Starting phenix.real_space_refine on Sun Apr 7 23:46:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox8_17260/04_2024/8ox8_17260_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox8_17260/04_2024/8ox8_17260.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox8_17260/04_2024/8ox8_17260_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox8_17260/04_2024/8ox8_17260_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox8_17260/04_2024/8ox8_17260_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox8_17260/04_2024/8ox8_17260.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox8_17260/04_2024/8ox8_17260.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox8_17260/04_2024/8ox8_17260_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox8_17260/04_2024/8ox8_17260_updated.pdb" } resolution = 2.98 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 56 5.16 5 C 7628 2.51 5 N 1989 2.21 5 O 2193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11872 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1125, 9119 Classifications: {'peptide': 1125} Link IDs: {'PTRANS': 28, 'TRANS': 1096} Chain breaks: 5 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: "B" Number of atoms: 2633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2633 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 25, 'TRANS': 301} 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: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {' MG': 1, 'IP9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.55, per 1000 atoms: 0.55 Number of scatterers: 11872 At special positions: 0 Unit cell: (83.8512, 96.2736, 175.984, 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 56 16.00 P 5 15.00 Mg 1 11.99 O 2193 8.00 N 1989 7.00 C 7628 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: 4.81 Conformation dependent library (CDL) restraints added in 2.3 seconds 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2742 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 10 sheets defined 43.3% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.664A pdb=" N PHE A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 132 Processing helix chain 'A' and resid 144 through 174 removed outlier: 4.189A pdb=" N LEU A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP A 162 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 173 " --> pdb=" O MET A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' 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 249 Processing helix chain 'A' and resid 253 through 257 removed outlier: 3.749A pdb=" N ALA A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 257' 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 321 No H-bonds generated for 'chain 'A' and resid 318 through 321' Processing helix chain 'A' and resid 332 through 365 removed outlier: 4.272A pdb=" N GLN A 365 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 381 through 399 removed outlier: 4.013A pdb=" N TRP A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N THR A 398 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N MET A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 420 Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 511 through 518 Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 553 through 564 Processing helix chain 'A' and resid 622 through 626 Processing helix chain 'A' and resid 636 through 648 Processing helix chain 'A' and resid 663 through 678 removed outlier: 3.528A pdb=" N LYS A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 694 removed outlier: 3.547A pdb=" N LYS A 689 " --> pdb=" O GLU A 685 " (cutoff:3.500A) removed outlier: 3.726A 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: 4.029A pdb=" N LYS A 839 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG A 840 " --> pdb=" O THR A 836 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG A 841 " --> pdb=" O GLN A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 884 Processing helix chain 'A' and resid 895 through 903 removed outlier: 4.225A pdb=" N ASN A 899 " --> pdb=" O ASN A 896 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET A 900 " --> pdb=" O ASP A 897 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 903 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 920 No H-bonds generated for 'chain 'A' and resid 917 through 920' Processing helix chain 'A' and resid 929 through 937 removed outlier: 3.694A pdb=" N LEU A 935 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 936 " --> pdb=" O GLN A 933 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 937 " --> pdb=" O ARG A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 962 removed outlier: 3.560A pdb=" N ASN A 958 " --> pdb=" O PHE A 954 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 959 " --> pdb=" O PHE A 955 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 961 " --> pdb=" O LYS A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 970 removed outlier: 4.323A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 991 removed outlier: 3.734A pdb=" N THR A 986 " --> pdb=" O ASP A 982 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL A 990 " --> pdb=" O THR A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1003 removed outlier: 3.539A pdb=" N LEU A 998 " --> pdb=" O SER A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1013 Processing helix chain 'A' and resid 1016 through 1023 removed outlier: 3.543A pdb=" N ILE A1020 " --> pdb=" O GLY A1017 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A1021 " --> pdb=" O LEU A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1056 Proline residue: A1051 - end of helix Processing helix chain 'A' and resid 1069 through 1091 removed outlier: 3.616A pdb=" N GLY A1089 " --> pdb=" O ASN A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1117 removed outlier: 3.528A pdb=" N ILE A1107 " --> pdb=" O ILE A1103 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N PHE A1115 " --> pdb=" O PHE A1111 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A1116 " --> pdb=" O GLY A1112 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A1117 " --> pdb=" O ILE A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1139 No H-bonds generated for 'chain 'A' and resid 1136 through 1139' Processing helix chain 'A' and resid 1143 through 1170 removed outlier: 3.531A pdb=" N ILE A1149 " --> pdb=" O ILE A1145 " (cutoff:3.500A) Proline residue: A1159 - end of helix Processing helix chain 'A' and resid 1174 through 1180 Processing helix chain 'A' and resid 1182 through 1184 No H-bonds generated for 'chain 'A' and resid 1182 through 1184' Processing helix chain 'A' and resid 1217 through 1222 Processing helix chain 'B' and resid 47 through 74 removed outlier: 3.699A pdb=" N LEU B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Proline residue: B 52 - end of helix removed outlier: 3.611A pdb=" N GLY B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Proline residue: B 63 - end of helix Processing helix chain 'B' and resid 92 through 96 removed outlier: 3.820A pdb=" N SER B 96 " --> pdb=" O LYS B 93 " (cutoff:3.500A) 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 150 No H-bonds generated for 'chain 'B' and resid 147 through 150' Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' 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 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 sheet with id= A, first strand: chain 'A' and resid 64 through 66 Processing sheet with id= B, first strand: chain 'A' and resid 199 through 203 removed outlier: 6.453A pdb=" N LEU A 309 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N LEU A 214 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 237 through 240 removed outlier: 3.969A pdb=" N TYR A 225 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 277 through 280 removed outlier: 4.058A pdb=" N GLY A 277 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 924 through 926 removed outlier: 6.482A pdb=" N TYR A 450 " --> pdb=" O LEU A 889 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE A 891 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE A 452 " --> pdb=" O ILE A 891 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LYS A 727 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N SER A 453 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N TRP A 729 " --> pdb=" O SER A 453 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL A 863 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 862 " --> pdb=" O ARG A 797 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N THR A 754 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ILE A 800 " --> pdb=" O THR A 754 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS A 756 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR A 802 " --> pdb=" O CYS A 756 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 474 through 476 removed outlier: 6.711A pdb=" N ALA A 705 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N CYS A 469 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA A 703 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ILE A 471 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N LEU A 701 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU A 656 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE A 614 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG A 608 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL A 590 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 538 through 540 Processing sheet with id= H, first strand: chain 'A' and resid 567 through 569 Processing sheet with id= I, first strand: chain 'B' and resid 78 through 81 removed outlier: 5.950A pdb=" N TYR B 122 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU B 272 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU B 124 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ARG B 270 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 102 through 109 removed outlier: 4.241A pdb=" N CYS B 102 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG B 290 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 182 " --> pdb=" O THR B 296 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1269 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: 4.05 Time building geometry restraints manager: 5.23 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: 1904 1.31 - 1.43: 3396 1.43 - 1.56: 6751 1.56 - 1.69: 7 1.69 - 1.81: 87 Bond restraints: 12145 Sorted by residual: bond pdb=" OD1 PHD A 454 " pdb=" P PHD A 454 " ideal model delta sigma weight residual 1.816 1.641 0.175 2.00e-02 2.50e+03 7.64e+01 bond pdb=" CG PHD A 454 " pdb=" OD1 PHD A 454 " ideal model delta sigma weight residual 1.300 1.395 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.561 -0.042 2.00e-02 2.50e+03 4.34e+00 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 2.62e+00 bond pdb=" CB GLN A 928 " pdb=" CG GLN A 928 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.85e+00 ... (remaining 12140 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.55: 276 106.55 - 113.41: 6619 113.41 - 120.27: 4465 120.27 - 127.13: 4966 127.13 - 133.98: 129 Bond angle restraints: 16455 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 97.64 109.45 -11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CB PHD A 454 " pdb=" CG PHD A 454 " pdb=" OD1 PHD A 454 " ideal model delta sigma weight residual 112.45 120.11 -7.66 3.00e+00 1.11e-01 6.52e+00 angle pdb=" OP2 PHD A 454 " pdb=" P PHD A 454 " pdb=" OP3 PHD A 454 " ideal model delta sigma weight residual 116.75 109.68 7.07 3.00e+00 1.11e-01 5.55e+00 angle pdb=" C3 BMA C 3 " pdb=" C2 BMA C 3 " pdb=" O2 BMA C 3 " ideal model delta sigma weight residual 112.95 106.08 6.87 3.00e+00 1.11e-01 5.24e+00 angle pdb=" CG PHD A 454 " pdb=" OD1 PHD A 454 " pdb=" P PHD A 454 " ideal model delta sigma weight residual 125.58 118.74 6.84 3.00e+00 1.11e-01 5.20e+00 ... (remaining 16450 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.41: 6798 22.41 - 44.82: 429 44.82 - 67.24: 27 67.24 - 89.65: 25 89.65 - 112.06: 6 Dihedral angle restraints: 7285 sinusoidal: 3031 harmonic: 4254 Sorted by residual: dihedral pdb=" CA ASN A1029 " pdb=" C ASN A1029 " pdb=" N TYR A1030 " pdb=" CA TYR A1030 " ideal model delta harmonic sigma weight residual 180.00 158.36 21.64 0 5.00e+00 4.00e-02 1.87e+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 -59.11 112.06 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" O4 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual 288.71 177.96 110.75 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 7282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1542 0.052 - 0.104: 231 0.104 - 0.155: 56 0.155 - 0.207: 0 0.207 - 0.259: 1 Chirality restraints: 1830 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 -2.53 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C2 BMA C 3 " pdb=" C1 BMA C 3 " pdb=" C3 BMA C 3 " pdb=" O2 BMA C 3 " both_signs ideal model delta sigma weight residual False 2.47 2.62 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA ILE A 706 " pdb=" N ILE A 706 " pdb=" C ILE A 706 " pdb=" CB ILE A 706 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 1827 not shown) Planarity restraints: 2081 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 995 " -0.052 5.00e-02 4.00e+02 7.87e-02 9.90e+00 pdb=" N PRO A 996 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 996 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 996 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 169 " -0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO B 170 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 170 " -0.027 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=" C ILE B 62 " 0.025 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO B 63 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 63 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 63 " 0.022 5.00e-02 4.00e+02 ... (remaining 2078 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 99 2.51 - 3.11: 9186 3.11 - 3.71: 18216 3.71 - 4.30: 27861 4.30 - 4.90: 46716 Nonbonded interactions: 102078 Sorted by model distance: nonbonded pdb=" O LEU A 441 " pdb=" OH TYR A 924 " model vdw 1.913 2.440 nonbonded pdb=" OD2 PHD A 454 " pdb="MG MG A1301 " model vdw 1.919 2.170 nonbonded pdb=" O3 NAG C 2 " pdb=" O2 BMA C 3 " model vdw 2.023 2.440 nonbonded pdb=" OG SER A 403 " pdb=" O HOH A1401 " model vdw 2.027 2.440 nonbonded pdb=" NH2 ARG B 162 " pdb=" O ASP B 165 " model vdw 2.069 2.520 ... (remaining 102073 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: 0.730 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: 3.620 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 34.750 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:11.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 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 : 0.005 0.175 12145 Z= 0.302 Angle : 0.546 11.809 16455 Z= 0.281 Chirality : 0.040 0.259 1830 Planarity : 0.004 0.079 2078 Dihedral : 14.912 112.059 4534 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: -0.95 (0.21), residues: 1435 helix: -0.38 (0.20), residues: 608 sheet: -0.05 (0.37), residues: 195 loop : -0.94 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 317 HIS 0.004 0.001 HIS A 74 PHE 0.010 0.001 PHE A 961 TYR 0.011 0.001 TYR A 924 ARG 0.003 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.299 Fit side-chains REVERT: A 168 LYS cc_start: 0.7845 (tmmt) cc_final: 0.7584 (ptpt) REVERT: A 834 MET cc_start: 0.5922 (tpp) cc_final: 0.5661 (tpt) REVERT: A 847 GLU cc_start: 0.7109 (tt0) cc_final: 0.6897 (tt0) REVERT: A 982 ASP cc_start: 0.7716 (t0) cc_final: 0.7389 (t0) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 1.2190 time to fit residues: 233.6712 Evaluate side-chains 127 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 115 GLN A 442 ASN A 526 GLN A 771 ASN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12145 Z= 0.198 Angle : 0.548 9.489 16455 Z= 0.281 Chirality : 0.042 0.325 1830 Planarity : 0.004 0.058 2078 Dihedral : 9.046 98.120 1723 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.18 % Allowed : 7.60 % Favored : 91.22 % 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: -0.10 (0.22), residues: 1435 helix: 0.58 (0.21), residues: 621 sheet: 0.35 (0.38), residues: 185 loop : -0.78 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 260 HIS 0.003 0.001 HIS A 307 PHE 0.020 0.001 PHE A 666 TYR 0.009 0.001 TYR B 82 ARG 0.005 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 1.313 Fit side-chains REVERT: A 168 LYS cc_start: 0.7691 (tmmt) cc_final: 0.7418 (ptpt) REVERT: A 190 LYS cc_start: 0.7882 (mtpp) cc_final: 0.7538 (mtpt) REVERT: A 345 PHE cc_start: 0.7208 (t80) cc_final: 0.6979 (t80) REVERT: A 392 TYR cc_start: 0.8607 (m-80) cc_final: 0.8057 (m-80) REVERT: A 464 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7418 (mtm) REVERT: A 701 LEU cc_start: 0.8290 (mt) cc_final: 0.7964 (mt) REVERT: A 982 ASP cc_start: 0.7529 (t0) cc_final: 0.7113 (t0) REVERT: B 42 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7407 (mp10) outliers start: 15 outliers final: 7 residues processed: 155 average time/residue: 0.9868 time to fit residues: 170.3116 Evaluate side-chains 140 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 242 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.2980 chunk 40 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 141 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 129 optimal weight: 0.0970 chunk 44 optimal weight: 0.0980 chunk 105 optimal weight: 0.7980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 115 GLN A 613 ASN A 771 ASN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 GLN B 152 ASN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12145 Z= 0.144 Angle : 0.494 9.518 16455 Z= 0.249 Chirality : 0.040 0.285 1830 Planarity : 0.003 0.046 2078 Dihedral : 8.066 96.852 1723 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.88 % Allowed : 10.19 % Favored : 87.93 % 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: 0.24 (0.22), residues: 1435 helix: 1.00 (0.22), residues: 622 sheet: 0.52 (0.39), residues: 185 loop : -0.76 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 260 HIS 0.003 0.001 HIS A1181 PHE 0.018 0.001 PHE A 666 TYR 0.011 0.001 TYR B 121 ARG 0.006 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 1.278 Fit side-chains REVERT: A 168 LYS cc_start: 0.7672 (tmmt) cc_final: 0.7281 (ptpt) REVERT: A 190 LYS cc_start: 0.7821 (mtpp) cc_final: 0.7142 (mtpt) REVERT: A 325 LYS cc_start: 0.7288 (tmtt) cc_final: 0.7050 (tmtm) REVERT: A 345 PHE cc_start: 0.7207 (t80) cc_final: 0.6983 (t80) REVERT: A 392 TYR cc_start: 0.8573 (m-80) cc_final: 0.8111 (m-80) REVERT: A 464 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7365 (mtm) REVERT: A 591 LEU cc_start: 0.9114 (mp) cc_final: 0.8911 (mp) REVERT: A 701 LEU cc_start: 0.8277 (mt) cc_final: 0.8001 (mt) REVERT: A 769 MET cc_start: 0.6988 (OUTLIER) cc_final: 0.6785 (tpt) REVERT: A 982 ASP cc_start: 0.7497 (t0) cc_final: 0.7172 (t0) REVERT: A 1010 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.8030 (ttmt) REVERT: A 1020 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8089 (mt) REVERT: B 42 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7371 (mp10) outliers start: 24 outliers final: 9 residues processed: 150 average time/residue: 0.9752 time to fit residues: 164.0101 Evaluate side-chains 143 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 242 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 87 optimal weight: 0.2980 chunk 131 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 37 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 115 GLN A 613 ASN A 771 ASN A 958 ASN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1087 GLN B 152 ASN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12145 Z= 0.163 Angle : 0.487 9.590 16455 Z= 0.245 Chirality : 0.040 0.267 1830 Planarity : 0.003 0.041 2078 Dihedral : 7.419 94.389 1723 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.96 % Allowed : 12.70 % Favored : 85.34 % 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: 0.42 (0.23), residues: 1435 helix: 1.16 (0.22), residues: 624 sheet: 0.68 (0.39), residues: 185 loop : -0.71 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 260 HIS 0.004 0.001 HIS A1181 PHE 0.016 0.001 PHE A1072 TYR 0.010 0.001 TYR B 121 ARG 0.005 0.000 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 1.373 Fit side-chains REVERT: A 168 LYS cc_start: 0.7707 (tmmt) cc_final: 0.7273 (ptpt) REVERT: A 190 LYS cc_start: 0.7861 (mtpp) cc_final: 0.7181 (mtpt) REVERT: A 345 PHE cc_start: 0.7209 (t80) cc_final: 0.7005 (t80) REVERT: A 409 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6370 (mp0) REVERT: A 464 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7386 (mtm) REVERT: A 465 THR cc_start: 0.8075 (p) cc_final: 0.7787 (p) REVERT: A 701 LEU cc_start: 0.8262 (mt) cc_final: 0.8015 (mt) REVERT: A 769 MET cc_start: 0.6982 (OUTLIER) cc_final: 0.6703 (tpt) REVERT: A 834 MET cc_start: 0.6233 (mmm) cc_final: 0.5832 (tpt) REVERT: B 42 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7355 (mp10) outliers start: 25 outliers final: 10 residues processed: 146 average time/residue: 0.9034 time to fit residues: 148.3391 Evaluate side-chains 142 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 682 ASN Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 242 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 0.2980 chunk 118 optimal weight: 30.0000 chunk 96 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 115 GLN ** A 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN A1138 ASN B 152 ASN B 176 ASN B 235 ASN ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 12145 Z= 0.474 Angle : 0.615 9.669 16455 Z= 0.309 Chirality : 0.046 0.274 1830 Planarity : 0.004 0.036 2078 Dihedral : 7.498 90.457 1723 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.98 % Allowed : 13.64 % Favored : 83.39 % 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: 1435 helix: 0.74 (0.21), residues: 617 sheet: 0.43 (0.38), residues: 198 loop : -0.87 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 64 HIS 0.006 0.001 HIS A 417 PHE 0.021 0.002 PHE A 527 TYR 0.015 0.002 TYR A 123 ARG 0.006 0.001 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 132 time to evaluate : 1.312 Fit side-chains REVERT: A 98 LYS cc_start: 0.7095 (mmmm) cc_final: 0.6771 (mmtt) REVERT: A 108 ILE cc_start: 0.7884 (mm) cc_final: 0.7630 (mp) REVERT: A 112 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7182 (mp) REVERT: A 168 LYS cc_start: 0.8055 (tmmt) cc_final: 0.7543 (ptpt) REVERT: A 345 PHE cc_start: 0.7291 (t80) cc_final: 0.7072 (t80) REVERT: A 409 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6467 (mp0) REVERT: A 465 THR cc_start: 0.8289 (p) cc_final: 0.8044 (p) REVERT: A 701 LEU cc_start: 0.8394 (mt) cc_final: 0.8105 (mt) REVERT: A 769 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.6719 (tpt) REVERT: A 834 MET cc_start: 0.6236 (mmm) cc_final: 0.5923 (tpt) REVERT: A 982 ASP cc_start: 0.7619 (t0) cc_final: 0.7156 (t0) REVERT: A 1215 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7763 (mtp-110) REVERT: B 42 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7365 (mp10) outliers start: 38 outliers final: 14 residues processed: 156 average time/residue: 0.9229 time to fit residues: 161.5287 Evaluate side-chains 147 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 682 ASN Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1215 ARG Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 7.9990 chunk 125 optimal weight: 0.0070 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 115 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 134 optimal weight: 4.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 ASN A 771 ASN A 977 GLN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN B 152 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 12145 Z= 0.158 Angle : 0.495 9.588 16455 Z= 0.250 Chirality : 0.040 0.261 1830 Planarity : 0.003 0.035 2078 Dihedral : 7.094 89.507 1723 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.04 % Allowed : 15.36 % Favored : 82.60 % 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: 0.32 (0.23), residues: 1435 helix: 1.06 (0.22), residues: 624 sheet: 0.73 (0.40), residues: 185 loop : -0.79 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 260 HIS 0.004 0.001 HIS A1181 PHE 0.015 0.001 PHE A1072 TYR 0.011 0.001 TYR A 123 ARG 0.005 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 137 time to evaluate : 1.451 Fit side-chains REVERT: A 98 LYS cc_start: 0.6930 (mmmm) cc_final: 0.6630 (mmtt) REVERT: A 108 ILE cc_start: 0.7892 (mm) cc_final: 0.7674 (mp) REVERT: A 168 LYS cc_start: 0.7945 (tmmt) cc_final: 0.7496 (ptpt) REVERT: A 190 LYS cc_start: 0.7964 (mtmm) cc_final: 0.7306 (mtpt) REVERT: A 345 PHE cc_start: 0.7235 (t80) cc_final: 0.7025 (t80) REVERT: A 409 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6347 (mp0) REVERT: A 464 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8082 (mtt) REVERT: A 465 THR cc_start: 0.8207 (p) cc_final: 0.7950 (p) REVERT: A 591 LEU cc_start: 0.9199 (mt) cc_final: 0.8983 (mp) REVERT: A 701 LEU cc_start: 0.8336 (mt) cc_final: 0.8077 (mt) REVERT: A 834 MET cc_start: 0.6180 (mmm) cc_final: 0.5873 (tpt) REVERT: A 982 ASP cc_start: 0.7541 (t0) cc_final: 0.7075 (t0) REVERT: B 42 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7229 (mp10) outliers start: 26 outliers final: 12 residues processed: 155 average time/residue: 0.9191 time to fit residues: 160.1733 Evaluate side-chains 147 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 0.0670 chunk 77 optimal weight: 0.9980 chunk 138 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 115 GLN A 479 HIS A 670 ASN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN B 152 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12145 Z= 0.182 Angle : 0.495 9.585 16455 Z= 0.248 Chirality : 0.041 0.262 1830 Planarity : 0.003 0.035 2078 Dihedral : 6.930 88.591 1723 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.57 % Allowed : 16.61 % Favored : 81.82 % 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: 0.39 (0.23), residues: 1435 helix: 1.17 (0.22), residues: 624 sheet: 0.77 (0.40), residues: 184 loop : -0.81 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 260 HIS 0.004 0.001 HIS A1181 PHE 0.014 0.001 PHE A1072 TYR 0.011 0.001 TYR A 123 ARG 0.005 0.000 ARG A 480 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.513 Fit side-chains REVERT: A 70 ASP cc_start: 0.6825 (OUTLIER) cc_final: 0.6338 (m-30) REVERT: A 98 LYS cc_start: 0.6976 (mmmm) cc_final: 0.6683 (mmtt) REVERT: A 108 ILE cc_start: 0.7907 (mm) cc_final: 0.7649 (mp) REVERT: A 168 LYS cc_start: 0.7992 (tmmt) cc_final: 0.7502 (ptpt) REVERT: A 190 LYS cc_start: 0.7982 (mtmm) cc_final: 0.7321 (mtpt) REVERT: A 345 PHE cc_start: 0.7262 (t80) cc_final: 0.7053 (t80) REVERT: A 409 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6477 (mp0) REVERT: A 464 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8082 (mtt) REVERT: A 465 THR cc_start: 0.8188 (p) cc_final: 0.7920 (p) REVERT: A 701 LEU cc_start: 0.8326 (mt) cc_final: 0.8089 (mt) REVERT: A 834 MET cc_start: 0.6169 (mmm) cc_final: 0.5867 (tpt) REVERT: B 42 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7234 (mp10) outliers start: 20 outliers final: 11 residues processed: 150 average time/residue: 0.9390 time to fit residues: 159.2877 Evaluate side-chains 148 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 5.9990 chunk 82 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 109 optimal weight: 0.0670 chunk 126 optimal weight: 4.9990 overall best weight: 0.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 115 GLN A 479 HIS A 613 ASN A 670 ASN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN B 152 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 12145 Z= 0.167 Angle : 0.488 9.570 16455 Z= 0.245 Chirality : 0.040 0.261 1830 Planarity : 0.003 0.036 2078 Dihedral : 6.750 87.203 1723 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.88 % Allowed : 16.61 % Favored : 81.50 % 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: 0.44 (0.23), residues: 1435 helix: 1.19 (0.22), residues: 630 sheet: 0.81 (0.40), residues: 185 loop : -0.77 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 260 HIS 0.004 0.001 HIS A1181 PHE 0.015 0.001 PHE A1072 TYR 0.016 0.001 TYR A 342 ARG 0.006 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 1.363 Fit side-chains REVERT: A 70 ASP cc_start: 0.6809 (OUTLIER) cc_final: 0.6366 (m-30) REVERT: A 98 LYS cc_start: 0.6952 (mmmm) cc_final: 0.6642 (mmtt) REVERT: A 108 ILE cc_start: 0.7842 (mm) cc_final: 0.7634 (mp) REVERT: A 168 LYS cc_start: 0.8020 (tmmt) cc_final: 0.7464 (ptpt) REVERT: A 325 LYS cc_start: 0.7205 (tmtt) cc_final: 0.7005 (tmtm) REVERT: A 345 PHE cc_start: 0.7253 (t80) cc_final: 0.7033 (t80) REVERT: A 392 TYR cc_start: 0.8454 (m-80) cc_final: 0.8152 (m-80) REVERT: A 409 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6500 (mp0) REVERT: A 465 THR cc_start: 0.8081 (p) cc_final: 0.7784 (p) REVERT: A 701 LEU cc_start: 0.8281 (mt) cc_final: 0.8031 (mt) REVERT: A 834 MET cc_start: 0.6260 (mmm) cc_final: 0.5938 (tpt) REVERT: A 1215 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7640 (ptp-110) REVERT: B 42 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7277 (mp10) REVERT: B 166 LYS cc_start: 0.7561 (pttm) cc_final: 0.7325 (ptpp) outliers start: 24 outliers final: 12 residues processed: 156 average time/residue: 0.9133 time to fit residues: 160.8693 Evaluate side-chains 148 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1215 ARG Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 115 GLN A 547 ASN A 670 ASN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 12145 Z= 0.182 Angle : 0.493 9.570 16455 Z= 0.247 Chirality : 0.040 0.261 1830 Planarity : 0.003 0.037 2078 Dihedral : 6.715 86.373 1723 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.33 % Allowed : 17.55 % 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: 0.44 (0.23), residues: 1435 helix: 1.18 (0.22), residues: 630 sheet: 0.83 (0.41), residues: 180 loop : -0.76 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 260 HIS 0.005 0.001 HIS A1181 PHE 0.014 0.001 PHE A1072 TYR 0.010 0.001 TYR B 121 ARG 0.006 0.000 ARG A 480 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 1.432 Fit side-chains REVERT: A 70 ASP cc_start: 0.6811 (OUTLIER) cc_final: 0.6409 (m-30) REVERT: A 98 LYS cc_start: 0.6949 (mmmm) cc_final: 0.6637 (mmtt) REVERT: A 108 ILE cc_start: 0.7848 (mm) cc_final: 0.7639 (mp) REVERT: A 168 LYS cc_start: 0.7999 (tmmt) cc_final: 0.7435 (ptpt) REVERT: A 325 LYS cc_start: 0.7243 (tmtt) cc_final: 0.7013 (tmtm) REVERT: A 345 PHE cc_start: 0.7247 (t80) cc_final: 0.7037 (t80) REVERT: A 392 TYR cc_start: 0.8498 (m-80) cc_final: 0.8244 (m-80) REVERT: A 409 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6516 (mp0) REVERT: A 465 THR cc_start: 0.8080 (p) cc_final: 0.7786 (p) REVERT: A 701 LEU cc_start: 0.8286 (mt) cc_final: 0.8029 (mt) REVERT: A 834 MET cc_start: 0.6301 (mmm) cc_final: 0.5965 (tpt) REVERT: B 42 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7208 (mp10) REVERT: B 166 LYS cc_start: 0.7603 (pttm) cc_final: 0.7347 (ptpp) outliers start: 17 outliers final: 12 residues processed: 150 average time/residue: 0.9632 time to fit residues: 161.8179 Evaluate side-chains 147 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 95 optimal weight: 0.5980 chunk 143 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 115 GLN A 547 ASN A 613 ASN A 670 ASN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12145 Z= 0.234 Angle : 0.519 9.591 16455 Z= 0.259 Chirality : 0.041 0.263 1830 Planarity : 0.003 0.036 2078 Dihedral : 6.768 84.936 1723 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.41 % Allowed : 17.79 % Favored : 80.80 % 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: 0.33 (0.23), residues: 1435 helix: 1.07 (0.21), residues: 629 sheet: 0.81 (0.41), residues: 179 loop : -0.81 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 260 HIS 0.006 0.001 HIS A1181 PHE 0.015 0.001 PHE A 527 TYR 0.020 0.001 TYR A 342 ARG 0.005 0.000 ARG A 282 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 1.313 Fit side-chains REVERT: A 70 ASP cc_start: 0.6804 (OUTLIER) cc_final: 0.6372 (m-30) REVERT: A 98 LYS cc_start: 0.6980 (mmmm) cc_final: 0.6645 (mmtt) REVERT: A 110 MET cc_start: 0.6581 (ttm) cc_final: 0.6265 (mtp) REVERT: A 168 LYS cc_start: 0.7979 (tmmt) cc_final: 0.7390 (ptpt) REVERT: A 190 LYS cc_start: 0.8111 (mtpp) cc_final: 0.7462 (mtpp) REVERT: A 193 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7616 (mt-10) REVERT: A 345 PHE cc_start: 0.7257 (t80) cc_final: 0.7050 (t80) REVERT: A 392 TYR cc_start: 0.8559 (m-80) cc_final: 0.7927 (m-80) REVERT: A 409 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6514 (mp0) REVERT: A 465 THR cc_start: 0.8046 (p) cc_final: 0.7745 (p) REVERT: A 701 LEU cc_start: 0.8328 (mt) cc_final: 0.8080 (mt) REVERT: A 834 MET cc_start: 0.6288 (mmm) cc_final: 0.5945 (tpt) REVERT: A 1215 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7676 (ptp-110) REVERT: B 42 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7219 (mp10) outliers start: 18 outliers final: 11 residues processed: 148 average time/residue: 0.9541 time to fit residues: 158.2054 Evaluate side-chains 144 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1215 ARG Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 547 ASN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.162016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.116673 restraints weight = 13396.977| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.33 r_work: 0.3253 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12145 Z= 0.185 Angle : 0.502 9.570 16455 Z= 0.251 Chirality : 0.040 0.261 1830 Planarity : 0.003 0.036 2078 Dihedral : 6.700 84.241 1723 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.33 % Allowed : 18.18 % Favored : 80.49 % 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: 0.38 (0.23), residues: 1435 helix: 1.15 (0.22), residues: 627 sheet: 0.77 (0.41), residues: 180 loop : -0.81 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 260 HIS 0.006 0.001 HIS A1181 PHE 0.014 0.001 PHE A1072 TYR 0.011 0.001 TYR B 121 ARG 0.006 0.000 ARG A 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3843.29 seconds wall clock time: 70 minutes 17.15 seconds (4217.15 seconds total)