Starting phenix.real_space_refine on Fri Mar 15 13:30:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox7_17259/03_2024/8ox7_17259_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox7_17259/03_2024/8ox7_17259.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox7_17259/03_2024/8ox7_17259_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox7_17259/03_2024/8ox7_17259_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox7_17259/03_2024/8ox7_17259_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox7_17259/03_2024/8ox7_17259.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox7_17259/03_2024/8ox7_17259.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox7_17259/03_2024/8ox7_17259_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox7_17259/03_2024/8ox7_17259_updated.pdb" } resolution = 2.56 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= 1.000 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 55 5.16 5 C 7556 2.51 5 N 1968 2.21 5 O 2170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 111": "OE1" <-> "OE2" Residue "B TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A ASP 291": "OD1" <-> "OD2" Residue "A ASP 304": "OD1" <-> "OD2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 712": "OD1" <-> "OD2" Residue "A GLU 759": "OE1" <-> "OE2" Residue "A GLU 914": "OE1" <-> "OE2" Residue "A ASP 1219": "OD1" <-> "OD2" 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: 11755 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2642 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 25, 'TRANS': 302} Chain: "A" Number of atoms: 8993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8993 Classifications: {'peptide': 1112} Link IDs: {'PTRANS': 28, 'TRANS': 1083} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {' MG': 1, 'IP9': 1} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} Time building chain proxies: 6.57, per 1000 atoms: 0.56 Number of scatterers: 11755 At special positions: 0 Unit cell: (83.8512, 97.3088, 178.054, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 5 15.00 Mg 1 11.99 O 2170 8.00 N 1968 7.00 C 7556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 102 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.04 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 401 " - " ASN B 107 " " NAG B 402 " - " ASN B 294 " " NAG C 1 " - " ASN B 180 " Time building additional restraints: 4.82 Conformation dependent library (CDL) restraints added in 2.1 seconds 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2716 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 11 sheets defined 43.1% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'B' and resid 47 through 73 removed outlier: 3.730A pdb=" N LEU B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Proline residue: B 52 - end of helix removed outlier: 3.955A pdb=" N GLY B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) Proline residue: B 63 - end of helix Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 132 through 135 No H-bonds generated for 'chain 'B' and resid 132 through 135' Processing helix chain 'B' and resid 140 through 143 No H-bonds generated for 'chain 'B' and resid 140 through 143' Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.691A pdb=" N LEU B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 147 through 151' Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 173 through 176 No H-bonds generated for 'chain 'B' and resid 173 through 176' Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 223 through 226 No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 255 through 261 Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 323 through 349 Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 119 through 131 Processing helix chain 'A' and resid 141 through 173 removed outlier: 3.751A pdb=" N LEU A 145 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N VAL A 146 " --> pdb=" O THR A 143 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.585A pdb=" N VAL A 150 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP A 162 " --> pdb=" O ASP A 159 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 166 " --> pdb=" O ASP A 163 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 171 " --> pdb=" O LYS A 168 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU A 172 " --> pdb=" O MET A 169 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A 173 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 244 through 247 No H-bonds generated for 'chain 'A' and resid 244 through 247' Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.584A pdb=" N THR A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 332 through 365 removed outlier: 3.504A pdb=" N ASN A 338 " --> pdb=" O ASP A 334 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN A 365 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 399 removed outlier: 3.999A pdb=" N TRP A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N THR A 398 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N MET A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 421 removed outlier: 3.664A pdb=" N ILE A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 446 Processing helix chain 'A' and resid 511 through 518 Processing helix chain 'A' and resid 522 through 531 removed outlier: 3.649A pdb=" N LEU A 531 " --> pdb=" O PHE A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 564 Processing helix chain 'A' and resid 622 through 627 removed outlier: 3.570A pdb=" N GLU A 627 " --> pdb=" O THR A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 648 removed outlier: 4.256A pdb=" N GLN A 637 " --> pdb=" O PRO A 634 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A 639 " --> pdb=" O LYS A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 678 removed outlier: 3.595A pdb=" N LYS A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 694 removed outlier: 3.605A pdb=" N GLU A 693 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 694 " --> pdb=" O VAL A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 723 Processing helix chain 'A' and resid 736 through 745 Processing helix chain 'A' and resid 758 through 772 Processing helix chain 'A' and resid 803 through 809 Processing helix chain 'A' and resid 834 through 859 removed outlier: 4.011A pdb=" N ARG A 840 " --> pdb=" O THR A 836 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG A 841 " --> pdb=" O GLN A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 883 Processing helix chain 'A' and resid 895 through 903 removed outlier: 3.543A pdb=" N VAL A 898 " --> pdb=" O ALA A 895 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ASN A 899 " --> pdb=" O ASN A 896 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET A 900 " --> pdb=" O ASP A 897 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 902 " --> pdb=" O ASN A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 937 removed outlier: 3.698A pdb=" N LEU A 935 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 936 " --> pdb=" O GLN A 933 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU A 937 " --> pdb=" O ARG A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 971 removed outlier: 3.687A pdb=" N TYR A 956 " --> pdb=" O ARG A 952 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 958 " --> pdb=" O PHE A 954 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 961 " --> pdb=" O LYS A 957 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL A 964 " --> pdb=" O ALA A 960 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N HIS A 965 " --> pdb=" O PHE A 961 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A 966 " --> pdb=" O THR A 962 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE A 971 " --> pdb=" O TRP A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 987 Processing helix chain 'A' and resid 995 through 1003 Processing helix chain 'A' and resid 1009 through 1013 Processing helix chain 'A' and resid 1016 through 1023 removed outlier: 3.510A pdb=" N ILE A1020 " --> pdb=" O GLY A1017 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A1021 " --> pdb=" O LEU A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1055 Proline residue: A1051 - end of helix Processing helix chain 'A' and resid 1069 through 1091 removed outlier: 3.541A pdb=" N ILE A1088 " --> pdb=" O VAL A1084 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A1089 " --> pdb=" O ASN A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1117 Processing helix chain 'A' and resid 1120 through 1125 removed outlier: 3.810A pdb=" N LEU A1125 " --> pdb=" O GLY A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1141 removed outlier: 3.580A pdb=" N ARG A1141 " --> pdb=" O SER A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1170 Proline residue: A1159 - end of helix Processing helix chain 'A' and resid 1174 through 1180 Processing helix chain 'A' and resid 1217 through 1222 Processing sheet with id= A, first strand: chain 'B' and resid 77 through 81 removed outlier: 6.002A pdb=" N TYR B 122 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU B 272 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU B 124 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ARG B 270 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 102 through 110 removed outlier: 4.289A pdb=" N CYS B 102 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG B 290 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 64 through 67 removed outlier: 4.042A pdb=" N GLY A 277 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 177 through 181 Processing sheet with id= E, first strand: chain 'A' and resid 199 through 203 removed outlier: 6.358A pdb=" N LEU A 309 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU A 214 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 237 through 241 removed outlier: 3.994A pdb=" N TYR A 225 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 906 through 909 removed outlier: 6.332A pdb=" N TYR A 450 " --> pdb=" O LEU A 889 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE A 891 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE A 452 " --> pdb=" O ILE A 891 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LYS A 727 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N SER A 453 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TRP A 729 " --> pdb=" O SER A 453 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL A 863 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 862 " --> pdb=" O ARG A 797 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR A 754 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE A 800 " --> pdb=" O THR A 754 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N CYS A 756 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N THR A 802 " --> pdb=" O CYS A 756 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 474 through 476 removed outlier: 6.651A pdb=" N LEU A 656 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA A 703 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU A 654 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA A 705 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ARG A 652 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE A 614 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARG A 608 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL A 590 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 538 through 540 Processing sheet with id= J, first strand: chain 'A' and resid 567 through 569 Processing sheet with id= K, first strand: chain 'A' and resid 460 through 466 removed outlier: 7.216A pdb=" N LYS A 709 " --> pdb=" O GLN A 461 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE A 463 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU A 707 " --> pdb=" O ILE A 463 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1212 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: 4.59 Time building geometry restraints manager: 5.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1886 1.31 - 1.44: 3358 1.44 - 1.57: 6688 1.57 - 1.69: 8 1.69 - 1.82: 85 Bond restraints: 12025 Sorted by residual: bond pdb=" OD1 PHD A 454 " pdb=" P PHD A 454 " ideal model delta sigma weight residual 1.816 1.642 0.174 2.00e-02 2.50e+03 7.53e+01 bond pdb=" CG PHD A 454 " pdb=" OD1 PHD A 454 " ideal model delta sigma weight residual 1.300 1.397 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.595 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" CG PHD A 454 " pdb=" OD2 PHD A 454 " ideal model delta sigma weight residual 1.218 1.186 0.032 2.00e-02 2.50e+03 2.55e+00 bond pdb=" C1 NAG B 402 " pdb=" O5 NAG B 402 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 ... (remaining 12020 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.37: 261 106.37 - 113.27: 6498 113.27 - 120.18: 4291 120.18 - 127.08: 5113 127.08 - 133.99: 132 Bond angle restraints: 16295 Sorted by residual: angle pdb=" OD1 PHD A 454 " pdb=" P PHD A 454 " pdb=" OP1 PHD A 454 " ideal model delta sigma weight residual 97.64 108.57 -10.93 3.00e+00 1.11e-01 1.33e+01 angle pdb=" N VAL B 50 " pdb=" CA VAL B 50 " pdb=" C VAL B 50 " ideal model delta sigma weight residual 112.96 109.70 3.26 1.00e+00 1.00e+00 1.06e+01 angle pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sigma weight residual 113.24 105.27 7.97 3.00e+00 1.11e-01 7.06e+00 angle pdb=" C1 BMA C 3 " pdb=" O5 BMA C 3 " pdb=" C5 BMA C 3 " ideal model delta sigma weight residual 118.82 110.87 7.95 3.00e+00 1.11e-01 7.02e+00 angle pdb=" C ARG B 26 " pdb=" N ARG B 27 " pdb=" CA ARG B 27 " ideal model delta sigma weight residual 120.49 124.16 -3.67 1.42e+00 4.96e-01 6.69e+00 ... (remaining 16290 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.77: 6786 23.77 - 47.55: 362 47.55 - 71.32: 42 71.32 - 95.10: 17 95.10 - 118.87: 5 Dihedral angle restraints: 7212 sinusoidal: 2999 harmonic: 4213 Sorted by residual: dihedral pdb=" CB CYS B 91 " pdb=" SG CYS B 91 " pdb=" SG CYS B 104 " pdb=" CB CYS B 104 " ideal model delta sinusoidal sigma weight residual -86.00 -47.54 -38.46 1 1.00e+01 1.00e-02 2.08e+01 dihedral pdb=" CA ASN A1029 " pdb=" C ASN A1029 " pdb=" N TYR A1030 " pdb=" CA TYR A1030 " ideal model delta harmonic sigma weight residual 180.00 158.21 21.79 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" C2 IP9 A1302 " pdb=" C3 IP9 A1302 " pdb=" C4 IP9 A1302 " pdb=" C5 IP9 A1302 " ideal model delta sinusoidal sigma weight residual 52.95 -65.92 118.87 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 7209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1431 0.044 - 0.088: 290 0.088 - 0.133: 87 0.133 - 0.177: 8 0.177 - 0.221: 1 Chirality restraints: 1817 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.50 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA CYS B 91 " pdb=" N CYS B 91 " pdb=" C CYS B 91 " pdb=" CB CYS B 91 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA VAL A 133 " pdb=" N VAL A 133 " pdb=" C VAL A 133 " pdb=" CB VAL A 133 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 1814 not shown) Planarity restraints: 2061 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 100 " -0.044 5.00e-02 4.00e+02 6.74e-02 7.27e+00 pdb=" N PRO B 101 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 101 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 101 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 169 " -0.035 5.00e-02 4.00e+02 5.22e-02 4.37e+00 pdb=" N PRO B 170 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 170 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 170 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 317 " -0.017 2.00e-02 2.50e+03 1.20e-02 3.63e+00 pdb=" CG TRP B 317 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP B 317 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP B 317 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 317 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 317 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 317 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 317 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 317 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 317 " -0.002 2.00e-02 2.50e+03 ... (remaining 2058 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 109 2.54 - 3.13: 9419 3.13 - 3.72: 18681 3.72 - 4.31: 28698 4.31 - 4.90: 46501 Nonbonded interactions: 103408 Sorted by model distance: nonbonded pdb=" OD2 PHD A 454 " pdb="MG MG A1301 " model vdw 1.947 2.170 nonbonded pdb=" O3 NAG C 2 " pdb=" O2 BMA C 3 " model vdw 1.977 2.440 nonbonded pdb=" O THR A 456 " pdb="MG MG A1301 " model vdw 1.977 2.170 nonbonded pdb=" O LEU A 441 " pdb=" OH TYR A 924 " model vdw 2.001 2.440 nonbonded pdb=" OP3 PHD A 454 " pdb="MG MG A1301 " model vdw 2.009 2.170 ... (remaining 103403 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.510 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 35.270 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 0.174 12025 Z= 0.238 Angle : 0.557 10.932 16295 Z= 0.277 Chirality : 0.040 0.221 1817 Planarity : 0.004 0.070 2058 Dihedral : 14.910 118.872 4487 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.08 % Allowed : 0.24 % Favored : 99.68 % 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: -0.45 (0.22), residues: 1425 helix: 0.07 (0.21), residues: 608 sheet: 0.70 (0.38), residues: 192 loop : -0.90 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 317 HIS 0.004 0.001 HIS A1213 PHE 0.014 0.001 PHE A1126 TYR 0.028 0.001 TYR A 968 ARG 0.008 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 1.302 Fit side-chains REVERT: B 76 ARG cc_start: 0.7342 (mmt90) cc_final: 0.7140 (mtt-85) REVERT: A 276 THR cc_start: 0.7484 (m) cc_final: 0.7179 (p) REVERT: A 478 ASP cc_start: 0.7239 (m-30) cc_final: 0.7011 (m-30) REVERT: A 603 MET cc_start: 0.8127 (ptm) cc_final: 0.7875 (ptp) REVERT: A 1214 GLN cc_start: 0.7813 (mt0) cc_final: 0.7583 (pt0) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 1.3299 time to fit residues: 235.9872 Evaluate side-chains 135 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN A 18 ASN ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN A 549 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12025 Z= 0.237 Angle : 0.580 9.070 16295 Z= 0.299 Chirality : 0.044 0.305 1817 Planarity : 0.005 0.055 2058 Dihedral : 9.653 109.610 1708 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.58 % Allowed : 8.47 % Favored : 89.95 % 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: -0.05 (0.22), residues: 1425 helix: 0.51 (0.21), residues: 635 sheet: 0.72 (0.37), residues: 201 loop : -0.83 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 317 HIS 0.004 0.001 HIS A 965 PHE 0.016 0.002 PHE A1126 TYR 0.023 0.001 TYR A 968 ARG 0.008 0.000 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 1.155 Fit side-chains REVERT: B 318 MET cc_start: 0.6207 (tpp) cc_final: 0.4448 (mmm) REVERT: A 163 ASP cc_start: 0.6898 (t70) cc_final: 0.6650 (t0) REVERT: A 206 ASP cc_start: 0.7456 (m-30) cc_final: 0.7225 (m-30) REVERT: A 241 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7449 (tpt) REVERT: A 478 ASP cc_start: 0.7216 (m-30) cc_final: 0.7011 (m-30) REVERT: A 622 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7194 (p0) REVERT: A 637 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7624 (tp-100) REVERT: A 772 GLN cc_start: 0.6297 (mm110) cc_final: 0.5649 (mt0) REVERT: A 813 LYS cc_start: 0.7534 (mmtm) cc_final: 0.7200 (mmtm) REVERT: A 1214 GLN cc_start: 0.7838 (mt0) cc_final: 0.7415 (pt0) outliers start: 20 outliers final: 10 residues processed: 164 average time/residue: 1.2460 time to fit residues: 221.9005 Evaluate side-chains 148 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 672 LYS Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1223 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 140 optimal weight: 0.2980 chunk 115 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 104 optimal weight: 20.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN A 549 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12025 Z= 0.262 Angle : 0.568 9.702 16295 Z= 0.291 Chirality : 0.045 0.400 1817 Planarity : 0.004 0.053 2058 Dihedral : 9.147 106.816 1708 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.29 % Allowed : 11.47 % Favored : 86.23 % 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: 0.01 (0.22), residues: 1425 helix: 0.60 (0.21), residues: 634 sheet: 0.99 (0.38), residues: 189 loop : -0.89 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 317 HIS 0.005 0.001 HIS A1213 PHE 0.017 0.002 PHE A 305 TYR 0.022 0.002 TYR A 968 ARG 0.009 0.000 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 148 time to evaluate : 1.211 Fit side-chains REVERT: B 242 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6992 (pmm) REVERT: B 318 MET cc_start: 0.6157 (tpp) cc_final: 0.4742 (mmm) REVERT: A 163 ASP cc_start: 0.7021 (t70) cc_final: 0.6783 (t0) REVERT: A 206 ASP cc_start: 0.7453 (m-30) cc_final: 0.7221 (m-30) REVERT: A 241 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7649 (tpt) REVERT: A 478 ASP cc_start: 0.7244 (m-30) cc_final: 0.7038 (m-30) REVERT: A 622 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7226 (p0) REVERT: A 636 LYS cc_start: 0.8320 (tttt) cc_final: 0.8078 (ttpt) REVERT: A 637 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7550 (tp-100) REVERT: A 772 GLN cc_start: 0.6380 (mm110) cc_final: 0.5542 (mt0) REVERT: A 813 LYS cc_start: 0.7595 (mmtm) cc_final: 0.7371 (mttm) outliers start: 29 outliers final: 12 residues processed: 165 average time/residue: 1.2316 time to fit residues: 220.8191 Evaluate side-chains 150 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1223 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 138 optimal weight: 0.0170 chunk 68 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN A 549 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12025 Z= 0.249 Angle : 0.543 10.083 16295 Z= 0.279 Chirality : 0.044 0.405 1817 Planarity : 0.004 0.053 2058 Dihedral : 8.739 103.758 1708 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.01 % Allowed : 12.90 % Favored : 84.10 % 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: 0.04 (0.22), residues: 1425 helix: 0.70 (0.21), residues: 624 sheet: 0.99 (0.38), residues: 189 loop : -0.95 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 317 HIS 0.004 0.001 HIS A 965 PHE 0.014 0.002 PHE A 666 TYR 0.014 0.001 TYR A 968 ARG 0.008 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 144 time to evaluate : 1.347 Fit side-chains revert: symmetry clash REVERT: B 76 ARG cc_start: 0.7461 (mmt90) cc_final: 0.7152 (mtt-85) REVERT: B 226 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.7299 (mtp180) REVERT: B 241 TYR cc_start: 0.6292 (OUTLIER) cc_final: 0.6058 (m-10) REVERT: B 242 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6991 (pmm) REVERT: B 318 MET cc_start: 0.6171 (tpp) cc_final: 0.4934 (mmt) REVERT: A 163 ASP cc_start: 0.7059 (t70) cc_final: 0.6810 (t0) REVERT: A 206 ASP cc_start: 0.7399 (m-30) cc_final: 0.7161 (m-30) REVERT: A 241 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7444 (tpt) REVERT: A 478 ASP cc_start: 0.7236 (m-30) cc_final: 0.7031 (m-30) REVERT: A 523 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6640 (mt-10) REVERT: A 622 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7210 (p0) REVERT: A 637 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7548 (tp-100) REVERT: A 638 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6373 (mp0) REVERT: A 772 GLN cc_start: 0.6125 (mm110) cc_final: 0.5591 (mt0) REVERT: A 813 LYS cc_start: 0.7615 (mmtm) cc_final: 0.7303 (mttm) REVERT: A 1215 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7041 (mtp85) outliers start: 38 outliers final: 16 residues processed: 169 average time/residue: 1.2361 time to fit residues: 227.6756 Evaluate side-chains 163 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 139 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1215 ARG Chi-restraints excluded: chain A residue 1223 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN A 515 GLN A 549 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12025 Z= 0.240 Angle : 0.540 10.408 16295 Z= 0.277 Chirality : 0.043 0.349 1817 Planarity : 0.004 0.051 2058 Dihedral : 8.429 100.727 1708 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.32 % Allowed : 13.53 % Favored : 83.15 % 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: 0.07 (0.22), residues: 1425 helix: 0.70 (0.21), residues: 630 sheet: 1.10 (0.39), residues: 184 loop : -0.94 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 317 HIS 0.004 0.001 HIS A 965 PHE 0.017 0.002 PHE A 305 TYR 0.013 0.001 TYR B 297 ARG 0.007 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 145 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: B 226 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7307 (mtp180) REVERT: B 309 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.8060 (mtm180) REVERT: B 318 MET cc_start: 0.6179 (tpp) cc_final: 0.5007 (mmt) REVERT: A 125 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7775 (mp) REVERT: A 163 ASP cc_start: 0.7077 (t70) cc_final: 0.6807 (t0) REVERT: A 206 ASP cc_start: 0.7399 (m-30) cc_final: 0.7160 (m-30) REVERT: A 241 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7534 (tpt) REVERT: A 350 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7729 (mp) REVERT: A 478 ASP cc_start: 0.7241 (m-30) cc_final: 0.7033 (m-30) REVERT: A 514 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7171 (tm-30) REVERT: A 622 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7185 (p0) REVERT: A 637 GLN cc_start: 0.7769 (mm-40) cc_final: 0.7562 (tp-100) REVERT: A 638 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6363 (mp0) REVERT: A 772 GLN cc_start: 0.6128 (mm110) cc_final: 0.5543 (mt0) REVERT: A 813 LYS cc_start: 0.7613 (mmtm) cc_final: 0.7403 (mttm) REVERT: A 956 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.8017 (t80) outliers start: 42 outliers final: 17 residues processed: 175 average time/residue: 1.2247 time to fit residues: 233.0466 Evaluate side-chains 163 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 137 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 956 TYR Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1223 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 72 optimal weight: 0.0170 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN A 515 GLN A 549 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12025 Z= 0.222 Angle : 0.527 10.030 16295 Z= 0.271 Chirality : 0.043 0.373 1817 Planarity : 0.004 0.050 2058 Dihedral : 8.103 98.185 1708 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.40 % Allowed : 14.72 % Favored : 81.88 % 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: 0.16 (0.22), residues: 1425 helix: 0.81 (0.21), residues: 624 sheet: 1.26 (0.39), residues: 182 loop : -0.96 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 983 HIS 0.004 0.001 HIS A 965 PHE 0.020 0.002 PHE A 305 TYR 0.013 0.001 TYR B 297 ARG 0.009 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 141 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 76 ARG cc_start: 0.7364 (mmt90) cc_final: 0.7086 (mtt-85) REVERT: B 226 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7281 (mtp180) REVERT: B 309 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8023 (mtm180) REVERT: A 110 MET cc_start: 0.4750 (OUTLIER) cc_final: 0.3666 (mpp) REVERT: A 163 ASP cc_start: 0.7116 (t70) cc_final: 0.6837 (t0) REVERT: A 206 ASP cc_start: 0.7437 (m-30) cc_final: 0.7196 (m-30) REVERT: A 241 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7466 (tpt) REVERT: A 271 ARG cc_start: 0.7299 (ptm-80) cc_final: 0.7004 (ttt-90) REVERT: A 280 PHE cc_start: 0.7850 (m-80) cc_final: 0.7522 (m-80) REVERT: A 350 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7719 (mp) REVERT: A 478 ASP cc_start: 0.7246 (m-30) cc_final: 0.7032 (m-30) REVERT: A 622 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7181 (p0) REVERT: A 637 GLN cc_start: 0.7725 (mm-40) cc_final: 0.7500 (tp-100) REVERT: A 638 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6299 (mp0) REVERT: A 769 MET cc_start: 0.5314 (OUTLIER) cc_final: 0.4519 (tpt) REVERT: A 772 GLN cc_start: 0.6106 (mm110) cc_final: 0.5520 (mt0) REVERT: A 956 TYR cc_start: 0.8707 (OUTLIER) cc_final: 0.8023 (t80) REVERT: A 1215 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7027 (mtp85) outliers start: 43 outliers final: 16 residues processed: 171 average time/residue: 1.1746 time to fit residues: 218.8573 Evaluate side-chains 164 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 956 TYR Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1215 ARG Chi-restraints excluded: chain A residue 1223 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 0.0670 chunk 101 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 chunk 85 optimal weight: 2.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN A 515 GLN A 549 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12025 Z= 0.168 Angle : 0.494 9.687 16295 Z= 0.254 Chirality : 0.041 0.331 1817 Planarity : 0.004 0.058 2058 Dihedral : 7.716 96.323 1708 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.69 % Allowed : 15.51 % Favored : 81.80 % 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: 0.25 (0.22), residues: 1425 helix: 0.92 (0.22), residues: 622 sheet: 1.08 (0.38), residues: 191 loop : -0.89 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1095 HIS 0.003 0.001 HIS A 965 PHE 0.021 0.001 PHE A 305 TYR 0.012 0.001 TYR B 297 ARG 0.008 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 141 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 226 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7278 (mtp180) REVERT: B 241 TYR cc_start: 0.6264 (OUTLIER) cc_final: 0.5990 (m-10) REVERT: B 309 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7900 (mtm180) REVERT: A 163 ASP cc_start: 0.7112 (t70) cc_final: 0.6838 (t0) REVERT: A 241 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7256 (tpt) REVERT: A 280 PHE cc_start: 0.7888 (m-80) cc_final: 0.7611 (m-80) REVERT: A 350 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7697 (mp) REVERT: A 478 ASP cc_start: 0.7231 (m-30) cc_final: 0.7017 (m-30) REVERT: A 622 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7180 (p0) REVERT: A 638 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6200 (mp0) REVERT: A 769 MET cc_start: 0.5301 (OUTLIER) cc_final: 0.4512 (tpt) REVERT: A 772 GLN cc_start: 0.6062 (mm110) cc_final: 0.5397 (mt0) REVERT: A 813 LYS cc_start: 0.7620 (mttm) cc_final: 0.7394 (mttm) REVERT: A 956 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.8068 (t80) REVERT: A 1215 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.6899 (mtp85) outliers start: 34 outliers final: 14 residues processed: 164 average time/residue: 1.2214 time to fit residues: 218.3770 Evaluate side-chains 163 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 139 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 956 TYR Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1144 TYR Chi-restraints excluded: chain A residue 1215 ARG Chi-restraints excluded: chain A residue 1223 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN A 515 GLN A 549 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12025 Z= 0.183 Angle : 0.498 10.257 16295 Z= 0.256 Chirality : 0.042 0.351 1817 Planarity : 0.004 0.068 2058 Dihedral : 7.476 94.718 1708 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.53 % Allowed : 15.98 % Favored : 81.49 % 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: 0.27 (0.22), residues: 1425 helix: 0.96 (0.21), residues: 622 sheet: 1.03 (0.39), residues: 186 loop : -0.88 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1095 HIS 0.003 0.001 HIS A 965 PHE 0.021 0.001 PHE A 305 TYR 0.012 0.001 TYR B 297 ARG 0.009 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 ARG cc_start: 0.7311 (mmt90) cc_final: 0.7031 (mtt-85) REVERT: B 226 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7281 (mtp180) REVERT: B 241 TYR cc_start: 0.6205 (OUTLIER) cc_final: 0.5987 (m-10) REVERT: B 309 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7907 (mtm180) REVERT: A 163 ASP cc_start: 0.7105 (t70) cc_final: 0.6822 (t0) REVERT: A 241 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7415 (tpt) REVERT: A 328 PHE cc_start: 0.8152 (t80) cc_final: 0.7945 (t80) REVERT: A 350 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7697 (mp) REVERT: A 478 ASP cc_start: 0.7231 (m-30) cc_final: 0.7013 (m-30) REVERT: A 622 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7172 (p0) REVERT: A 638 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6183 (mp0) REVERT: A 769 MET cc_start: 0.5323 (OUTLIER) cc_final: 0.4548 (tpt) REVERT: A 772 GLN cc_start: 0.6053 (mm110) cc_final: 0.5444 (mt0) REVERT: A 813 LYS cc_start: 0.7598 (mttm) cc_final: 0.7229 (mttm) REVERT: A 956 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.8062 (t80) REVERT: A 1215 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.6878 (mtp85) outliers start: 32 outliers final: 17 residues processed: 165 average time/residue: 1.1852 time to fit residues: 213.8790 Evaluate side-chains 165 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 138 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 956 TYR Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1144 TYR Chi-restraints excluded: chain A residue 1215 ARG Chi-restraints excluded: chain A residue 1223 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN A 549 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12025 Z= 0.238 Angle : 0.529 10.174 16295 Z= 0.272 Chirality : 0.043 0.313 1817 Planarity : 0.004 0.056 2058 Dihedral : 7.360 92.703 1708 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.61 % Allowed : 16.22 % Favored : 81.17 % 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: 0.14 (0.22), residues: 1425 helix: 0.79 (0.21), residues: 633 sheet: 1.10 (0.39), residues: 183 loop : -0.93 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1095 HIS 0.005 0.001 HIS A 965 PHE 0.022 0.002 PHE A 305 TYR 0.013 0.001 TYR A 392 ARG 0.009 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 141 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 76 ARG cc_start: 0.7344 (mmt90) cc_final: 0.7068 (mtt-85) REVERT: B 226 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7330 (mtp180) REVERT: B 241 TYR cc_start: 0.6306 (OUTLIER) cc_final: 0.6014 (m-10) REVERT: B 309 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7945 (mtm180) REVERT: A 163 ASP cc_start: 0.7076 (t70) cc_final: 0.6797 (t0) REVERT: A 241 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7437 (tpt) REVERT: A 350 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7720 (mp) REVERT: A 478 ASP cc_start: 0.7252 (m-30) cc_final: 0.7033 (m-30) REVERT: A 622 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7217 (p0) REVERT: A 638 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6148 (mp0) REVERT: A 769 MET cc_start: 0.5335 (OUTLIER) cc_final: 0.4543 (tpt) REVERT: A 772 GLN cc_start: 0.6090 (mm110) cc_final: 0.5417 (mt0) REVERT: A 813 LYS cc_start: 0.7586 (mttm) cc_final: 0.7223 (mttm) REVERT: A 956 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.8006 (t80) REVERT: A 1215 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.6769 (mtp85) outliers start: 33 outliers final: 18 residues processed: 164 average time/residue: 1.2172 time to fit residues: 217.6169 Evaluate side-chains 165 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 956 TYR Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1144 TYR Chi-restraints excluded: chain A residue 1215 ARG Chi-restraints excluded: chain A residue 1223 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN A 549 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12025 Z= 0.278 Angle : 0.557 10.304 16295 Z= 0.287 Chirality : 0.044 0.346 1817 Planarity : 0.004 0.057 2058 Dihedral : 7.271 89.617 1708 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.53 % Allowed : 16.46 % Favored : 81.01 % 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: 0.06 (0.22), residues: 1425 helix: 0.70 (0.21), residues: 633 sheet: 1.26 (0.40), residues: 177 loop : -1.01 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1095 HIS 0.005 0.001 HIS A 965 PHE 0.025 0.002 PHE A 305 TYR 0.014 0.002 TYR A 392 ARG 0.009 0.000 ARG B 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 76 ARG cc_start: 0.7390 (mmt90) cc_final: 0.7106 (mtt-85) REVERT: B 226 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7318 (mtp180) REVERT: B 241 TYR cc_start: 0.6344 (OUTLIER) cc_final: 0.6028 (m-10) REVERT: B 309 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8039 (mtm180) REVERT: A 163 ASP cc_start: 0.7094 (t70) cc_final: 0.6808 (t0) REVERT: A 241 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7492 (tpt) REVERT: A 350 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7727 (mp) REVERT: A 478 ASP cc_start: 0.7229 (m-30) cc_final: 0.6991 (m-30) REVERT: A 622 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7353 (p0) REVERT: A 638 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6212 (mp0) REVERT: A 674 MET cc_start: 0.7453 (mtp) cc_final: 0.7002 (mtp) REVERT: A 769 MET cc_start: 0.5485 (OUTLIER) cc_final: 0.4710 (tpt) REVERT: A 772 GLN cc_start: 0.6038 (mm110) cc_final: 0.5370 (mt0) REVERT: A 813 LYS cc_start: 0.7562 (mttm) cc_final: 0.7198 (mttm) REVERT: A 956 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.8069 (t80) REVERT: A 1215 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.6731 (mtp85) outliers start: 32 outliers final: 19 residues processed: 163 average time/residue: 1.1349 time to fit residues: 202.1868 Evaluate side-chains 166 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 956 TYR Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1144 TYR Chi-restraints excluded: chain A residue 1215 ARG Chi-restraints excluded: chain A residue 1223 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 16 optimal weight: 0.0970 chunk 31 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 14 optimal weight: 0.0000 chunk 20 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN A 517 GLN A 549 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.178755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.135184 restraints weight = 10898.452| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.62 r_work: 0.3338 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12025 Z= 0.148 Angle : 0.484 10.017 16295 Z= 0.250 Chirality : 0.041 0.304 1817 Planarity : 0.004 0.052 2058 Dihedral : 6.932 88.608 1708 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.29 % Allowed : 17.01 % Favored : 80.70 % 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: 0.26 (0.22), residues: 1425 helix: 0.92 (0.21), residues: 633 sheet: 1.09 (0.39), residues: 186 loop : -0.89 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1095 HIS 0.003 0.001 HIS A 535 PHE 0.026 0.001 PHE A 305 TYR 0.012 0.001 TYR B 297 ARG 0.009 0.000 ARG B 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4257.81 seconds wall clock time: 76 minutes 11.60 seconds (4571.60 seconds total)