Starting phenix.real_space_refine on Sun Mar 17 14:02:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qed_18352/03_2024/8qed_18352_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qed_18352/03_2024/8qed_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qed_18352/03_2024/8qed_18352.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qed_18352/03_2024/8qed_18352.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qed_18352/03_2024/8qed_18352_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qed_18352/03_2024/8qed_18352_trim_updated.pdb" } 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 Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1068": "OE1" <-> "OE2" Residue "A PHE 1077": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1087": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.53, per 1000 atoms: 0.42 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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: 14.95 Conformation dependent library (CDL) restraints added in 1.9 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... running ksdssp... Secondary structure from input PDB file: 47 helices and 4 sheets defined 53.1% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.23 Creating SS restraints... Processing helix chain 'A' and resid 54 through 63 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 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 78 through 95 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 99 through 114 Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 148 through 155 Processing helix chain 'A' and resid 168 through 172 removed outlier: 4.000A pdb=" N ILE A 172 " --> pdb=" O MET A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 257 through 278 removed outlier: 3.888A pdb=" N TYR A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 336 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 340 through 358 removed outlier: 3.786A pdb=" N THR A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 376 through 388 removed outlier: 3.643A pdb=" N LYS A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 424 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 434 through 436 No H-bonds generated for 'chain 'A' and resid 434 through 436' Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 466 through 475 Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 516 through 530 Processing helix chain 'A' and resid 547 through 554 removed outlier: 3.741A pdb=" N ASN A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 575 Processing helix chain 'A' and resid 585 through 608 removed outlier: 3.545A pdb=" N LEU A 608 " --> pdb=" O GLY A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 645 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) removed outlier: 4.433A pdb=" N ASP A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASN A 632 " --> pdb=" O ILE A 628 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) 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 652 through 662 removed outlier: 3.505A pdb=" N ILE A 657 " --> pdb=" O ASP A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 683 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) removed outlier: 3.944A pdb=" N PHE A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 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 711 through 722 removed outlier: 3.711A pdb=" N LYS A 720 " --> pdb=" O SER A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 747 No H-bonds generated for 'chain 'A' and resid 745 through 747' Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 776 through 779 No H-bonds generated for 'chain 'A' and resid 776 through 779' Processing helix chain 'A' and resid 785 through 796 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) Processing helix chain 'A' and resid 815 through 820 removed outlier: 4.097A pdb=" N LYS A 820 " --> pdb=" O GLN A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 removed outlier: 4.460A pdb=" N HIS A 842 " --> pdb=" O GLU A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 861 removed outlier: 3.640A pdb=" N LEU A 861 " --> pdb=" O TYR A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 918 removed outlier: 3.731A pdb=" N TYR A 913 " --> pdb=" O PHE A 910 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 915 " --> pdb=" O GLU A 912 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 918 " --> pdb=" O SER A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 932 No H-bonds generated for 'chain 'A' and resid 929 through 932' Processing helix chain 'A' and resid 959 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 997 through 1020 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 1023 through 1047 removed outlier: 3.738A pdb=" N LEU A1028 " --> pdb=" O ARG A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1078 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 1088 through 1098 Processing helix chain 'A' and resid 1100 through 1105 Processing helix chain 'A' and resid 1108 through 1119 removed outlier: 3.976A pdb=" N VAL A1117 " --> pdb=" O ILE A1113 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU A1118 " --> pdb=" O GLY A1114 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA A1119 " --> pdb=" O VAL A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1129 Processing helix chain 'A' and resid 1132 through 1154 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 Processing sheet with id= A, first strand: chain 'A' and resid 127 through 129 Processing sheet with id= B, first strand: chain 'A' and resid 199 through 203 removed outlier: 6.325A pdb=" N ASP A 141 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ILE A 124 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N PHE A 143 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL A 122 " --> pdb=" O PHE A 143 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 504 through 507 Processing sheet with id= D, first strand: chain 'A' and resid 980 through 985 removed outlier: 4.178A pdb=" N ASP A 980 " --> pdb=" O LYS A 808 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 949 " --> pdb=" O MET A 805 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL A 938 " --> pdb=" O SER A 945 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 1068 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: 6.33 Time building geometry restraints manager: 15.52 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: 73.98 - 85.98: 3 85.98 - 97.99: 1 97.99 - 110.00: 15213 110.00 - 122.00: 14383 122.00 - 134.01: 2774 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: 824 2.19 - 2.79: 35611 2.79 - 3.39: 48867 3.39 - 4.00: 62899 4.00 - 4.60: 97251 Nonbonded interactions: 245452 Sorted by model distance: nonbonded pdb=" OE1 GLU A 551 " pdb=" HG SER A 784 " model vdw 1.582 1.850 nonbonded pdb=" OE1 GLU A 410 " pdb=" H GLU A 410 " model vdw 1.608 1.850 nonbonded pdb=" HG SER A 547 " pdb=" OH TYR A 785 " model vdw 1.619 1.850 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 1.850 ... (remaining 245447 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '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: 0.830 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: 0.250 Extract box with map and model: 4.270 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 60.030 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.000 ------------------------------------------------------------------------------- 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 9256 Z= 0.235 Angle : 0.501 6.551 12565 Z= 0.249 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 73 average time/residue: 0.3523 time to fit residues: 40.3192 Evaluate side-chains 69 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 1.455 ------------------------------------------------------------------------------- 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: 0.0770 chunk 83 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.0652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9256 Z= 0.178 Angle : 0.512 5.235 12565 Z= 0.270 Chirality : 0.040 0.399 1440 Planarity : 0.003 0.031 1563 Dihedral : 6.594 54.320 1519 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.11 % Favored : 95.80 % Rotamer: Outliers : 0.51 % Allowed : 11.84 % 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 (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: 0.48 (0.26), residues: 1095 helix: 1.15 (0.22), residues: 582 sheet: -1.13 (0.66), residues: 71 loop : -0.47 (0.30), residues: 442 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 0.018 0.001 PHE A 505 TYR 0.011 0.001 TYR A 571 ARG 0.002 0.000 ARG A 815 *********************** 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 78 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 1.437 Fit side-chains revert: symmetry clash REVERT: A 567 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8012 (mtp) REVERT: A 859 MET cc_start: 0.8726 (mmm) cc_final: 0.8456 (mmm) outliers start: 5 outliers final: 3 residues processed: 77 average time/residue: 0.3367 time to fit residues: 41.4027 Evaluate side-chains 69 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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 951 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 chunk 83 optimal weight: 0.0770 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 9256 Z= 0.160 Angle : 0.456 5.015 12565 Z= 0.236 Chirality : 0.038 0.396 1440 Planarity : 0.003 0.031 1563 Dihedral : 6.140 56.333 1519 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.75 % Favored : 95.16 % Rotamer: Outliers : 0.91 % Allowed : 11.03 % Favored : 88.06 % 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: 0.60 (0.26), residues: 1095 helix: 1.28 (0.22), residues: 585 sheet: -1.11 (0.66), residues: 71 loop : -0.46 (0.30), residues: 439 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 0.013 0.001 PHE A 743 TYR 0.014 0.001 TYR A 228 ARG 0.001 0.000 ARG A 662 *********************** 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 83 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 1.519 Fit side-chains REVERT: A 89 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8286 (pm20) REVERT: A 567 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8187 (mtt) REVERT: A 859 MET cc_start: 0.8655 (mmm) cc_final: 0.8371 (mmm) outliers start: 9 outliers final: 4 residues processed: 81 average time/residue: 0.3279 time to fit residues: 42.0526 Evaluate side-chains 76 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 ASN A 555 ASN ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9256 Z= 0.323 Angle : 0.518 5.820 12565 Z= 0.270 Chirality : 0.041 0.413 1440 Planarity : 0.003 0.032 1563 Dihedral : 6.476 57.169 1519 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.84 % Favored : 94.98 % Rotamer: Outliers : 1.11 % Allowed : 12.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.26), residues: 1095 helix: 1.17 (0.22), residues: 586 sheet: -1.21 (0.71), residues: 61 loop : -0.64 (0.30), residues: 448 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 0.021 0.001 PHE A 982 TYR 0.009 0.001 TYR A 409 ARG 0.002 0.000 ARG A 584 *********************** 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 82 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 1.462 Fit side-chains revert: symmetry clash REVERT: A 567 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8029 (mtp) REVERT: A 650 TYR cc_start: 0.7412 (m-10) cc_final: 0.6998 (m-10) REVERT: A 859 MET cc_start: 0.8704 (mmm) cc_final: 0.8359 (mmm) outliers start: 11 outliers final: 10 residues processed: 81 average time/residue: 0.3340 time to fit residues: 43.1383 Evaluate side-chains 78 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 1.374 ------------------------------------------------------------------------------- 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 555 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 79 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9256 Z= 0.174 Angle : 0.466 5.437 12565 Z= 0.240 Chirality : 0.039 0.400 1440 Planarity : 0.003 0.031 1563 Dihedral : 6.253 59.002 1519 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.75 % Favored : 95.07 % Rotamer: Outliers : 1.01 % Allowed : 12.25 % Favored : 86.74 % 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: 0.58 (0.26), residues: 1095 helix: 1.35 (0.22), residues: 585 sheet: -1.21 (0.70), residues: 61 loop : -0.61 (0.30), residues: 449 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 0.016 0.001 PHE A 505 TYR 0.009 0.001 TYR A 228 ARG 0.001 0.000 ARG A 843 *********************** 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 83 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 567 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8252 (mtt) REVERT: A 859 MET cc_start: 0.8690 (mmm) cc_final: 0.8335 (mmm) outliers start: 10 outliers final: 8 residues processed: 82 average time/residue: 0.3231 time to fit residues: 42.2082 Evaluate side-chains 80 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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 951 THR Chi-restraints excluded: chain A residue 1110 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 21 optimal weight: 0.0870 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9256 Z= 0.209 Angle : 0.473 6.417 12565 Z= 0.243 Chirality : 0.039 0.400 1440 Planarity : 0.003 0.031 1563 Dihedral : 6.209 59.590 1519 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.02 % Favored : 94.79 % Rotamer: Outliers : 1.52 % Allowed : 11.74 % Favored : 86.74 % 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: 0.61 (0.26), residues: 1095 helix: 1.39 (0.22), residues: 586 sheet: -1.26 (0.70), residues: 61 loop : -0.62 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 415 HIS 0.004 0.001 HIS A 954 PHE 0.017 0.001 PHE A 505 TYR 0.009 0.001 TYR A 409 ARG 0.001 0.000 ARG A 584 *********************** 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 88 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 1.469 Fit side-chains revert: symmetry clash REVERT: A 567 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8235 (mtt) REVERT: A 650 TYR cc_start: 0.7341 (m-10) cc_final: 0.6987 (m-10) REVERT: A 859 MET cc_start: 0.8698 (mmm) cc_final: 0.8331 (mmm) outliers start: 15 outliers final: 13 residues processed: 85 average time/residue: 0.3501 time to fit residues: 47.0731 Evaluate side-chains 84 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 1.395 ------------------------------------------------------------------------------- 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 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 1110 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9256 Z= 0.252 Angle : 0.489 6.381 12565 Z= 0.252 Chirality : 0.039 0.404 1440 Planarity : 0.003 0.032 1563 Dihedral : 6.381 58.964 1519 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.30 % Favored : 94.52 % Rotamer: Outliers : 1.52 % Allowed : 12.25 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.26), residues: 1095 helix: 1.35 (0.22), residues: 585 sheet: -1.29 (0.70), residues: 61 loop : -0.69 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 415 HIS 0.004 0.001 HIS A 954 PHE 0.018 0.001 PHE A 505 TYR 0.016 0.001 TYR A 228 ARG 0.002 0.000 ARG A 584 *********************** 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 86 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 1.457 Fit side-chains revert: symmetry clash REVERT: A 859 MET cc_start: 0.8713 (mmm) cc_final: 0.8332 (mmm) outliers start: 15 outliers final: 14 residues processed: 83 average time/residue: 0.3354 time to fit residues: 43.9843 Evaluate side-chains 84 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 1.437 ------------------------------------------------------------------------------- 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 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 1110 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9256 Z= 0.194 Angle : 0.468 5.925 12565 Z= 0.239 Chirality : 0.039 0.397 1440 Planarity : 0.003 0.032 1563 Dihedral : 6.278 57.491 1519 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.11 % Favored : 94.70 % Rotamer: Outliers : 1.42 % Allowed : 12.45 % Favored : 86.13 % 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: 0.62 (0.26), residues: 1095 helix: 1.43 (0.22), residues: 586 sheet: -1.37 (0.66), residues: 68 loop : -0.62 (0.30), residues: 441 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 0.016 0.001 PHE A 505 TYR 0.010 0.001 TYR A 228 ARG 0.001 0.000 ARG A 584 *********************** 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 88 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 567 MET cc_start: 0.8484 (mtt) cc_final: 0.8183 (mtp) REVERT: A 650 TYR cc_start: 0.7392 (m-10) cc_final: 0.6987 (m-10) REVERT: A 859 MET cc_start: 0.8709 (mmm) cc_final: 0.8320 (mmm) outliers start: 14 outliers final: 11 residues processed: 87 average time/residue: 0.3254 time to fit residues: 44.8601 Evaluate side-chains 83 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 1.440 ------------------------------------------------------------------------------- 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 672 LEU Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 981 MET Chi-restraints excluded: chain A residue 1110 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9990 chunk 101 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 93 optimal weight: 0.0670 chunk 64 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9256 Z= 0.143 Angle : 0.449 6.013 12565 Z= 0.228 Chirality : 0.038 0.390 1440 Planarity : 0.003 0.032 1563 Dihedral : 6.036 55.306 1519 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.38 % Favored : 95.53 % Rotamer: Outliers : 1.11 % Allowed : 12.96 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1095 helix: 1.57 (0.22), residues: 589 sheet: -1.31 (0.66), residues: 68 loop : -0.59 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 415 HIS 0.004 0.001 HIS A 954 PHE 0.012 0.001 PHE A 112 TYR 0.008 0.001 TYR A 409 ARG 0.001 0.000 ARG A 662 *********************** 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 89 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 567 MET cc_start: 0.8491 (mtt) cc_final: 0.8191 (mtp) REVERT: A 859 MET cc_start: 0.8704 (mmm) cc_final: 0.8322 (mmm) outliers start: 11 outliers final: 10 residues processed: 88 average time/residue: 0.3254 time to fit residues: 45.9207 Evaluate side-chains 83 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 1.382 ------------------------------------------------------------------------------- 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 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 49 optimal weight: 0.9980 chunk 72 optimal weight: 0.0770 chunk 109 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9256 Z= 0.166 Angle : 0.458 6.318 12565 Z= 0.233 Chirality : 0.038 0.396 1440 Planarity : 0.003 0.032 1563 Dihedral : 6.017 54.001 1519 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.38 % Favored : 95.53 % Rotamer: Outliers : 1.01 % Allowed : 13.16 % Favored : 85.83 % 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: 0.80 (0.26), residues: 1095 helix: 1.59 (0.22), residues: 589 sheet: -1.16 (0.71), residues: 61 loop : -0.63 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 415 HIS 0.004 0.001 HIS A 954 PHE 0.012 0.001 PHE A 505 TYR 0.009 0.001 TYR A 228 ARG 0.001 0.000 ARG A 584 ********************** 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 83 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 567 MET cc_start: 0.8495 (mtt) cc_final: 0.8238 (mtp) REVERT: A 650 TYR cc_start: 0.7383 (m-10) cc_final: 0.6967 (m-10) REVERT: A 859 MET cc_start: 0.8715 (mmm) cc_final: 0.8334 (mmm) outliers start: 10 outliers final: 10 residues processed: 82 average time/residue: 0.3363 time to fit residues: 43.6634 Evaluate side-chains 82 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 1.521 ------------------------------------------------------------------------------- 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 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 80 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 76 optimal weight: 0.5980 chunk 4 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.148522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.099882 restraints weight = 36297.938| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.22 r_work: 0.3011 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9256 Z= 0.195 Angle : 0.469 6.948 12565 Z= 0.238 Chirality : 0.039 0.398 1440 Planarity : 0.003 0.032 1563 Dihedral : 6.095 54.016 1519 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.93 % Favored : 94.98 % Rotamer: Outliers : 1.11 % Allowed : 13.36 % 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: 0.78 (0.26), residues: 1095 helix: 1.60 (0.22), residues: 587 sheet: -1.20 (0.70), residues: 61 loop : -0.66 (0.30), residues: 447 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 0.016 0.001 PHE A 505 TYR 0.009 0.001 TYR A 409 ARG 0.001 0.000 ARG A 584 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3807.21 seconds wall clock time: 68 minutes 3.19 seconds (4083.19 seconds total)