Starting phenix.real_space_refine on Mon May 19 13:39:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qed_18352/05_2025/8qed_18352_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qed_18352/05_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_18352/05_2025/8qed_18352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qed_18352/05_2025/8qed_18352.map" model { file = "/net/cci-nas-00/data/ceres_data/8qed_18352/05_2025/8qed_18352_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qed_18352/05_2025/8qed_18352_trim.cif" } resolution = 3.27 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= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.10, per 1000 atoms: 0.46 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: 4.63 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.64 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: 6.57 Time building geometry restraints manager: 5.62 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: 0.740 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: 0.290 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 38.220 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.040 ------------------------------------------------------------------------------- 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 : 4.27 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 (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 (0.26), 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 TRP 0.005 0.001 TRP A 415 HIS 0.004 0.001 HIS A 954 PHE 0.014 0.001 PHE A 982 TYR 0.009 0.001 TYR A 789 ARG 0.001 0.000 ARG A 539 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 4) link_NAG-ASN : angle 1.59264 ( 12) link_BETA1-4 : bond 0.01233 ( 4) link_BETA1-4 : angle 5.13304 ( 12) hydrogen bonds : bond 0.24762 ( 438) hydrogen bonds : angle 8.26543 ( 1257) SS BOND : bond 0.00174 ( 14) SS BOND : angle 0.41814 ( 28) covalent geometry : bond 0.00361 ( 9256) covalent geometry : angle 0.50125 (12565) *********************** 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 : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 73 average time/residue: 0.3449 time to fit residues: 39.6184 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 : 1.295 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.148055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105280 restraints weight = 36331.417| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.42 r_work: 0.2971 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9278 Z= 0.156 Angle : 0.571 7.809 12617 Z= 0.303 Chirality : 0.041 0.406 1440 Planarity : 0.003 0.031 1563 Dihedral : 6.633 53.160 1519 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.38 % Favored : 95.53 % Rotamer: Outliers : 0.71 % Allowed : 11.34 % 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 (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: 0.34 (0.26), residues: 1095 helix: 0.98 (0.21), residues: 596 sheet: -1.18 (0.66), residues: 71 loop : -0.49 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 521 HIS 0.004 0.001 HIS A 954 PHE 0.018 0.001 PHE A 505 TYR 0.012 0.001 TYR A 571 ARG 0.002 0.000 ARG A 662 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 4) link_NAG-ASN : angle 1.39453 ( 12) link_BETA1-4 : bond 0.00590 ( 4) link_BETA1-4 : angle 3.38523 ( 12) hydrogen bonds : bond 0.06132 ( 438) hydrogen bonds : angle 5.63585 ( 1257) SS BOND : bond 0.00238 ( 14) SS BOND : angle 0.50978 ( 28) covalent geometry : bond 0.00336 ( 9256) covalent geometry : angle 0.56073 (12565) *********************** 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 : 1.247 Fit side-chains revert: symmetry clash REVERT: A 158 ASN cc_start: 0.7997 (m-40) cc_final: 0.7294 (t0) REVERT: A 567 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8150 (mtp) REVERT: A 859 MET cc_start: 0.8807 (mmm) cc_final: 0.8541 (mmm) outliers start: 7 outliers final: 4 residues processed: 82 average time/residue: 0.3154 time to fit residues: 41.2287 Evaluate side-chains 77 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 28 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.145798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.102958 restraints weight = 36464.243| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.41 r_work: 0.2920 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 9278 Z= 0.258 Angle : 0.587 7.930 12617 Z= 0.307 Chirality : 0.043 0.434 1440 Planarity : 0.003 0.032 1563 Dihedral : 6.893 54.361 1519 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.30 % Favored : 94.61 % Rotamer: Outliers : 1.32 % Allowed : 12.04 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.26), residues: 1095 helix: 0.81 (0.21), residues: 596 sheet: -1.49 (0.64), residues: 71 loop : -0.64 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 415 HIS 0.004 0.001 HIS A 413 PHE 0.022 0.002 PHE A 505 TYR 0.012 0.002 TYR A 228 ARG 0.002 0.000 ARG A1075 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 4) link_NAG-ASN : angle 2.12107 ( 12) link_BETA1-4 : bond 0.00687 ( 4) link_BETA1-4 : angle 3.63007 ( 12) hydrogen bonds : bond 0.05842 ( 438) hydrogen bonds : angle 5.40442 ( 1257) SS BOND : bond 0.00320 ( 14) SS BOND : angle 0.67486 ( 28) covalent geometry : bond 0.00600 ( 9256) covalent geometry : angle 0.57321 (12565) *********************** 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 88 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 1.374 Fit side-chains revert: symmetry clash REVERT: A 227 GLN cc_start: 0.9109 (tt0) cc_final: 0.8889 (tt0) REVERT: A 567 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8314 (mtp) REVERT: A 859 MET cc_start: 0.8786 (mmm) cc_final: 0.8487 (mmm) outliers start: 13 outliers final: 9 residues processed: 84 average time/residue: 0.3420 time to fit residues: 45.6604 Evaluate side-chains 82 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 1.475 ------------------------------------------------------------------------------- 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 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 1110 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.148736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.105353 restraints weight = 36269.018| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.44 r_work: 0.3021 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9278 Z= 0.142 Angle : 0.519 7.670 12617 Z= 0.268 Chirality : 0.040 0.409 1440 Planarity : 0.003 0.030 1563 Dihedral : 6.497 54.222 1519 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.57 % Favored : 95.34 % Rotamer: Outliers : 0.81 % Allowed : 12.65 % Favored : 86.54 % 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 (0.26), residues: 1095 helix: 0.92 (0.21), residues: 600 sheet: -1.40 (0.62), residues: 71 loop : -0.55 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 415 HIS 0.004 0.001 HIS A 954 PHE 0.018 0.001 PHE A 505 TYR 0.009 0.001 TYR A 409 ARG 0.002 0.000 ARG A 841 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 4) link_NAG-ASN : angle 1.43337 ( 12) link_BETA1-4 : bond 0.00563 ( 4) link_BETA1-4 : angle 3.43472 ( 12) hydrogen bonds : bond 0.04729 ( 438) hydrogen bonds : angle 5.05756 ( 1257) SS BOND : bond 0.00225 ( 14) SS BOND : angle 0.45370 ( 28) covalent geometry : bond 0.00330 ( 9256) covalent geometry : angle 0.50634 (12565) *********************** 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 88 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8422 (pm20) REVERT: A 567 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8314 (mtp) REVERT: A 859 MET cc_start: 0.8737 (mmm) cc_final: 0.8414 (mmm) outliers start: 8 outliers final: 5 residues processed: 86 average time/residue: 0.3201 time to fit residues: 43.6596 Evaluate side-chains 81 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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 951 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 9 optimal weight: 20.0000 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.148054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.105620 restraints weight = 36569.568| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.43 r_work: 0.3048 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9278 Z= 0.134 Angle : 0.506 7.255 12617 Z= 0.260 Chirality : 0.039 0.411 1440 Planarity : 0.003 0.033 1563 Dihedral : 6.329 53.956 1519 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.02 % Favored : 94.89 % Rotamer: Outliers : 1.42 % Allowed : 12.96 % 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 (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: 0.35 (0.26), residues: 1095 helix: 1.04 (0.21), residues: 600 sheet: -1.33 (0.62), residues: 71 loop : -0.54 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 415 HIS 0.004 0.001 HIS A 954 PHE 0.016 0.001 PHE A 505 TYR 0.008 0.001 TYR A 571 ARG 0.001 0.000 ARG A 662 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 4) link_NAG-ASN : angle 1.40988 ( 12) link_BETA1-4 : bond 0.00626 ( 4) link_BETA1-4 : angle 3.38452 ( 12) hydrogen bonds : bond 0.04425 ( 438) hydrogen bonds : angle 4.87824 ( 1257) SS BOND : bond 0.00181 ( 14) SS BOND : angle 0.42516 ( 28) covalent geometry : bond 0.00307 ( 9256) covalent geometry : angle 0.49361 (12565) *********************** 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 91 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 TYR cc_start: 0.6994 (m-10) cc_final: 0.6748 (m-10) REVERT: A 567 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8410 (mtt) REVERT: A 859 MET cc_start: 0.8739 (mmm) cc_final: 0.8406 (mmm) outliers start: 14 outliers final: 9 residues processed: 90 average time/residue: 0.3234 time to fit residues: 45.9618 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 : 1.358 ------------------------------------------------------------------------------- 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 757 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 16 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 97 optimal weight: 0.2980 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.146378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.103664 restraints weight = 36493.178| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.43 r_work: 0.2984 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9278 Z= 0.215 Angle : 0.552 7.337 12617 Z= 0.286 Chirality : 0.041 0.425 1440 Planarity : 0.003 0.034 1563 Dihedral : 6.641 54.533 1519 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.21 % Favored : 94.70 % Rotamer: Outliers : 1.82 % Allowed : 12.85 % 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 (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: 0.21 (0.26), residues: 1095 helix: 0.96 (0.21), residues: 598 sheet: -1.42 (0.63), residues: 71 loop : -0.67 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 415 HIS 0.004 0.001 HIS A 954 PHE 0.020 0.001 PHE A 982 TYR 0.009 0.001 TYR A 409 ARG 0.002 0.000 ARG A1075 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 4) link_NAG-ASN : angle 1.78181 ( 12) link_BETA1-4 : bond 0.00640 ( 4) link_BETA1-4 : angle 3.47147 ( 12) hydrogen bonds : bond 0.04512 ( 438) hydrogen bonds : angle 4.93121 ( 1257) SS BOND : bond 0.00282 ( 14) SS BOND : angle 0.65568 ( 28) covalent geometry : bond 0.00503 ( 9256) covalent geometry : angle 0.53941 (12565) *********************** 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 95 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8356 (mtt) REVERT: A 859 MET cc_start: 0.8786 (mmm) cc_final: 0.8446 (mmm) outliers start: 18 outliers final: 15 residues processed: 92 average time/residue: 0.3376 time to fit residues: 49.5364 Evaluate side-chains 91 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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 1009 ILE Chi-restraints excluded: chain A residue 1110 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 58 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.147525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.105061 restraints weight = 36307.020| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.44 r_work: 0.2980 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9278 Z= 0.133 Angle : 0.512 7.082 12617 Z= 0.263 Chirality : 0.039 0.410 1440 Planarity : 0.003 0.034 1563 Dihedral : 6.494 54.597 1519 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.48 % Favored : 94.43 % Rotamer: Outliers : 1.42 % Allowed : 13.06 % 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 (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 (0.26), residues: 1095 helix: 1.07 (0.21), residues: 600 sheet: -1.38 (0.63), residues: 71 loop : -0.63 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 415 HIS 0.004 0.001 HIS A 954 PHE 0.016 0.001 PHE A 505 TYR 0.010 0.001 TYR A 571 ARG 0.001 0.000 ARG A 662 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 4) link_NAG-ASN : angle 1.45799 ( 12) link_BETA1-4 : bond 0.00630 ( 4) link_BETA1-4 : angle 3.34983 ( 12) hydrogen bonds : bond 0.04198 ( 438) hydrogen bonds : angle 4.79763 ( 1257) SS BOND : bond 0.00215 ( 14) SS BOND : angle 0.47308 ( 28) covalent geometry : bond 0.00306 ( 9256) covalent geometry : angle 0.50046 (12565) *********************** 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 92 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 TYR cc_start: 0.6987 (m-10) cc_final: 0.6730 (m-10) REVERT: A 567 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8362 (mtt) REVERT: A 859 MET cc_start: 0.8783 (mmm) cc_final: 0.8437 (mmm) outliers start: 14 outliers final: 13 residues processed: 89 average time/residue: 0.3300 time to fit residues: 46.7382 Evaluate side-chains 90 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 1.340 ------------------------------------------------------------------------------- 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 951 THR Chi-restraints excluded: chain A residue 981 MET Chi-restraints excluded: chain A residue 1009 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 41 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 93 optimal weight: 0.0000 chunk 73 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 97 optimal weight: 0.2980 chunk 102 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 101 optimal weight: 0.0770 chunk 94 optimal weight: 0.9980 overall best weight: 0.2542 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.151304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.107495 restraints weight = 36299.733| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.51 r_work: 0.2987 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9278 Z= 0.090 Angle : 0.478 6.854 12617 Z= 0.241 Chirality : 0.039 0.393 1440 Planarity : 0.003 0.034 1563 Dihedral : 5.941 54.255 1519 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.20 % Favored : 95.71 % Rotamer: Outliers : 1.01 % Allowed : 13.66 % 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 (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: 0.71 (0.26), residues: 1095 helix: 1.37 (0.22), residues: 600 sheet: -1.12 (0.64), residues: 71 loop : -0.46 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 415 HIS 0.004 0.001 HIS A 954 PHE 0.013 0.001 PHE A 743 TYR 0.014 0.001 TYR A 228 ARG 0.002 0.000 ARG A 957 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 4) link_NAG-ASN : angle 0.94982 ( 12) link_BETA1-4 : bond 0.00644 ( 4) link_BETA1-4 : angle 3.16661 ( 12) hydrogen bonds : bond 0.03623 ( 438) hydrogen bonds : angle 4.51420 ( 1257) SS BOND : bond 0.00143 ( 14) SS BOND : angle 0.31169 ( 28) covalent geometry : bond 0.00197 ( 9256) covalent geometry : angle 0.46817 (12565) *********************** 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 90 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8405 (mtt) REVERT: A 859 MET cc_start: 0.8773 (mmm) cc_final: 0.8440 (mmm) outliers start: 10 outliers final: 8 residues processed: 88 average time/residue: 0.3193 time to fit residues: 44.8012 Evaluate side-chains 85 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 10 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.150072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.106172 restraints weight = 36476.920| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.49 r_work: 0.3049 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9278 Z= 0.122 Angle : 0.492 6.316 12617 Z= 0.248 Chirality : 0.039 0.409 1440 Planarity : 0.003 0.036 1563 Dihedral : 6.046 54.533 1519 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.93 % Favored : 94.98 % Rotamer: Outliers : 1.32 % Allowed : 13.87 % Favored : 84.82 % 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: 0.73 (0.26), residues: 1095 helix: 1.40 (0.22), residues: 600 sheet: -1.14 (0.64), residues: 71 loop : -0.47 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 415 HIS 0.003 0.001 HIS A 954 PHE 0.012 0.001 PHE A 505 TYR 0.009 0.001 TYR A 571 ARG 0.001 0.000 ARG A 957 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 4) link_NAG-ASN : angle 1.26260 ( 12) link_BETA1-4 : bond 0.00620 ( 4) link_BETA1-4 : angle 3.12667 ( 12) hydrogen bonds : bond 0.03680 ( 438) hydrogen bonds : angle 4.50688 ( 1257) SS BOND : bond 0.00167 ( 14) SS BOND : angle 0.39015 ( 28) covalent geometry : bond 0.00282 ( 9256) covalent geometry : angle 0.48116 (12565) *********************** 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 90 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 PHE cc_start: 0.7667 (m-10) cc_final: 0.7430 (m-10) REVERT: A 567 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8399 (mtt) REVERT: A 859 MET cc_start: 0.8773 (mmm) cc_final: 0.8442 (mmm) outliers start: 13 outliers final: 10 residues processed: 88 average time/residue: 0.4009 time to fit residues: 54.1907 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 : 1.503 ------------------------------------------------------------------------------- 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 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 20 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 30 optimal weight: 0.0570 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 76 optimal weight: 0.0040 chunk 64 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.5312 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.149882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106305 restraints weight = 36316.827| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.45 r_work: 0.3073 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9278 Z= 0.100 Angle : 0.486 6.140 12617 Z= 0.245 Chirality : 0.039 0.405 1440 Planarity : 0.003 0.035 1563 Dihedral : 5.942 54.445 1519 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.29 % Favored : 95.62 % Rotamer: Outliers : 0.91 % Allowed : 14.17 % Favored : 84.92 % 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: 0.79 (0.26), residues: 1095 helix: 1.44 (0.22), residues: 600 sheet: -1.07 (0.64), residues: 71 loop : -0.44 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 415 HIS 0.004 0.001 HIS A 954 PHE 0.017 0.001 PHE A 185 TYR 0.008 0.001 TYR A 571 ARG 0.001 0.000 ARG A 957 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 4) link_NAG-ASN : angle 1.12357 ( 12) link_BETA1-4 : bond 0.00609 ( 4) link_BETA1-4 : angle 3.02942 ( 12) hydrogen bonds : bond 0.03591 ( 438) hydrogen bonds : angle 4.42328 ( 1257) SS BOND : bond 0.00143 ( 14) SS BOND : angle 0.34202 ( 28) covalent geometry : bond 0.00225 ( 9256) covalent geometry : angle 0.47682 (12565) ********************** 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 85 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 PHE cc_start: 0.7549 (m-10) cc_final: 0.7300 (m-10) REVERT: A 567 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8452 (mtt) REVERT: A 859 MET cc_start: 0.8761 (mmm) cc_final: 0.8458 (mmm) outliers start: 9 outliers final: 8 residues processed: 83 average time/residue: 0.3623 time to fit residues: 46.9557 Evaluate side-chains 83 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 1.454 ------------------------------------------------------------------------------- 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 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 45 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 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 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.148195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.105156 restraints weight = 36204.167| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.43 r_work: 0.3040 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9278 Z= 0.121 Angle : 0.494 6.785 12617 Z= 0.250 Chirality : 0.039 0.410 1440 Planarity : 0.003 0.036 1563 Dihedral : 5.982 54.233 1519 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.21 % Favored : 94.70 % Rotamer: Outliers : 1.11 % Allowed : 13.87 % Favored : 85.02 % 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: 0.78 (0.26), residues: 1095 helix: 1.44 (0.22), residues: 600 sheet: -1.10 (0.64), residues: 71 loop : -0.45 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 415 HIS 0.003 0.001 HIS A 954 PHE 0.013 0.001 PHE A 505 TYR 0.009 0.001 TYR A 571 ARG 0.001 0.000 ARG A 957 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 4) link_NAG-ASN : angle 1.23576 ( 12) link_BETA1-4 : bond 0.00602 ( 4) link_BETA1-4 : angle 3.03704 ( 12) hydrogen bonds : bond 0.03612 ( 438) hydrogen bonds : angle 4.42753 ( 1257) SS BOND : bond 0.00161 ( 14) SS BOND : angle 0.37536 ( 28) covalent geometry : bond 0.00280 ( 9256) covalent geometry : angle 0.48450 (12565) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9015.97 seconds wall clock time: 155 minutes 15.48 seconds (9315.48 seconds total)