Starting phenix.real_space_refine on Sun Aug 24 08:55:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qed_18352/08_2025/8qed_18352_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qed_18352/08_2025/8qed_18352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qed_18352/08_2025/8qed_18352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qed_18352/08_2025/8qed_18352.map" model { file = "/net/cci-nas-00/data/ceres_data/8qed_18352/08_2025/8qed_18352_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qed_18352/08_2025/8qed_18352_trim.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.001 sd= 0.030 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 1 5.49 5 S 57 5.16 5 C 5901 2.51 5 N 1406 2.21 5 O 1666 1.98 5 H 8712 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17743 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 17523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 17523 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 47, 'TRANS': 1053} Chain breaks: 2 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: "C" 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: "D" 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: "E" 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: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 108 Unusual residues: {'ERG': 2, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.59, per 1000 atoms: 0.20 Number of scatterers: 17743 At special positions: 0 Unit cell: (84.63, 104.16, 161.448, 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 57 16.00 P 1 15.00 O 1666 8.00 N 1406 7.00 C 5901 6.00 H 8712 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 75 " distance=2.03 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 41 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 110 " distance=2.03 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 235 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 438 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 480 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 828 " distance=2.03 Simple disulfide: pdb=" SG CYS A 868 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A 869 " - pdb=" SG CYS A 891 " distance=2.03 Simple disulfide: pdb=" SG CYS A 879 " - pdb=" SG CYS A 888 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B 1 " - " ASN A 900 " " NAG C 1 " - " ASN A 513 " " NAG D 1 " - " ASN A 940 " " NAG E 1 " - " ASN A 401 " Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 604.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 7 sheets defined 60.7% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.675A pdb=" N LEU A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.540A pdb=" N TRP A 68 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 96 removed outlier: 3.507A pdb=" N VAL A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 98 through 115 Processing helix chain 'A' and resid 117 through 121 removed outlier: 4.385A pdb=" N PHE A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 117 through 121' Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 256 through 279 removed outlier: 3.888A pdb=" N TYR A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 279 " --> pdb=" O MET A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 337 removed outlier: 3.797A pdb=" N ASN A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLU A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 359 removed outlier: 3.786A pdb=" N THR A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 375 through 389 removed outlier: 3.643A pdb=" N LYS A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 425 removed outlier: 3.553A pdb=" N ASN A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'A' and resid 451 through 457 Processing helix chain 'A' and resid 465 through 476 Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 515 through 531 removed outlier: 3.691A pdb=" N ASN A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 553 removed outlier: 3.741A pdb=" N ASN A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 576 Processing helix chain 'A' and resid 584 through 609 removed outlier: 3.675A pdb=" N GLY A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 608 " --> pdb=" O GLY A 604 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 630 removed outlier: 3.873A pdb=" N VAL A 620 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE A 621 " --> pdb=" O ILE A 617 " (cutoff:3.500A) Proline residue: A 622 - end of helix removed outlier: 3.523A pdb=" N ILE A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 646 removed outlier: 3.675A pdb=" N PHE A 634 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 635 " --> pdb=" O ASP A 631 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU A 645 " --> pdb=" O ASP A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 663 removed outlier: 3.505A pdb=" N ILE A 657 " --> pdb=" O ASP A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 682 removed outlier: 3.527A pdb=" N CYS A 677 " --> pdb=" O CYS A 673 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N PHE A 678 " --> pdb=" O GLN A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 710 removed outlier: 3.572A pdb=" N PHE A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN A 703 " --> pdb=" O SER A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 723 removed outlier: 3.711A pdb=" N LYS A 720 " --> pdb=" O SER A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 747 Processing helix chain 'A' and resid 748 through 765 removed outlier: 3.724A pdb=" N VAL A 765 " --> pdb=" O PHE A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 770 Processing helix chain 'A' and resid 775 through 780 removed outlier: 3.838A pdb=" N ALA A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 797 removed outlier: 4.111A pdb=" N ASP A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR A 789 " --> pdb=" O TYR A 785 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER A 795 " --> pdb=" O LYS A 791 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 797 " --> pdb=" O VAL A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 819 Processing helix chain 'A' and resid 832 through 841 Processing helix chain 'A' and resid 852 through 861 removed outlier: 3.582A pdb=" N ASP A 856 " --> pdb=" O ASN A 852 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 861 " --> pdb=" O TYR A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 897 removed outlier: 3.932A pdb=" N TRP A 897 " --> pdb=" O GLN A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 919 removed outlier: 4.320A pdb=" N MET A 911 " --> pdb=" O GLY A 907 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE A 916 " --> pdb=" O GLU A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 974 removed outlier: 3.571A pdb=" N SER A 973 " --> pdb=" O GLY A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1021 removed outlier: 3.571A pdb=" N LEU A1002 " --> pdb=" O GLY A 998 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A1005 " --> pdb=" O THR A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1048 removed outlier: 3.738A pdb=" N LEU A1028 " --> pdb=" O ARG A1024 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A1048 " --> pdb=" O MET A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1079 removed outlier: 4.003A pdb=" N VAL A1063 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY A1064 " --> pdb=" O ILE A1060 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A1069 " --> pdb=" O LEU A1065 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS A1070 " --> pdb=" O GLY A1066 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N HIS A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE A1073 " --> pdb=" O PHE A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1099 Processing helix chain 'A' and resid 1099 through 1106 Processing helix chain 'A' and resid 1107 through 1117 removed outlier: 3.810A pdb=" N LYS A1111 " --> pdb=" O ILE A1107 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A1117 " --> pdb=" O ILE A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1120 No H-bonds generated for 'chain 'A' and resid 1118 through 1120' Processing helix chain 'A' and resid 1123 through 1130 removed outlier: 3.944A pdb=" N ASP A1127 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1155 removed outlier: 3.689A pdb=" N TRP A1134 " --> pdb=" O TYR A1130 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A1146 " --> pdb=" O ALA A1142 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU A1149 " --> pdb=" O ALA A1145 " (cutoff:3.500A) Proline residue: A1150 - end of helix removed outlier: 3.870A pdb=" N LEU A1155 " --> pdb=" O ALA A1151 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 4.428A pdb=" N GLY A 30 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 129 removed outlier: 6.547A pdb=" N VAL A 122 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 142 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE A 124 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU A 140 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LYS A 126 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N GLN A 199 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA A 138 " --> pdb=" O GLN A 199 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ASN A 201 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU A 140 " --> pdb=" O ASN A 201 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LYS A 203 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL A 142 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 160 through 161 Processing sheet with id=AA4, first strand: chain 'A' and resid 393 through 394 Processing sheet with id=AA5, first strand: chain 'A' and resid 393 through 394 Processing sheet with id=AA6, first strand: chain 'A' and resid 937 through 939 removed outlier: 6.733A pdb=" N VAL A 938 " --> pdb=" O SER A 945 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 949 " --> pdb=" O MET A 805 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP A 980 " --> pdb=" O LYS A 808 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 871 through 872 440 hydrogen bonds defined for protein. 1257 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: 4.34 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 8702 1.04 - 1.23: 188 1.23 - 1.43: 3732 1.43 - 1.63: 5268 1.63 - 1.82: 78 Bond restraints: 17968 Sorted by residual: bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.18e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.96e+00 bond pdb=" C6 ERG A1201 " pdb=" C7 ERG A1201 " ideal model delta sigma weight residual 1.452 1.411 0.041 2.00e-02 2.50e+03 4.23e+00 bond pdb=" C6 ERG A1200 " pdb=" C7 ERG A1200 " ideal model delta sigma weight residual 1.452 1.414 0.038 2.00e-02 2.50e+03 3.60e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.53e+00 ... (remaining 17963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.00: 32371 7.00 - 14.01: 0 14.01 - 21.01: 0 21.01 - 28.02: 0 28.02 - 35.02: 3 Bond angle restraints: 32374 Sorted by residual: angle pdb=" C GLU A 551 " pdb=" CA GLU A 551 " pdb=" HA GLU A 551 " ideal model delta sigma weight residual 109.00 73.98 35.02 3.00e+00 1.11e-01 1.36e+02 angle pdb=" N GLU A 551 " pdb=" CA GLU A 551 " pdb=" HA GLU A 551 " ideal model delta sigma weight residual 110.00 75.53 34.47 3.00e+00 1.11e-01 1.32e+02 angle pdb=" CB GLU A 551 " pdb=" CA GLU A 551 " pdb=" HA GLU A 551 " ideal model delta sigma weight residual 109.00 76.41 32.59 3.00e+00 1.11e-01 1.18e+02 angle pdb=" N THR A 942 " pdb=" CA THR A 942 " pdb=" C THR A 942 " ideal model delta sigma weight residual 114.62 111.04 3.58 1.14e+00 7.69e-01 9.87e+00 angle pdb=" N GLU A 551 " pdb=" CA GLU A 551 " pdb=" C GLU A 551 " ideal model delta sigma weight residual 113.23 116.14 -2.91 1.24e+00 6.50e-01 5.52e+00 ... (remaining 32369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 7855 17.64 - 35.29: 686 35.29 - 52.93: 186 52.93 - 70.58: 57 70.58 - 88.22: 18 Dihedral angle restraints: 8802 sinusoidal: 4806 harmonic: 3996 Sorted by residual: dihedral pdb=" CB CYS A 98 " pdb=" SG CYS A 98 " pdb=" SG CYS A 230 " pdb=" CB CYS A 230 " ideal model delta sinusoidal sigma weight residual -86.00 -142.90 56.90 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CB CYS A 223 " pdb=" SG CYS A 223 " pdb=" SG CYS A 235 " pdb=" CB CYS A 235 " ideal model delta sinusoidal sigma weight residual -86.00 -37.67 -48.33 1 1.00e+01 1.00e-02 3.22e+01 dihedral pdb=" CB CYS A 822 " pdb=" SG CYS A 822 " pdb=" SG CYS A 828 " pdb=" CB CYS A 828 " ideal model delta sinusoidal sigma weight residual -86.00 -131.50 45.50 1 1.00e+01 1.00e-02 2.87e+01 ... (remaining 8799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1359 0.082 - 0.164: 77 0.164 - 0.247: 1 0.247 - 0.329: 2 0.329 - 0.411: 1 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CA GLU A 551 " pdb=" N GLU A 551 " pdb=" C GLU A 551 " pdb=" CB GLU A 551 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" C20 ERG A1200 " pdb=" C17 ERG A1200 " pdb=" C21 ERG A1200 " pdb=" C22 ERG A1200 " both_signs ideal model delta sigma weight residual False 2.58 2.30 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 900 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1437 not shown) Planarity restraints: 2618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 621 " -0.019 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO A 622 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 622 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 622 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 931 " 0.015 5.00e-02 4.00e+02 2.28e-02 8.32e-01 pdb=" N PRO A 932 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 932 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 932 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 239 " -0.014 5.00e-02 4.00e+02 2.17e-02 7.50e-01 pdb=" N PRO A 240 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 240 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 240 " -0.012 5.00e-02 4.00e+02 ... (remaining 2615 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 798 2.19 - 2.79: 35561 2.79 - 3.39: 48799 3.39 - 4.00: 62796 4.00 - 4.60: 97150 Nonbonded interactions: 245104 Sorted by model distance: nonbonded pdb=" OE1 GLU A 551 " pdb=" HG SER A 784 " model vdw 1.582 2.450 nonbonded pdb=" OE1 GLU A 410 " pdb=" H GLU A 410 " model vdw 1.608 2.450 nonbonded pdb=" HG SER A 547 " pdb=" OH TYR A 785 " model vdw 1.619 2.450 nonbonded pdb=" H GLU A 551 " pdb=" HA GLU A 551 " model vdw 1.628 1.816 nonbonded pdb=" OD1 ASN A 898 " pdb=" HG SER A 902 " model vdw 1.631 2.450 ... (remaining 245099 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 0.120 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.700 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 0.046 9278 Z= 0.161 Angle : 0.527 10.248 12617 Z= 0.255 Chirality : 0.040 0.411 1440 Planarity : 0.002 0.029 1563 Dihedral : 15.814 88.221 3591 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.75 % Favored : 95.07 % Rotamer: Outliers : 0.10 % Allowed : 11.94 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.26), residues: 1095 helix: 1.19 (0.23), residues: 574 sheet: -1.18 (0.66), residues: 71 loop : -0.56 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 539 TYR 0.009 0.001 TYR A 789 PHE 0.014 0.001 PHE A 982 TRP 0.005 0.001 TRP A 415 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 9256) covalent geometry : angle 0.50125 (12565) SS BOND : bond 0.00174 ( 14) SS BOND : angle 0.41814 ( 28) hydrogen bonds : bond 0.24762 ( 438) hydrogen bonds : angle 8.26543 ( 1257) link_BETA1-4 : bond 0.01233 ( 4) link_BETA1-4 : angle 5.13304 ( 12) link_NAG-ASN : bond 0.00231 ( 4) link_NAG-ASN : angle 1.59264 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 73 average time/residue: 0.1601 time to fit residues: 18.5180 Evaluate side-chains 69 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 951 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.147013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104333 restraints weight = 36179.996| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.41 r_work: 0.2936 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9278 Z= 0.183 Angle : 0.575 8.176 12617 Z= 0.307 Chirality : 0.041 0.410 1440 Planarity : 0.003 0.031 1563 Dihedral : 6.771 55.176 1519 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.43 % Rotamer: Outliers : 0.71 % Allowed : 11.64 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.26), residues: 1095 helix: 1.03 (0.21), residues: 596 sheet: -1.19 (0.66), residues: 71 loop : -0.52 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 662 TYR 0.011 0.001 TYR A 571 PHE 0.018 0.001 PHE A 505 TRP 0.010 0.001 TRP A 415 HIS 0.004 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 9256) covalent geometry : angle 0.56345 (12565) SS BOND : bond 0.00291 ( 14) SS BOND : angle 0.50508 ( 28) hydrogen bonds : bond 0.07019 ( 438) hydrogen bonds : angle 5.80659 ( 1257) link_BETA1-4 : bond 0.00570 ( 4) link_BETA1-4 : angle 3.54767 ( 12) link_NAG-ASN : bond 0.00267 ( 4) link_NAG-ASN : angle 1.51327 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 PHE cc_start: 0.8039 (m-10) cc_final: 0.7827 (m-10) REVERT: A 567 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8263 (mtp) REVERT: A 859 MET cc_start: 0.8826 (mmm) cc_final: 0.8596 (mmm) outliers start: 7 outliers final: 5 residues processed: 81 average time/residue: 0.1591 time to fit residues: 20.7994 Evaluate side-chains 77 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 951 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 10 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 387 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.147290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.104643 restraints weight = 36371.375| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.41 r_work: 0.2982 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9278 Z= 0.168 Angle : 0.530 7.974 12617 Z= 0.275 Chirality : 0.040 0.409 1440 Planarity : 0.003 0.032 1563 Dihedral : 6.504 53.199 1519 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.21 % Favored : 94.70 % Rotamer: Outliers : 1.01 % Allowed : 12.04 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.26), residues: 1095 helix: 0.94 (0.21), residues: 598 sheet: -1.30 (0.64), residues: 71 loop : -0.54 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 524 TYR 0.014 0.001 TYR A 228 PHE 0.018 0.001 PHE A 505 TRP 0.014 0.001 TRP A 415 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 9256) covalent geometry : angle 0.51668 (12565) SS BOND : bond 0.00303 ( 14) SS BOND : angle 0.53948 ( 28) hydrogen bonds : bond 0.05466 ( 438) hydrogen bonds : angle 5.26796 ( 1257) link_BETA1-4 : bond 0.00655 ( 4) link_BETA1-4 : angle 3.50023 ( 12) link_NAG-ASN : bond 0.00347 ( 4) link_NAG-ASN : angle 1.62050 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 85 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 227 GLN cc_start: 0.9144 (tt0) cc_final: 0.8918 (tt0) REVERT: A 567 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8336 (mtp) REVERT: A 650 TYR cc_start: 0.7407 (m-10) cc_final: 0.7205 (m-10) REVERT: A 859 MET cc_start: 0.8743 (mmm) cc_final: 0.8473 (mmm) outliers start: 10 outliers final: 7 residues processed: 82 average time/residue: 0.1533 time to fit residues: 20.3199 Evaluate side-chains 81 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 1110 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 0.0170 chunk 91 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 28 optimal weight: 0.0970 chunk 107 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 overall best weight: 0.6216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.148644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.106308 restraints weight = 36133.541| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.38 r_work: 0.3007 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9278 Z= 0.114 Angle : 0.494 7.360 12617 Z= 0.254 Chirality : 0.039 0.401 1440 Planarity : 0.003 0.030 1563 Dihedral : 6.135 52.987 1519 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.57 % Favored : 95.34 % Rotamer: Outliers : 1.01 % Allowed : 12.15 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.26), residues: 1095 helix: 1.09 (0.21), residues: 600 sheet: -1.19 (0.63), residues: 71 loop : -0.45 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 662 TYR 0.008 0.001 TYR A 409 PHE 0.013 0.001 PHE A 505 TRP 0.013 0.001 TRP A 415 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9256) covalent geometry : angle 0.48195 (12565) SS BOND : bond 0.00199 ( 14) SS BOND : angle 0.41604 ( 28) hydrogen bonds : bond 0.04513 ( 438) hydrogen bonds : angle 4.94962 ( 1257) link_BETA1-4 : bond 0.00581 ( 4) link_BETA1-4 : angle 3.31103 ( 12) link_NAG-ASN : bond 0.00259 ( 4) link_NAG-ASN : angle 1.23231 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8403 (pm20) REVERT: A 567 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8366 (mtt) REVERT: A 859 MET cc_start: 0.8727 (mmm) cc_final: 0.8446 (mmm) outliers start: 10 outliers final: 6 residues processed: 85 average time/residue: 0.1635 time to fit residues: 22.1304 Evaluate side-chains 82 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 951 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.148124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.105642 restraints weight = 36219.358| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.40 r_work: 0.3051 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9278 Z= 0.136 Angle : 0.500 6.942 12617 Z= 0.256 Chirality : 0.039 0.402 1440 Planarity : 0.003 0.033 1563 Dihedral : 6.068 53.029 1519 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.11 % Favored : 94.79 % Rotamer: Outliers : 1.11 % Allowed : 13.16 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.26), residues: 1095 helix: 1.17 (0.21), residues: 600 sheet: -1.20 (0.63), residues: 71 loop : -0.49 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 524 TYR 0.011 0.001 TYR A 571 PHE 0.016 0.001 PHE A 743 TRP 0.012 0.001 TRP A 415 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9256) covalent geometry : angle 0.48815 (12565) SS BOND : bond 0.00180 ( 14) SS BOND : angle 0.43948 ( 28) hydrogen bonds : bond 0.04243 ( 438) hydrogen bonds : angle 4.76943 ( 1257) link_BETA1-4 : bond 0.00637 ( 4) link_BETA1-4 : angle 3.25872 ( 12) link_NAG-ASN : bond 0.00280 ( 4) link_NAG-ASN : angle 1.45977 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8344 (mtt) REVERT: A 859 MET cc_start: 0.8733 (mmm) cc_final: 0.8437 (mmm) outliers start: 11 outliers final: 8 residues processed: 88 average time/residue: 0.1600 time to fit residues: 22.6516 Evaluate side-chains 82 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 951 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.148375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.105723 restraints weight = 36168.129| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.42 r_work: 0.3047 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9278 Z= 0.130 Angle : 0.495 6.901 12617 Z= 0.254 Chirality : 0.039 0.401 1440 Planarity : 0.003 0.033 1563 Dihedral : 6.037 52.867 1519 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.75 % Favored : 95.16 % Rotamer: Outliers : 1.52 % Allowed : 12.85 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.26), residues: 1095 helix: 1.22 (0.21), residues: 599 sheet: -1.21 (0.63), residues: 71 loop : -0.49 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 662 TYR 0.010 0.001 TYR A 571 PHE 0.015 0.001 PHE A 505 TRP 0.012 0.001 TRP A 415 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9256) covalent geometry : angle 0.48362 (12565) SS BOND : bond 0.00182 ( 14) SS BOND : angle 0.40437 ( 28) hydrogen bonds : bond 0.04038 ( 438) hydrogen bonds : angle 4.69641 ( 1257) link_BETA1-4 : bond 0.00596 ( 4) link_BETA1-4 : angle 3.21772 ( 12) link_NAG-ASN : bond 0.00253 ( 4) link_NAG-ASN : angle 1.34987 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8373 (mtt) REVERT: A 859 MET cc_start: 0.8748 (mmm) cc_final: 0.8417 (mmm) outliers start: 15 outliers final: 12 residues processed: 88 average time/residue: 0.1533 time to fit residues: 21.8001 Evaluate side-chains 88 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 981 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 ASN ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.147357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.104731 restraints weight = 36575.850| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.43 r_work: 0.3018 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9278 Z= 0.174 Angle : 0.522 6.925 12617 Z= 0.267 Chirality : 0.040 0.405 1440 Planarity : 0.003 0.034 1563 Dihedral : 6.269 53.760 1519 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.30 % Favored : 94.61 % Rotamer: Outliers : 1.72 % Allowed : 13.06 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.26), residues: 1095 helix: 1.18 (0.21), residues: 599 sheet: -1.29 (0.63), residues: 71 loop : -0.57 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1075 TYR 0.012 0.001 TYR A 571 PHE 0.017 0.001 PHE A 505 TRP 0.011 0.001 TRP A 415 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 9256) covalent geometry : angle 0.51029 (12565) SS BOND : bond 0.00243 ( 14) SS BOND : angle 0.57849 ( 28) hydrogen bonds : bond 0.04107 ( 438) hydrogen bonds : angle 4.70640 ( 1257) link_BETA1-4 : bond 0.00623 ( 4) link_BETA1-4 : angle 3.27296 ( 12) link_NAG-ASN : bond 0.00309 ( 4) link_NAG-ASN : angle 1.57092 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8363 (mtt) REVERT: A 859 MET cc_start: 0.8772 (mmm) cc_final: 0.8427 (mmm) outliers start: 17 outliers final: 14 residues processed: 90 average time/residue: 0.1507 time to fit residues: 21.9674 Evaluate side-chains 91 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 981 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 25 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.149544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.105513 restraints weight = 36286.857| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.48 r_work: 0.3027 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9278 Z= 0.120 Angle : 0.500 6.686 12617 Z= 0.255 Chirality : 0.039 0.402 1440 Planarity : 0.003 0.033 1563 Dihedral : 6.218 53.825 1519 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.93 % Favored : 94.98 % Rotamer: Outliers : 1.52 % Allowed : 12.96 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.26), residues: 1095 helix: 1.26 (0.21), residues: 599 sheet: -1.25 (0.63), residues: 71 loop : -0.54 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 843 TYR 0.010 0.001 TYR A 571 PHE 0.015 0.001 PHE A 505 TRP 0.013 0.001 TRP A 415 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9256) covalent geometry : angle 0.48884 (12565) SS BOND : bond 0.00199 ( 14) SS BOND : angle 0.45368 ( 28) hydrogen bonds : bond 0.03914 ( 438) hydrogen bonds : angle 4.63233 ( 1257) link_BETA1-4 : bond 0.00578 ( 4) link_BETA1-4 : angle 3.17751 ( 12) link_NAG-ASN : bond 0.00230 ( 4) link_NAG-ASN : angle 1.38367 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 PHE cc_start: 0.7784 (m-10) cc_final: 0.7514 (m-10) REVERT: A 567 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8402 (mtt) REVERT: A 859 MET cc_start: 0.8766 (mmm) cc_final: 0.8421 (mmm) outliers start: 15 outliers final: 14 residues processed: 88 average time/residue: 0.1573 time to fit residues: 22.4150 Evaluate side-chains 91 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 981 MET Chi-restraints excluded: chain A residue 1009 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 0.3980 chunk 93 optimal weight: 0.0870 chunk 14 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 97 optimal weight: 0.1980 chunk 105 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.150948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.107026 restraints weight = 36226.121| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.53 r_work: 0.3052 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 0.024 9278 Z= 0.095 Angle : 0.481 7.193 12617 Z= 0.242 Chirality : 0.038 0.393 1440 Planarity : 0.003 0.034 1563 Dihedral : 5.902 53.247 1519 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.75 % Favored : 95.16 % Rotamer: Outliers : 1.21 % Allowed : 13.26 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.26), residues: 1095 helix: 1.46 (0.22), residues: 600 sheet: -1.14 (0.63), residues: 71 loop : -0.47 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 957 TYR 0.008 0.001 TYR A 571 PHE 0.012 0.001 PHE A 112 TRP 0.013 0.001 TRP A 415 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 9256) covalent geometry : angle 0.47108 (12565) SS BOND : bond 0.00157 ( 14) SS BOND : angle 0.33791 ( 28) hydrogen bonds : bond 0.03597 ( 438) hydrogen bonds : angle 4.47577 ( 1257) link_BETA1-4 : bond 0.00624 ( 4) link_BETA1-4 : angle 3.07110 ( 12) link_NAG-ASN : bond 0.00301 ( 4) link_NAG-ASN : angle 1.07348 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 PHE cc_start: 0.7763 (m-10) cc_final: 0.7537 (m-10) REVERT: A 158 ASN cc_start: 0.7846 (m-40) cc_final: 0.7117 (t0) REVERT: A 567 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8413 (mtt) REVERT: A 859 MET cc_start: 0.8753 (mmm) cc_final: 0.8418 (mmm) outliers start: 12 outliers final: 9 residues processed: 89 average time/residue: 0.1688 time to fit residues: 23.3106 Evaluate side-chains 87 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 981 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 71 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 76 optimal weight: 0.0770 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 22 optimal weight: 0.0000 chunk 87 optimal weight: 0.7980 overall best weight: 0.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.148886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.106116 restraints weight = 36065.004| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.46 r_work: 0.3059 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9278 Z= 0.102 Angle : 0.483 6.882 12617 Z= 0.243 Chirality : 0.038 0.399 1440 Planarity : 0.003 0.034 1563 Dihedral : 5.884 52.877 1519 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.29 % Favored : 95.62 % Rotamer: Outliers : 1.11 % Allowed : 13.66 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.26), residues: 1095 helix: 1.51 (0.22), residues: 600 sheet: -1.05 (0.69), residues: 61 loop : -0.46 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 957 TYR 0.009 0.001 TYR A 571 PHE 0.012 0.001 PHE A 112 TRP 0.012 0.001 TRP A 415 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 9256) covalent geometry : angle 0.47329 (12565) SS BOND : bond 0.00146 ( 14) SS BOND : angle 0.35516 ( 28) hydrogen bonds : bond 0.03544 ( 438) hydrogen bonds : angle 4.42722 ( 1257) link_BETA1-4 : bond 0.00605 ( 4) link_BETA1-4 : angle 3.02892 ( 12) link_NAG-ASN : bond 0.00223 ( 4) link_NAG-ASN : angle 1.16787 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 PHE cc_start: 0.7679 (m-10) cc_final: 0.7466 (m-10) REVERT: A 158 ASN cc_start: 0.7801 (m-40) cc_final: 0.7073 (t0) REVERT: A 567 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8393 (mtt) REVERT: A 859 MET cc_start: 0.8778 (mmm) cc_final: 0.8471 (mmm) outliers start: 11 outliers final: 9 residues processed: 87 average time/residue: 0.1547 time to fit residues: 21.8286 Evaluate side-chains 87 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 981 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 48 optimal weight: 0.0030 chunk 4 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.147506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.105079 restraints weight = 36364.402| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.42 r_work: 0.3048 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9278 Z= 0.156 Angle : 0.511 7.090 12617 Z= 0.260 Chirality : 0.040 0.409 1440 Planarity : 0.003 0.033 1563 Dihedral : 6.110 53.249 1519 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.75 % Favored : 94.16 % Rotamer: Outliers : 1.32 % Allowed : 13.36 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.26), residues: 1095 helix: 1.42 (0.22), residues: 600 sheet: -1.10 (0.70), residues: 61 loop : -0.52 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1075 TYR 0.011 0.001 TYR A 571 PHE 0.017 0.001 PHE A 505 TRP 0.010 0.001 TRP A 415 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9256) covalent geometry : angle 0.50109 (12565) SS BOND : bond 0.00205 ( 14) SS BOND : angle 0.44877 ( 28) hydrogen bonds : bond 0.03739 ( 438) hydrogen bonds : angle 4.50162 ( 1257) link_BETA1-4 : bond 0.00594 ( 4) link_BETA1-4 : angle 3.04800 ( 12) link_NAG-ASN : bond 0.00244 ( 4) link_NAG-ASN : angle 1.43165 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4958.87 seconds wall clock time: 85 minutes 3.12 seconds (5103.12 seconds total)