7483 (p90) REVERT: B 150 ASP cc_start: 0.6754 (t0) cc_final: 0.6328 (t0) REVERT: B 971 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8637 (tp30) outliers start: 2 outliers final: 2 residues processed: 166 average time/residue: 0.2168 time to fit residues: 54.7775 Evaluate side-chains 144 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain B residue 1083 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS A 580 HIS ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1096 ASN ** B 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 HIS B 858 ASN B 882 GLN ** B 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1007 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.100 13524 Z= 0.697 Angle : 0.846 14.062 18272 Z= 0.432 Chirality : 0.052 0.231 2063 Planarity : 0.006 0.059 2344 Dihedral : 7.509 83.895 1890 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.99 % Favored : 93.95 % Rotamer: Outliers : 5.83 % Allowed : 16.88 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.53 (0.20), residues: 1669 helix: 0.83 (0.21), residues: 621 sheet: 0.07 (0.28), residues: 339 loop : -1.64 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 368 HIS 0.012 0.003 HIS B 325 PHE 0.029 0.003 PHE B 427 TYR 0.044 0.003 TYR A 243 ARG 0.007 0.001 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 134 time to evaluate : 1.586 Fit side-chains revert: symmetry clash REVERT: A 257 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8006 (mm) REVERT: A 566 MET cc_start: 0.5916 (mmm) cc_final: 0.5595 (tmm) REVERT: A 574 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.6483 (t80) REVERT: A 913 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7270 (mm) REVERT: A 969 MET cc_start: 0.5973 (OUTLIER) cc_final: 0.5711 (ttp) REVERT: B 150 ASP cc_start: 0.6643 (t0) cc_final: 0.6284 (t0) REVERT: B 202 TYR cc_start: 0.6065 (OUTLIER) cc_final: 0.5348 (m-80) REVERT: B 387 TYR cc_start: 0.8148 (t80) cc_final: 0.7697 (t80) REVERT: B 520 ASP cc_start: 0.6570 (OUTLIER) cc_final: 0.6329 (p0) REVERT: B 574 TYR cc_start: 0.7206 (OUTLIER) cc_final: 0.6699 (t80) REVERT: B 764 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8360 (pp) outliers start: 84 outliers final: 47 residues processed: 202 average time/residue: 0.2082 time to fit residues: 65.5314 Evaluate side-chains 178 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 123 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 441 ASN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 791 HIS Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 969 MET Chi-restraints excluded: chain A residue 983 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 882 GLN Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 949 ILE Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 1063 HIS Chi-restraints excluded: chain B residue 1101 MET Chi-restraints excluded: chain B residue 1115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 152 optimal weight: 7.9990 chunk 165 optimal weight: 9.9990 chunk 136 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN B 882 GLN B 883 HIS B 947 ASN ** B1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13524 Z= 0.191 Angle : 0.583 12.989 18272 Z= 0.282 Chirality : 0.042 0.151 2063 Planarity : 0.004 0.052 2344 Dihedral : 5.993 77.152 1887 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.19 % Allowed : 20.49 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.21), residues: 1669 helix: 1.68 (0.21), residues: 619 sheet: 0.31 (0.29), residues: 340 loop : -1.34 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 524 HIS 0.012 0.001 HIS B 325 PHE 0.012 0.001 PHE A 873 TYR 0.014 0.001 TYR A 243 ARG 0.005 0.000 ARG B 898 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 149 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7252 (mmm160) REVERT: A 574 TYR cc_start: 0.7292 (OUTLIER) cc_final: 0.6605 (t80) REVERT: A 913 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7229 (mm) REVERT: A 966 ASP cc_start: 0.7504 (t0) cc_final: 0.6848 (p0) REVERT: A 1059 LEU cc_start: 0.8875 (tp) cc_final: 0.8662 (pp) REVERT: B 150 ASP cc_start: 0.6959 (t0) cc_final: 0.6570 (t0) REVERT: B 203 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.7188 (pttp) REVERT: B 520 ASP cc_start: 0.6593 (OUTLIER) cc_final: 0.6364 (p0) REVERT: B 875 HIS cc_start: 0.8580 (OUTLIER) cc_final: 0.8223 (p-80) REVERT: B 971 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8631 (tp30) outliers start: 46 outliers final: 16 residues processed: 189 average time/residue: 0.2138 time to fit residues: 61.7022 Evaluate side-chains 158 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 136 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 875 HIS Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 1119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 30.0000 chunk 102 optimal weight: 0.0000 chunk 153 optimal weight: 20.0000 chunk 162 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 882 GLN ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1081 ASN ** B1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 13524 Z= 0.457 Angle : 0.703 12.403 18272 Z= 0.350 Chirality : 0.047 0.244 2063 Planarity : 0.005 0.053 2344 Dihedral : 6.305 79.027 1887 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.57 % Favored : 94.37 % Rotamer: Outliers : 5.56 % Allowed : 20.49 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.21), residues: 1669 helix: 1.35 (0.21), residues: 616 sheet: 0.07 (0.29), residues: 342 loop : -1.50 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 368 HIS 0.006 0.002 HIS A 883 PHE 0.020 0.002 PHE B 427 TYR 0.030 0.002 TYR A 243 ARG 0.004 0.000 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 137 time to evaluate : 1.525 Fit side-chains revert: symmetry clash REVERT: A 289 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7706 (mmm160) REVERT: A 574 TYR cc_start: 0.7588 (OUTLIER) cc_final: 0.6606 (t80) REVERT: A 913 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7270 (mm) REVERT: A 966 ASP cc_start: 0.7476 (t0) cc_final: 0.6759 (p0) REVERT: A 1059 LEU cc_start: 0.8839 (tp) cc_final: 0.8625 (pp) REVERT: B 150 ASP cc_start: 0.6874 (t0) cc_final: 0.6381 (t0) REVERT: B 202 TYR cc_start: 0.6040 (OUTLIER) cc_final: 0.5399 (m-80) REVERT: B 203 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7464 (pttp) REVERT: B 362 GLN cc_start: 0.5592 (tm-30) cc_final: 0.5317 (tm-30) REVERT: B 574 TYR cc_start: 0.7130 (OUTLIER) cc_final: 0.6525 (t80) REVERT: B 994 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8302 (mp) REVERT: B 1091 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7763 (mm) outliers start: 80 outliers final: 47 residues processed: 208 average time/residue: 0.2192 time to fit residues: 69.6116 Evaluate side-chains 184 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 129 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 506 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 325 HIS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 949 ILE Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain B residue 1091 LEU Chi-restraints excluded: chain B residue 1101 MET Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 2 optimal weight: 8.9990 chunk 120 optimal weight: 0.3980 chunk 67 optimal weight: 0.5980 chunk 138 optimal weight: 0.4980 chunk 112 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 145 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 HIS ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 875 HIS ** B1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13524 Z= 0.154 Angle : 0.574 12.695 18272 Z= 0.273 Chirality : 0.042 0.164 2063 Planarity : 0.004 0.051 2344 Dihedral : 5.425 72.199 1887 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.71 % Favored : 96.23 % Rotamer: Outliers : 3.33 % Allowed : 22.71 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.21), residues: 1669 helix: 1.84 (0.22), residues: 623 sheet: 0.34 (0.29), residues: 336 loop : -1.29 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 524 HIS 0.006 0.001 HIS B 907 PHE 0.011 0.001 PHE B 873 TYR 0.012 0.001 TYR A 574 ARG 0.003 0.000 ARG B 898 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 146 time to evaluate : 1.541 Fit side-chains revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8693 (pt0) REVERT: A 289 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7222 (mmm160) REVERT: A 574 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.6596 (t80) REVERT: A 913 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7143 (mm) REVERT: A 933 MET cc_start: 0.7158 (tpp) cc_final: 0.6948 (tpp) REVERT: A 966 ASP cc_start: 0.7432 (t0) cc_final: 0.6747 (p0) REVERT: A 1059 LEU cc_start: 0.8900 (tp) cc_final: 0.8602 (pp) REVERT: B 150 ASP cc_start: 0.6877 (t0) cc_final: 0.6396 (t0) REVERT: B 362 GLN cc_start: 0.5567 (tm-30) cc_final: 0.5258 (tm-30) REVERT: B 574 TYR cc_start: 0.6954 (OUTLIER) cc_final: 0.6408 (t80) REVERT: B 971 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8639 (tp30) REVERT: B 1091 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7636 (mm) outliers start: 48 outliers final: 24 residues processed: 189 average time/residue: 0.2215 time to fit residues: 63.5795 Evaluate side-chains 169 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 1091 LEU Chi-restraints excluded: chain B residue 1119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.9980 chunk 146 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 HIS ** A 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13524 Z= 0.214 Angle : 0.583 12.943 18272 Z= 0.279 Chirality : 0.043 0.155 2063 Planarity : 0.004 0.052 2344 Dihedral : 5.348 72.462 1887 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.55 % Favored : 95.39 % Rotamer: Outliers : 3.75 % Allowed : 22.43 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.21), residues: 1669 helix: 1.96 (0.22), residues: 618 sheet: 0.30 (0.29), residues: 335 loop : -1.32 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.007 0.001 HIS A 907 PHE 0.013 0.001 PHE A 281 TYR 0.017 0.001 TYR A 243 ARG 0.002 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 139 time to evaluate : 1.495 Fit side-chains revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8647 (pt0) REVERT: A 574 TYR cc_start: 0.7266 (OUTLIER) cc_final: 0.6672 (t80) REVERT: A 913 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7176 (mm) REVERT: A 966 ASP cc_start: 0.7499 (t0) cc_final: 0.6870 (p0) REVERT: A 1059 LEU cc_start: 0.8895 (tp) cc_final: 0.8591 (pp) REVERT: B 150 ASP cc_start: 0.6944 (t0) cc_final: 0.6455 (t0) REVERT: B 362 GLN cc_start: 0.5629 (tm-30) cc_final: 0.5345 (tm-30) REVERT: B 574 TYR cc_start: 0.6974 (OUTLIER) cc_final: 0.6352 (t80) REVERT: B 1091 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7711 (mm) outliers start: 54 outliers final: 27 residues processed: 186 average time/residue: 0.2177 time to fit residues: 61.9142 Evaluate side-chains 167 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 1091 LEU Chi-restraints excluded: chain B residue 1119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 7.9990 chunk 18 optimal weight: 0.0980 chunk 92 optimal weight: 0.2980 chunk 118 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 136 optimal weight: 0.2980 chunk 90 optimal weight: 0.8980 chunk 161 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 HIS ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1096 ASN ** B1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13524 Z= 0.141 Angle : 0.566 13.167 18272 Z= 0.266 Chirality : 0.041 0.163 2063 Planarity : 0.003 0.050 2344 Dihedral : 4.969 67.723 1887 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.71 % Favored : 96.23 % Rotamer: Outliers : 3.19 % Allowed : 23.19 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.22), residues: 1669 helix: 2.06 (0.22), residues: 632 sheet: 0.45 (0.29), residues: 334 loop : -1.16 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 477 HIS 0.007 0.001 HIS A 907 PHE 0.010 0.001 PHE B 873 TYR 0.014 0.001 TYR A 574 ARG 0.003 0.000 ARG B 898 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 143 time to evaluate : 1.546 Fit side-chains REVERT: A 289 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7971 (tpt-90) REVERT: A 574 TYR cc_start: 0.7097 (OUTLIER) cc_final: 0.6654 (t80) REVERT: A 900 LYS cc_start: 0.8913 (ttmm) cc_final: 0.8650 (mtpp) REVERT: A 913 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7130 (mm) REVERT: A 966 ASP cc_start: 0.7389 (t0) cc_final: 0.6813 (p0) REVERT: A 1005 MET cc_start: 0.6586 (tpt) cc_final: 0.5824 (ptt) REVERT: A 1059 LEU cc_start: 0.8889 (tp) cc_final: 0.8564 (pp) REVERT: B 150 ASP cc_start: 0.6908 (t0) cc_final: 0.6471 (t0) REVERT: B 574 TYR cc_start: 0.6980 (OUTLIER) cc_final: 0.6352 (t80) REVERT: B 749 ARG cc_start: 0.7354 (ptp90) cc_final: 0.7112 (ptp90) REVERT: B 971 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8663 (tp30) REVERT: B 994 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8279 (mp) REVERT: B 1091 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7691 (mm) outliers start: 46 outliers final: 21 residues processed: 181 average time/residue: 0.2300 time to fit residues: 63.3557 Evaluate side-chains 161 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 441 ASN Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 872 CYS Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain B residue 1091 LEU Chi-restraints excluded: chain B residue 1119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 HIS ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13524 Z= 0.171 Angle : 0.576 13.179 18272 Z= 0.270 Chirality : 0.042 0.161 2063 Planarity : 0.003 0.049 2344 Dihedral : 4.911 66.694 1887 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.07 % Favored : 95.87 % Rotamer: Outliers : 3.61 % Allowed : 22.29 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.22), residues: 1669 helix: 2.09 (0.22), residues: 630 sheet: 0.52 (0.29), residues: 334 loop : -1.13 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 477 HIS 0.006 0.001 HIS A 907 PHE 0.016 0.001 PHE A 281 TYR 0.013 0.001 TYR A 243 ARG 0.002 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 138 time to evaluate : 1.516 Fit side-chains REVERT: A 289 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.8015 (tpt-90) REVERT: A 566 MET cc_start: 0.6066 (tmm) cc_final: 0.5764 (tmm) REVERT: A 574 TYR cc_start: 0.7145 (OUTLIER) cc_final: 0.6631 (t80) REVERT: A 900 LYS cc_start: 0.8937 (ttmm) cc_final: 0.8664 (mtpp) REVERT: A 913 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7158 (mm) REVERT: A 933 MET cc_start: 0.7092 (tpp) cc_final: 0.6781 (tpp) REVERT: A 966 ASP cc_start: 0.7402 (t0) cc_final: 0.6832 (p0) REVERT: A 1059 LEU cc_start: 0.8898 (tp) cc_final: 0.8580 (pp) REVERT: B 150 ASP cc_start: 0.6945 (t0) cc_final: 0.6440 (t0) REVERT: B 574 TYR cc_start: 0.7020 (OUTLIER) cc_final: 0.6340 (t80) REVERT: B 749 ARG cc_start: 0.7460 (ptp90) cc_final: 0.7125 (ptp90) REVERT: B 967 LEU cc_start: 0.7391 (mt) cc_final: 0.7105 (mt) REVERT: B 971 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8670 (tp30) REVERT: B 994 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8277 (mp) REVERT: B 1091 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7683 (mm) outliers start: 52 outliers final: 37 residues processed: 183 average time/residue: 0.2185 time to fit residues: 60.8802 Evaluate side-chains 181 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 138 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 441 ASN Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 872 CYS Chi-restraints excluded: chain B residue 902 PHE Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain B residue 1063 HIS Chi-restraints excluded: chain B residue 1091 LEU Chi-restraints excluded: chain B residue 1119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 136 optimal weight: 0.0870 chunk 142 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13524 Z= 0.248 Angle : 0.616 14.437 18272 Z= 0.292 Chirality : 0.043 0.167 2063 Planarity : 0.004 0.048 2344 Dihedral : 5.174 68.867 1887 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.37 % Favored : 95.57 % Rotamer: Outliers : 3.54 % Allowed : 22.36 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.21), residues: 1669 helix: 2.01 (0.22), residues: 619 sheet: 0.36 (0.29), residues: 338 loop : -1.16 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 477 HIS 0.006 0.001 HIS B 759 PHE 0.013 0.001 PHE A 871 TYR 0.021 0.002 TYR A 243 ARG 0.002 0.000 ARG A1060 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 136 time to evaluate : 1.198 Fit side-chains REVERT: A 289 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7411 (mmm160) REVERT: A 566 MET cc_start: 0.6051 (tmm) cc_final: 0.5708 (tmm) REVERT: A 574 TYR cc_start: 0.7269 (OUTLIER) cc_final: 0.6721 (t80) REVERT: A 900 LYS cc_start: 0.8940 (ttmm) cc_final: 0.8655 (mtpp) REVERT: A 913 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7204 (mm) REVERT: A 933 MET cc_start: 0.7075 (tpp) cc_final: 0.6780 (tpp) REVERT: A 966 ASP cc_start: 0.7477 (t0) cc_final: 0.6922 (p0) REVERT: A 1059 LEU cc_start: 0.8899 (tp) cc_final: 0.8590 (pp) REVERT: B 150 ASP cc_start: 0.6985 (t0) cc_final: 0.6445 (t0) REVERT: B 362 GLN cc_start: 0.5714 (tm-30) cc_final: 0.5413 (tm-30) REVERT: B 574 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.6385 (t80) REVERT: B 749 ARG cc_start: 0.7474 (ptp90) cc_final: 0.7162 (ptp90) REVERT: B 967 LEU cc_start: 0.7489 (mt) cc_final: 0.7105 (mt) REVERT: B 994 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8311 (mp) REVERT: B 1091 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7778 (mm) outliers start: 51 outliers final: 38 residues processed: 181 average time/residue: 0.2198 time to fit residues: 61.1675 Evaluate side-chains 181 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 137 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 441 ASN Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 872 CYS Chi-restraints excluded: chain B residue 902 PHE Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain B residue 1091 LEU Chi-restraints excluded: chain B residue 1119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 110 optimal weight: 0.0020 chunk 167 optimal weight: 8.9990 chunk 154 optimal weight: 6.9990 chunk 133 optimal weight: 0.0980 chunk 13 optimal weight: 0.0980 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 141 optimal weight: 0.0570 overall best weight: 0.4508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 13524 Z= 0.140 Angle : 0.574 14.238 18272 Z= 0.269 Chirality : 0.041 0.162 2063 Planarity : 0.003 0.049 2344 Dihedral : 4.891 64.128 1887 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.83 % Favored : 96.11 % Rotamer: Outliers : 2.85 % Allowed : 23.12 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.21), residues: 1669 helix: 2.10 (0.22), residues: 631 sheet: 0.53 (0.29), residues: 333 loop : -1.08 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 477 HIS 0.006 0.001 HIS B 759 PHE 0.012 0.001 PHE B 95 TYR 0.013 0.001 TYR A 574 ARG 0.002 0.000 ARG B 749 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 139 time to evaluate : 1.552 Fit side-chains REVERT: A 289 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7956 (tpt-90) REVERT: A 566 MET cc_start: 0.6174 (tmm) cc_final: 0.5901 (tmm) REVERT: A 574 TYR cc_start: 0.7034 (OUTLIER) cc_final: 0.6477 (t80) REVERT: A 900 LYS cc_start: 0.8920 (ttmm) cc_final: 0.8638 (mtpp) REVERT: A 913 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7128 (mm) REVERT: A 933 MET cc_start: 0.7199 (tpp) cc_final: 0.6942 (tpp) REVERT: A 966 ASP cc_start: 0.7464 (t0) cc_final: 0.7106 (p0) REVERT: A 1059 LEU cc_start: 0.8898 (tp) cc_final: 0.8583 (pp) REVERT: B 150 ASP cc_start: 0.6958 (t0) cc_final: 0.6438 (t0) REVERT: B 362 GLN cc_start: 0.5641 (tm-30) cc_final: 0.5373 (tm-30) REVERT: B 574 TYR cc_start: 0.7006 (OUTLIER) cc_final: 0.6331 (t80) REVERT: B 749 ARG cc_start: 0.7381 (ptp90) cc_final: 0.7123 (ptp90) REVERT: B 967 LEU cc_start: 0.7447 (mt) cc_final: 0.7065 (mt) REVERT: B 994 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8285 (mp) REVERT: B 1091 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7752 (mm) outliers start: 41 outliers final: 32 residues processed: 173 average time/residue: 0.2125 time to fit residues: 56.4984 Evaluate side-chains 176 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 138 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 441 ASN Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 872 CYS Chi-restraints excluded: chain B residue 902 PHE Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain B residue 1091 LEU Chi-restraints excluded: chain B residue 1119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 137 optimal weight: 0.0060 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 117 optimal weight: 0.0020 chunk 7 optimal weight: 3.9990 overall best weight: 0.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.200869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.134805 restraints weight = 18956.133| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 3.38 r_work: 0.3702 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 13524 Z= 0.137 Angle : 0.577 14.179 18272 Z= 0.267 Chirality : 0.041 0.158 2063 Planarity : 0.003 0.048 2344 Dihedral : 4.631 59.209 1887 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.71 % Favored : 96.23 % Rotamer: Outliers : 2.85 % Allowed : 23.33 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.22), residues: 1669 helix: 2.29 (0.22), residues: 622 sheet: 0.60 (0.29), residues: 334 loop : -1.01 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 477 HIS 0.006 0.001 HIS B 759 PHE 0.020 0.001 PHE A 281 TYR 0.010 0.001 TYR A 574 ARG 0.006 0.000 ARG B 898 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2786.91 seconds wall clock time: 51 minutes 3.81 seconds (3063.81 seconds total)