Starting phenix.real_space_refine on Mon Aug 25 12:56:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ymx_33946/08_2025/7ymx_33946.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ymx_33946/08_2025/7ymx_33946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ymx_33946/08_2025/7ymx_33946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ymx_33946/08_2025/7ymx_33946.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ymx_33946/08_2025/7ymx_33946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ymx_33946/08_2025/7ymx_33946.map" } resolution = 4.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.117 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: 4 Type Number sf(0) Gaussians S 153 5.16 5 C 17602 2.51 5 N 4511 2.21 5 O 5509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27775 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "B" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "C" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" 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: "G" 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: "H" 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: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.76, per 1000 atoms: 0.24 Number of scatterers: 27775 At special positions: 0 Unit cell: (151.8, 170.5, 179.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 153 16.00 O 5509 8.00 N 4511 7.00 C 17602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.03 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.02 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.03 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.03 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.05 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.02 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.04 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.03 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.03 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.03 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.03 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.03 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.03 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.03 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.03 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.05 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " 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 ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA I 3 " - " MAN I 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA I 3 " - " MAN I 5 " " BMA O 3 " - " MAN O 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A1401 " - " ASN A 222 " " NAG A1402 " - " ASN A 236 " " NAG A1403 " - " ASN A 244 " " NAG A1404 " - " ASN A 619 " " NAG A1405 " - " ASN A 719 " " NAG A1406 " - " ASN A 774 " " NAG A1407 " - " ASN A 785 " " NAG B1401 " - " ASN B 619 " " NAG B1402 " - " ASN B 774 " " NAG B1403 " - " ASN B 785 " " NAG B1404 " - " ASN B 244 " " NAG B1405 " - " ASN B 66 " " NAG B1406 " - " ASN B 719 " " NAG C1401 " - " ASN C 719 " " NAG C1402 " - " ASN C 870 " " NAG C1403 " - " ASN C 785 " " NAG C1404 " - " ASN C 166 " " NAG C1405 " - " ASN C 244 " " NAG C1406 " - " ASN C 619 " " NAG C1407 " - " ASN C 66 " " NAG D 1 " - " ASN A 66 " " NAG E 1 " - " ASN A 125 " " NAG F 1 " - " ASN A 166 " " NAG G 1 " - " ASN A 870 " " NAG H 1 " - " ASN A1213 " " NAG I 1 " - " ASN B 125 " " NAG J 1 " - " ASN B1213 " " NAG K 1 " - " ASN B 870 " " NAG L 1 " - " ASN B 222 " " NAG M 1 " - " ASN C1213 " " NAG N 1 " - " ASN C 222 " " NAG O 1 " - " ASN C 125 " Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 830.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6510 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 54 sheets defined 25.2% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 224 through 230 Processing helix chain 'A' and resid 342 through 352 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.813A pdb=" N PHE A 399 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 415 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'A' and resid 449 through 457 removed outlier: 3.556A pdb=" N MET A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER A 457 " --> pdb=" O SER A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.873A pdb=" N SER A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 529 " --> pdb=" O PRO A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 596 through 600 removed outlier: 4.164A pdb=" N LEU A 600 " --> pdb=" O ALA A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 812 Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 825 through 854 removed outlier: 4.411A pdb=" N SER A 829 " --> pdb=" O GLY A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 875 Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 915 Processing helix chain 'A' and resid 926 through 931 removed outlier: 4.082A pdb=" N ALA A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 959 removed outlier: 4.876A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 959 " --> pdb=" O ILE A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 983 Processing helix chain 'A' and resid 986 through 993 removed outlier: 3.803A pdb=" N LEU A 990 " --> pdb=" O THR A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1008 removed outlier: 3.585A pdb=" N ILE A 997 " --> pdb=" O ASN A 993 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET A1008 " --> pdb=" O ALA A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 3.717A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1106 removed outlier: 3.981A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 removed outlier: 4.153A pdb=" N PHE B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.556A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.676A pdb=" N ARG B 307 " --> pdb=" O GLN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 395 through 399 removed outlier: 3.656A pdb=" N PHE B 399 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 457 removed outlier: 3.980A pdb=" N MET B 452 " --> pdb=" O PRO B 449 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N SER B 454 " --> pdb=" O SER B 451 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 457 " --> pdb=" O SER B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 removed outlier: 3.587A pdb=" N ASN B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 591 through 595 removed outlier: 4.088A pdb=" N LYS B 595 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 600 removed outlier: 4.044A pdb=" N LEU B 600 " --> pdb=" O ALA B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 812 removed outlier: 3.615A pdb=" N TYR B 809 " --> pdb=" O ASP B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 820 Processing helix chain 'B' and resid 826 through 854 Processing helix chain 'B' and resid 888 through 898 removed outlier: 3.505A pdb=" N VAL B 898 " --> pdb=" O LEU B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 915 removed outlier: 3.846A pdb=" N GLN B 914 " --> pdb=" O ASP B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 959 removed outlier: 4.688A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B 959 " --> pdb=" O ILE B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 984 removed outlier: 3.698A pdb=" N GLY B 984 " --> pdb=" O LEU B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 993 removed outlier: 3.614A pdb=" N LEU B 990 " --> pdb=" O THR B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1008 removed outlier: 3.640A pdb=" N ILE B 997 " --> pdb=" O ASN B 993 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET B1008 " --> pdb=" O ALA B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1039 removed outlier: 3.699A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1042 No H-bonds generated for 'chain 'B' and resid 1040 through 1042' Processing helix chain 'B' and resid 1050 through 1058 Processing helix chain 'B' and resid 1059 through 1107 removed outlier: 4.152A pdb=" N ALA B1065 " --> pdb=" O PRO B1061 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B1107 " --> pdb=" O VAL B1103 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 342 through 352 Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 395 through 399 removed outlier: 3.908A pdb=" N PHE C 399 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 418 Processing helix chain 'C' and resid 431 through 436 Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 524 through 529 Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 591 through 600 removed outlier: 3.591A pdb=" N THR C 594 " --> pdb=" O ALA C 591 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS C 595 " --> pdb=" O ASN C 592 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE C 596 " --> pdb=" O ASP C 593 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA C 597 " --> pdb=" O THR C 594 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU C 600 " --> pdb=" O ALA C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 812 Processing helix chain 'C' and resid 814 through 822 Processing helix chain 'C' and resid 826 through 853 Processing helix chain 'C' and resid 888 through 898 Processing helix chain 'C' and resid 908 through 912 Processing helix chain 'C' and resid 926 through 931 removed outlier: 3.835A pdb=" N ALA C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 955 Processing helix chain 'C' and resid 971 through 983 removed outlier: 3.545A pdb=" N VAL C 983 " --> pdb=" O ARG C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 993 removed outlier: 3.749A pdb=" N LEU C 990 " --> pdb=" O THR C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1008 removed outlier: 4.013A pdb=" N MET C1008 " --> pdb=" O ALA C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1038 removed outlier: 3.887A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1039 through 1042 Processing helix chain 'C' and resid 1050 through 1058 Processing helix chain 'C' and resid 1059 through 1106 removed outlier: 3.944A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 75 removed outlier: 4.368A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.473A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.719A pdb=" N ALA A 146 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 279 through 284 removed outlier: 4.980A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 126 through 129 removed outlier: 4.087A pdb=" N SER A 126 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 359 through 362 removed outlier: 4.097A pdb=" N THR A 669 " --> pdb=" O ASP A 664 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 373 through 374 removed outlier: 6.207A pdb=" N VAL A 374 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL A 631 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 400 through 404 removed outlier: 6.542A pdb=" N THR A 483 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL A 420 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 513 through 515 removed outlier: 4.937A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 723 through 724 removed outlier: 3.635A pdb=" N GLY A 732 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ALA A 737 " --> pdb=" O PRO A 730 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.814A pdb=" N ILE A 768 " --> pdb=" O SER B 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 778 through 796 removed outlier: 6.870A pdb=" N LYS A 779 " --> pdb=" O VAL A1150 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A1150 " --> pdb=" O LYS A 779 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER A 781 " --> pdb=" O GLU A1148 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU A1148 " --> pdb=" O SER A 781 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N HIS A1146 " --> pdb=" O PRO A 783 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY A1133 " --> pdb=" O ASN A1129 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASN A1129 " --> pdb=" O GLY A1133 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TYR A1135 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL A1127 " --> pdb=" O TYR A1135 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N MET A1137 " --> pdb=" O SER A1125 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER A1125 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A1139 " --> pdb=" O ILE A1123 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A1121 " --> pdb=" O TYR A1141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AB6, first strand: chain 'A' and resid 857 through 858 removed outlier: 3.544A pdb=" N SER A 858 " --> pdb=" O ILE C 768 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1202 through 1204 removed outlier: 6.164A pdb=" N CYS A1156 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1170 through 1173 Processing sheet with id=AB9, first strand: chain 'B' and resid 67 through 75 removed outlier: 4.327A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 92 through 93 removed outlier: 3.518A pdb=" N THR B 93 " --> pdb=" O THR B 96 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.510A pdb=" N LYS B 110 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.510A pdb=" N LYS B 110 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 279 through 284 removed outlier: 5.209A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AC6, first strand: chain 'B' and resid 359 through 362 removed outlier: 3.655A pdb=" N TYR B 663 " --> pdb=" O GLY B 359 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR B 669 " --> pdb=" O ASP B 664 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 373 through 375 Processing sheet with id=AC8, first strand: chain 'B' and resid 400 through 404 removed outlier: 6.748A pdb=" N THR B 477 " --> pdb=" O CYS B 425 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N CYS B 425 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 479 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE B 423 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU B 481 " --> pdb=" O ASN B 421 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER B 419 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 513 through 515 removed outlier: 4.682A pdb=" N SER B 498 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL B 561 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ILE B 500 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N SER B 559 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER B 504 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL B 555 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 506 " --> pdb=" O TRP B 553 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 618 through 620 removed outlier: 3.977A pdb=" N TYR B 648 " --> pdb=" O CYS B 620 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 724 removed outlier: 6.416A pdb=" N VAL B 718 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N SER B 761 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N SER B 720 " --> pdb=" O SER B 761 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 768 through 769 removed outlier: 5.451A pdb=" N ILE B 768 " --> pdb=" O SER C 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 778 through 782 Processing sheet with id=AD5, first strand: chain 'B' and resid 785 through 795 removed outlier: 7.020A pdb=" N TYR B1135 " --> pdb=" O VAL B1127 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL B1127 " --> pdb=" O TYR B1135 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N MET B1137 " --> pdb=" O SER B1125 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N SER B1125 " --> pdb=" O MET B1137 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL B1139 " --> pdb=" O ILE B1123 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR B1121 " --> pdb=" O TYR B1141 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 802 through 804 Processing sheet with id=AD7, first strand: chain 'B' and resid 1202 through 1205 removed outlier: 3.873A pdb=" N CYS B1164 " --> pdb=" O VAL B1205 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N CYS B1156 " --> pdb=" O ILE B1214 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1170 through 1173 Processing sheet with id=AD9, first strand: chain 'C' and resid 67 through 75 removed outlier: 4.457A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AE2, first strand: chain 'C' and resid 279 through 284 removed outlier: 5.202A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG C 119 " --> pdb=" O TYR C 314 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR C 314 " --> pdb=" O ARG C 119 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AE4, first strand: chain 'C' and resid 232 through 235 Processing sheet with id=AE5, first strand: chain 'C' and resid 232 through 235 Processing sheet with id=AE6, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AE7, first strand: chain 'C' and resid 206 through 208 removed outlier: 6.182A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 359 through 361 removed outlier: 4.008A pdb=" N THR C 669 " --> pdb=" O ASP C 664 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 373 through 374 removed outlier: 6.543A pdb=" N VAL C 374 " --> pdb=" O SER C 607 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 400 through 405 removed outlier: 6.312A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 407 through 409 removed outlier: 3.621A pdb=" N CYS C 585 " --> pdb=" O CYS C 407 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 513 through 515 removed outlier: 5.129A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL C 555 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU C 506 " --> pdb=" O TRP C 553 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP C 553 " --> pdb=" O LEU C 506 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP C 539 " --> pdb=" O GLY C 558 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 618 through 619 removed outlier: 7.217A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 717 through 724 removed outlier: 3.568A pdb=" N VAL C 718 " --> pdb=" O MET C 757 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 759 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER C 720 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N SER C 761 " --> pdb=" O SER C 720 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU C 722 " --> pdb=" O SER C 761 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 778 through 795 removed outlier: 7.069A pdb=" N ASN C1145 " --> pdb=" O THR C 784 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N PHE C 786 " --> pdb=" O PRO C1143 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE C 788 " --> pdb=" O TYR C1141 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N TYR C1141 " --> pdb=" O PHE C 788 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL C 790 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL C1139 " --> pdb=" O VAL C 790 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLN C 792 " --> pdb=" O MET C1137 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N MET C1137 " --> pdb=" O GLN C 792 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TYR C 794 " --> pdb=" O TYR C1135 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR C1135 " --> pdb=" O TYR C 794 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 802 through 804 Processing sheet with id=AF8, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 3.795A pdb=" N CYS C1164 " --> pdb=" O VAL C1205 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1170 through 1174 1019 hydrogen bonds defined for protein. 2715 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: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8619 1.34 - 1.46: 7225 1.46 - 1.59: 12356 1.59 - 1.71: 1 1.71 - 1.84: 204 Bond restraints: 28405 Sorted by residual: bond pdb=" CA ASP B 213 " pdb=" C ASP B 213 " ideal model delta sigma weight residual 1.522 1.465 0.057 1.36e-02 5.41e+03 1.77e+01 bond pdb=" CA GLY C 908 " pdb=" C GLY C 908 " ideal model delta sigma weight residual 1.515 1.466 0.049 1.25e-02 6.40e+03 1.52e+01 bond pdb=" CA CYS B 214 " pdb=" C CYS B 214 " ideal model delta sigma weight residual 1.522 1.480 0.042 1.20e-02 6.94e+03 1.23e+01 bond pdb=" C1 MAN O 4 " pdb=" C2 MAN O 4 " ideal model delta sigma weight residual 1.526 1.594 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" CA ASP C 911 " pdb=" C ASP C 911 " ideal model delta sigma weight residual 1.522 1.478 0.044 1.32e-02 5.74e+03 1.11e+01 ... (remaining 28400 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 37664 2.37 - 4.74: 848 4.74 - 7.11: 104 7.11 - 9.49: 19 9.49 - 11.86: 7 Bond angle restraints: 38642 Sorted by residual: angle pdb=" N ASP C 911 " pdb=" CA ASP C 911 " pdb=" C ASP C 911 " ideal model delta sigma weight residual 113.50 102.10 11.40 1.23e+00 6.61e-01 8.59e+01 angle pdb=" N GLY C 908 " pdb=" CA GLY C 908 " pdb=" C GLY C 908 " ideal model delta sigma weight residual 113.37 101.58 11.79 1.34e+00 5.57e-01 7.74e+01 angle pdb=" N CYS C 912 " pdb=" CA CYS C 912 " pdb=" C CYS C 912 " ideal model delta sigma weight residual 113.16 103.20 9.96 1.24e+00 6.50e-01 6.45e+01 angle pdb=" N MET C 913 " pdb=" CA MET C 913 " pdb=" C MET C 913 " ideal model delta sigma weight residual 112.92 103.35 9.57 1.23e+00 6.61e-01 6.05e+01 angle pdb=" N TYR C 909 " pdb=" CA TYR C 909 " pdb=" C TYR C 909 " ideal model delta sigma weight residual 111.36 103.90 7.46 1.09e+00 8.42e-01 4.69e+01 ... (remaining 38637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.82: 16323 22.82 - 45.65: 1056 45.65 - 68.47: 148 68.47 - 91.29: 79 91.29 - 114.11: 19 Dihedral angle restraints: 17625 sinusoidal: 7434 harmonic: 10191 Sorted by residual: dihedral pdb=" CB CYS C 811 " pdb=" SG CYS C 811 " pdb=" SG CYS C 817 " pdb=" CB CYS C 817 " ideal model delta sinusoidal sigma weight residual -86.00 -161.15 75.15 1 1.00e+01 1.00e-02 7.14e+01 dihedral pdb=" CB CYS B 912 " pdb=" SG CYS B 912 " pdb=" SG CYS B 925 " pdb=" CB CYS B 925 " ideal model delta sinusoidal sigma weight residual 93.00 162.93 -69.93 1 1.00e+01 1.00e-02 6.31e+01 dihedral pdb=" CB CYS B 811 " pdb=" SG CYS B 811 " pdb=" SG CYS B 817 " pdb=" CB CYS B 817 " ideal model delta sinusoidal sigma weight residual -86.00 -155.88 69.88 1 1.00e+01 1.00e-02 6.30e+01 ... (remaining 17622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 4380 0.136 - 0.271: 93 0.271 - 0.407: 2 0.407 - 0.542: 1 0.542 - 0.678: 1 Chirality restraints: 4477 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN B 222 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" CA ASN B 222 " pdb=" N ASN B 222 " pdb=" C ASN B 222 " pdb=" CB ASN B 222 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.41e+00 chirality pdb=" CB VAL A 86 " pdb=" CA VAL A 86 " pdb=" CG1 VAL A 86 " pdb=" CG2 VAL A 86 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 4474 not shown) Planarity restraints: 4972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 212 " -0.023 2.00e-02 2.50e+03 4.78e-02 2.28e+01 pdb=" C THR B 212 " 0.083 2.00e-02 2.50e+03 pdb=" O THR B 212 " -0.031 2.00e-02 2.50e+03 pdb=" N ASP B 213 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 928 " 0.014 2.00e-02 2.50e+03 2.68e-02 1.43e+01 pdb=" CG TYR C 928 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR C 928 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR C 928 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR C 928 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 928 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR C 928 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 928 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 84 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.27e+00 pdb=" C MET A 84 " -0.053 2.00e-02 2.50e+03 pdb=" O MET A 84 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR A 85 " 0.018 2.00e-02 2.50e+03 ... (remaining 4969 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5461 2.77 - 3.30: 26658 3.30 - 3.84: 48568 3.84 - 4.37: 53419 4.37 - 4.90: 89487 Nonbonded interactions: 223593 Sorted by model distance: nonbonded pdb=" O SER A 350 " pdb=" OG SER B 829 " model vdw 2.240 3.040 nonbonded pdb=" OD1 ASN B 421 " pdb=" OG1 THR B 483 " model vdw 2.245 3.040 nonbonded pdb=" OD2 ASP C 664 " pdb=" OG1 THR C 667 " model vdw 2.250 3.040 nonbonded pdb=" O GLN B 346 " pdb=" OG SER B 350 " model vdw 2.252 3.040 nonbonded pdb=" OD2 ASP B 664 " pdb=" OG1 THR B 667 " model vdw 2.260 3.040 ... (remaining 223588 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 'A' and resid 19 through 1406) selection = chain 'B' selection = (chain 'C' and resid 19 through 1406) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'O' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 0.030 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 25.210 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 0.068 28506 Z= 0.224 Angle : 0.844 11.857 38897 Z= 0.438 Chirality : 0.054 0.678 4477 Planarity : 0.006 0.073 4940 Dihedral : 15.809 114.115 10971 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.08 % Rotamer: Outliers : 0.33 % Allowed : 0.60 % Favored : 99.07 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.13), residues: 3462 helix: 0.24 (0.19), residues: 686 sheet: -0.18 (0.20), residues: 584 loop : -1.36 (0.12), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 505 TYR 0.062 0.002 TYR C 928 PHE 0.027 0.002 PHE B1136 TRP 0.020 0.002 TRP A 553 HIS 0.005 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00446 (28405) covalent geometry : angle 0.82513 (38642) SS BOND : bond 0.00452 ( 48) SS BOND : angle 1.92449 ( 96) hydrogen bonds : bond 0.14277 ( 997) hydrogen bonds : angle 7.02211 ( 2715) link_ALPHA1-3 : bond 0.00553 ( 3) link_ALPHA1-3 : angle 1.58567 ( 9) link_ALPHA1-6 : bond 0.00295 ( 3) link_ALPHA1-6 : angle 1.69481 ( 9) link_BETA1-4 : bond 0.00718 ( 15) link_BETA1-4 : angle 2.85447 ( 45) link_NAG-ASN : bond 0.00702 ( 32) link_NAG-ASN : angle 2.61247 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 ASN cc_start: 0.9770 (t0) cc_final: 0.9502 (p0) REVERT: A 452 MET cc_start: 0.1376 (ttp) cc_final: 0.0946 (ptt) REVERT: B 673 LEU cc_start: 0.9082 (mp) cc_final: 0.8841 (tp) REVERT: B 943 MET cc_start: 0.8514 (mmm) cc_final: 0.7951 (tmm) REVERT: C 169 LEU cc_start: 0.9397 (tp) cc_final: 0.9113 (mt) REVERT: C 563 MET cc_start: 0.8087 (mmt) cc_final: 0.7525 (mmp) REVERT: C 569 MET cc_start: 0.9270 (pmm) cc_final: 0.8672 (pmm) REVERT: C 943 MET cc_start: 0.8368 (ppp) cc_final: 0.7955 (ppp) outliers start: 10 outliers final: 2 residues processed: 112 average time/residue: 0.1643 time to fit residues: 30.6888 Evaluate side-chains 79 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 50.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 647 ASN A 833 GLN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 HIS B 410 ASN B 576 GLN B 688 GLN B 733 GLN B 833 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 ASN C 808 GLN C1028 ASN C1029 ASN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1145 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.023270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2267 r_free = 0.2267 target = 0.014537 restraints weight = 546198.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2289 r_free = 0.2289 target = 0.014986 restraints weight = 352467.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2304 r_free = 0.2304 target = 0.015329 restraints weight = 267006.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2316 r_free = 0.2316 target = 0.015539 restraints weight = 220511.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2323 r_free = 0.2323 target = 0.015736 restraints weight = 193268.361| |-----------------------------------------------------------------------------| r_work (final): 0.2327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 28506 Z= 0.203 Angle : 0.650 12.481 38897 Z= 0.332 Chirality : 0.043 0.495 4477 Planarity : 0.005 0.064 4940 Dihedral : 9.251 111.041 4881 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.43 % Favored : 94.54 % Rotamer: Outliers : 0.10 % Allowed : 5.22 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.14), residues: 3462 helix: 1.19 (0.20), residues: 708 sheet: -0.63 (0.19), residues: 708 loop : -1.10 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 190 TYR 0.019 0.002 TYR B 351 PHE 0.021 0.002 PHE B 313 TRP 0.014 0.002 TRP B 960 HIS 0.005 0.001 HIS C1138 Details of bonding type rmsd covalent geometry : bond 0.00406 (28405) covalent geometry : angle 0.63070 (38642) SS BOND : bond 0.00302 ( 48) SS BOND : angle 1.08313 ( 96) hydrogen bonds : bond 0.03991 ( 997) hydrogen bonds : angle 5.90554 ( 2715) link_ALPHA1-3 : bond 0.00616 ( 3) link_ALPHA1-3 : angle 3.81227 ( 9) link_ALPHA1-6 : bond 0.00352 ( 3) link_ALPHA1-6 : angle 2.03908 ( 9) link_BETA1-4 : bond 0.00354 ( 15) link_BETA1-4 : angle 2.23471 ( 45) link_NAG-ASN : bond 0.00358 ( 32) link_NAG-ASN : angle 2.40622 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 939 MET cc_start: 0.6841 (mtp) cc_final: 0.5737 (ttm) REVERT: C 147 PHE cc_start: 0.9809 (m-80) cc_final: 0.9539 (m-80) REVERT: C 757 MET cc_start: 0.8677 (mtt) cc_final: 0.8243 (tpp) outliers start: 3 outliers final: 2 residues processed: 83 average time/residue: 0.1441 time to fit residues: 21.4236 Evaluate side-chains 70 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 158 optimal weight: 9.9990 chunk 320 optimal weight: 20.0000 chunk 264 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 18 optimal weight: 40.0000 chunk 6 optimal weight: 20.0000 chunk 261 optimal weight: 10.0000 chunk 174 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 67 optimal weight: 30.0000 chunk 45 optimal weight: 50.0000 overall best weight: 13.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 471 GLN ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1056 GLN A1129 ASN ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 GLN B 808 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 ASN ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1028 ASN ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 ASN C 681 HIS C 769 GLN C 833 GLN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1097 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.022065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2242 r_free = 0.2242 target = 0.013819 restraints weight = 594290.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2260 r_free = 0.2260 target = 0.014143 restraints weight = 384114.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2277 r_free = 0.2277 target = 0.014407 restraints weight = 290967.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.2288 r_free = 0.2288 target = 0.014680 restraints weight = 242514.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2294 r_free = 0.2294 target = 0.014833 restraints weight = 214000.912| |-----------------------------------------------------------------------------| r_work (final): 0.2292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 28506 Z= 0.323 Angle : 0.798 17.108 38897 Z= 0.408 Chirality : 0.046 0.541 4477 Planarity : 0.005 0.063 4940 Dihedral : 8.640 115.563 4881 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.48 % Favored : 92.49 % Rotamer: Outliers : 0.07 % Allowed : 6.51 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.14), residues: 3462 helix: 0.33 (0.18), residues: 785 sheet: -0.90 (0.19), residues: 696 loop : -1.45 (0.14), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 190 TYR 0.028 0.003 TYR B 689 PHE 0.027 0.003 PHE B 674 TRP 0.026 0.003 TRP A 44 HIS 0.010 0.002 HIS B1146 Details of bonding type rmsd covalent geometry : bond 0.00637 (28405) covalent geometry : angle 0.77806 (38642) SS BOND : bond 0.00470 ( 48) SS BOND : angle 1.38258 ( 96) hydrogen bonds : bond 0.04835 ( 997) hydrogen bonds : angle 6.45667 ( 2715) link_ALPHA1-3 : bond 0.00745 ( 3) link_ALPHA1-3 : angle 3.49363 ( 9) link_ALPHA1-6 : bond 0.00333 ( 3) link_ALPHA1-6 : angle 2.09506 ( 9) link_BETA1-4 : bond 0.00636 ( 15) link_BETA1-4 : angle 2.31337 ( 45) link_NAG-ASN : bond 0.00965 ( 32) link_NAG-ASN : angle 2.85697 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 1.157 Fit side-chains REVERT: B 939 MET cc_start: 0.7156 (mtp) cc_final: 0.6436 (mtp) REVERT: B 943 MET cc_start: 0.9023 (tpt) cc_final: 0.8657 (tmm) REVERT: C 147 PHE cc_start: 0.9784 (m-80) cc_final: 0.9549 (m-80) REVERT: C 757 MET cc_start: 0.8823 (mtt) cc_final: 0.8258 (tpp) REVERT: C 939 MET cc_start: 0.8798 (mmm) cc_final: 0.8320 (mmm) outliers start: 2 outliers final: 0 residues processed: 76 average time/residue: 0.1649 time to fit residues: 21.8463 Evaluate side-chains 63 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 79 optimal weight: 6.9990 chunk 236 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 243 optimal weight: 5.9990 chunk 145 optimal weight: 0.5980 chunk 264 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 346 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN B 421 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1208 GLN ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.022601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2251 r_free = 0.2251 target = 0.014058 restraints weight = 562810.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2277 r_free = 0.2277 target = 0.014539 restraints weight = 357102.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2293 r_free = 0.2293 target = 0.014877 restraints weight = 267653.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2304 r_free = 0.2304 target = 0.015068 restraints weight = 219659.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.2311 r_free = 0.2311 target = 0.015278 restraints weight = 192205.109| |-----------------------------------------------------------------------------| r_work (final): 0.2318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 28506 Z= 0.152 Angle : 0.618 11.725 38897 Z= 0.312 Chirality : 0.044 0.489 4477 Planarity : 0.004 0.059 4940 Dihedral : 7.979 114.575 4881 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.83 % Favored : 94.14 % Rotamer: Outliers : 0.03 % Allowed : 3.06 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.14), residues: 3462 helix: 0.92 (0.20), residues: 743 sheet: -0.83 (0.19), residues: 722 loop : -1.26 (0.14), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 629 TYR 0.025 0.002 TYR C 609 PHE 0.027 0.002 PHE A 164 TRP 0.029 0.002 TRP A 44 HIS 0.004 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00324 (28405) covalent geometry : angle 0.60153 (38642) SS BOND : bond 0.00300 ( 48) SS BOND : angle 1.22813 ( 96) hydrogen bonds : bond 0.03547 ( 997) hydrogen bonds : angle 5.94573 ( 2715) link_ALPHA1-3 : bond 0.01150 ( 3) link_ALPHA1-3 : angle 3.15672 ( 9) link_ALPHA1-6 : bond 0.00536 ( 3) link_ALPHA1-6 : angle 1.62160 ( 9) link_BETA1-4 : bond 0.00365 ( 15) link_BETA1-4 : angle 1.82984 ( 45) link_NAG-ASN : bond 0.00329 ( 32) link_NAG-ASN : angle 2.22871 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.988 Fit side-chains REVERT: B 943 MET cc_start: 0.8923 (tpt) cc_final: 0.8719 (mmm) REVERT: C 757 MET cc_start: 0.8692 (mtt) cc_final: 0.8218 (tpp) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.1377 time to fit residues: 18.3170 Evaluate side-chains 65 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 66 optimal weight: 30.0000 chunk 270 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 305 optimal weight: 8.9990 chunk 310 optimal weight: 20.0000 chunk 141 optimal weight: 0.5980 chunk 345 optimal weight: 20.0000 chunk 179 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 241 optimal weight: 1.9990 chunk 162 optimal weight: 10.0000 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 GLN A1085 GLN A1129 ASN B 792 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 ASN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN C 772 GLN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.022550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2254 r_free = 0.2254 target = 0.014022 restraints weight = 561812.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2283 r_free = 0.2283 target = 0.014490 restraints weight = 357029.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2295 r_free = 0.2295 target = 0.014843 restraints weight = 268491.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2306 r_free = 0.2306 target = 0.015088 restraints weight = 220036.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2313 r_free = 0.2313 target = 0.015260 restraints weight = 191437.038| |-----------------------------------------------------------------------------| r_work (final): 0.2324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28506 Z= 0.157 Angle : 0.601 11.998 38897 Z= 0.303 Chirality : 0.043 0.453 4477 Planarity : 0.004 0.070 4940 Dihedral : 7.582 112.687 4881 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.82 % Rotamer: Outliers : 0.03 % Allowed : 2.76 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.14), residues: 3462 helix: 1.00 (0.20), residues: 744 sheet: -0.92 (0.19), residues: 723 loop : -1.25 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.023 0.002 TYR B 947 PHE 0.022 0.001 PHE A 164 TRP 0.018 0.002 TRP A 44 HIS 0.005 0.001 HIS B1138 Details of bonding type rmsd covalent geometry : bond 0.00326 (28405) covalent geometry : angle 0.58435 (38642) SS BOND : bond 0.00296 ( 48) SS BOND : angle 1.16371 ( 96) hydrogen bonds : bond 0.03452 ( 997) hydrogen bonds : angle 5.86212 ( 2715) link_ALPHA1-3 : bond 0.01074 ( 3) link_ALPHA1-3 : angle 3.05608 ( 9) link_ALPHA1-6 : bond 0.00603 ( 3) link_ALPHA1-6 : angle 1.56100 ( 9) link_BETA1-4 : bond 0.00351 ( 15) link_BETA1-4 : angle 1.88915 ( 45) link_NAG-ASN : bond 0.00315 ( 32) link_NAG-ASN : angle 2.18383 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: B 906 MET cc_start: 0.9516 (mmp) cc_final: 0.9296 (tpp) REVERT: B 943 MET cc_start: 0.9116 (tpt) cc_final: 0.8888 (tpt) REVERT: C 569 MET cc_start: 0.9271 (pmm) cc_final: 0.8745 (pmm) outliers start: 1 outliers final: 1 residues processed: 72 average time/residue: 0.1352 time to fit residues: 17.2872 Evaluate side-chains 65 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 188 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 170 optimal weight: 40.0000 chunk 72 optimal weight: 20.0000 chunk 294 optimal weight: 8.9990 chunk 256 optimal weight: 7.9990 chunk 267 optimal weight: 20.0000 chunk 212 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 236 optimal weight: 2.9990 chunk 178 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1122 HIS ** 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 = 0.2628 r_free = 0.2628 target = 0.022320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2253 r_free = 0.2253 target = 0.013887 restraints weight = 573707.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.2278 r_free = 0.2278 target = 0.014362 restraints weight = 369054.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.2294 r_free = 0.2294 target = 0.014695 restraints weight = 278163.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2304 r_free = 0.2304 target = 0.014931 restraints weight = 229370.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2310 r_free = 0.2310 target = 0.015097 restraints weight = 200736.687| |-----------------------------------------------------------------------------| r_work (final): 0.2305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28506 Z= 0.180 Angle : 0.614 11.897 38897 Z= 0.311 Chirality : 0.043 0.444 4477 Planarity : 0.004 0.057 4940 Dihedral : 7.354 112.922 4881 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.21 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.14), residues: 3462 helix: 0.90 (0.19), residues: 762 sheet: -1.00 (0.19), residues: 713 loop : -1.23 (0.14), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 119 TYR 0.019 0.002 TYR B 947 PHE 0.022 0.002 PHE A 164 TRP 0.018 0.002 TRP A 535 HIS 0.006 0.001 HIS B1138 Details of bonding type rmsd covalent geometry : bond 0.00370 (28405) covalent geometry : angle 0.59743 (38642) SS BOND : bond 0.00302 ( 48) SS BOND : angle 1.28253 ( 96) hydrogen bonds : bond 0.03588 ( 997) hydrogen bonds : angle 5.87745 ( 2715) link_ALPHA1-3 : bond 0.00945 ( 3) link_ALPHA1-3 : angle 3.19381 ( 9) link_ALPHA1-6 : bond 0.00646 ( 3) link_ALPHA1-6 : angle 1.60996 ( 9) link_BETA1-4 : bond 0.00326 ( 15) link_BETA1-4 : angle 1.93384 ( 45) link_NAG-ASN : bond 0.00315 ( 32) link_NAG-ASN : angle 2.17279 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: B 906 MET cc_start: 0.9506 (mmp) cc_final: 0.9251 (tpp) REVERT: B 943 MET cc_start: 0.9096 (tpt) cc_final: 0.8867 (tpt) REVERT: C 757 MET cc_start: 0.8674 (mtt) cc_final: 0.8201 (tpp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1455 time to fit residues: 18.8146 Evaluate side-chains 64 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 131 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 chunk 168 optimal weight: 50.0000 chunk 175 optimal weight: 20.0000 chunk 303 optimal weight: 4.9990 chunk 205 optimal weight: 9.9990 chunk 184 optimal weight: 9.9990 chunk 214 optimal weight: 20.0000 chunk 220 optimal weight: 20.0000 chunk 136 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 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 = 0.2629 r_free = 0.2629 target = 0.022292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.2256 r_free = 0.2256 target = 0.013920 restraints weight = 572644.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2278 r_free = 0.2278 target = 0.014393 restraints weight = 368626.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2296 r_free = 0.2296 target = 0.014732 restraints weight = 277392.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2303 r_free = 0.2303 target = 0.014962 restraints weight = 229643.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2311 r_free = 0.2311 target = 0.015131 restraints weight = 199851.396| |-----------------------------------------------------------------------------| r_work (final): 0.2307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28506 Z= 0.169 Angle : 0.607 12.410 38897 Z= 0.306 Chirality : 0.043 0.444 4477 Planarity : 0.004 0.055 4940 Dihedral : 7.226 112.657 4881 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.53 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.14), residues: 3462 helix: 1.00 (0.19), residues: 752 sheet: -0.99 (0.19), residues: 699 loop : -1.21 (0.14), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 694 TYR 0.022 0.002 TYR B 642 PHE 0.023 0.002 PHE A 164 TRP 0.018 0.002 TRP A 535 HIS 0.006 0.001 HIS A 670 Details of bonding type rmsd covalent geometry : bond 0.00348 (28405) covalent geometry : angle 0.58929 (38642) SS BOND : bond 0.00291 ( 48) SS BOND : angle 1.22967 ( 96) hydrogen bonds : bond 0.03517 ( 997) hydrogen bonds : angle 5.86486 ( 2715) link_ALPHA1-3 : bond 0.00876 ( 3) link_ALPHA1-3 : angle 2.96160 ( 9) link_ALPHA1-6 : bond 0.00619 ( 3) link_ALPHA1-6 : angle 1.59665 ( 9) link_BETA1-4 : bond 0.00347 ( 15) link_BETA1-4 : angle 1.94004 ( 45) link_NAG-ASN : bond 0.00330 ( 32) link_NAG-ASN : angle 2.28445 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.856 Fit side-chains REVERT: B 906 MET cc_start: 0.9513 (mmp) cc_final: 0.9302 (tpp) REVERT: B 943 MET cc_start: 0.9087 (tpt) cc_final: 0.8870 (tpt) REVERT: C 147 PHE cc_start: 0.9771 (m-10) cc_final: 0.9519 (m-80) REVERT: C 569 MET cc_start: 0.9253 (pmm) cc_final: 0.8705 (pmm) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1364 time to fit residues: 16.9106 Evaluate side-chains 64 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 34 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 310 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 108 optimal weight: 20.0000 chunk 166 optimal weight: 7.9990 chunk 147 optimal weight: 20.0000 chunk 253 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 252 optimal weight: 20.0000 chunk 179 optimal weight: 30.0000 overall best weight: 9.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 GLN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1085 GLN ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 848 ASN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.021746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2243 r_free = 0.2243 target = 0.013659 restraints weight = 596300.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2266 r_free = 0.2266 target = 0.014021 restraints weight = 381424.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2282 r_free = 0.2282 target = 0.014337 restraints weight = 285078.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2291 r_free = 0.2291 target = 0.014576 restraints weight = 234661.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2297 r_free = 0.2297 target = 0.014686 restraints weight = 205331.750| |-----------------------------------------------------------------------------| r_work (final): 0.2302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 28506 Z= 0.247 Angle : 0.693 13.828 38897 Z= 0.354 Chirality : 0.044 0.448 4477 Planarity : 0.005 0.076 4940 Dihedral : 7.327 113.317 4881 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.14), residues: 3462 helix: 0.75 (0.19), residues: 752 sheet: -1.23 (0.18), residues: 729 loop : -1.33 (0.14), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 181 TYR 0.028 0.002 TYR B 947 PHE 0.026 0.002 PHE A 164 TRP 0.017 0.002 TRP A 535 HIS 0.008 0.002 HIS B1146 Details of bonding type rmsd covalent geometry : bond 0.00496 (28405) covalent geometry : angle 0.67559 (38642) SS BOND : bond 0.00387 ( 48) SS BOND : angle 1.45374 ( 96) hydrogen bonds : bond 0.04078 ( 997) hydrogen bonds : angle 6.25852 ( 2715) link_ALPHA1-3 : bond 0.00248 ( 3) link_ALPHA1-3 : angle 3.50996 ( 9) link_ALPHA1-6 : bond 0.00491 ( 3) link_ALPHA1-6 : angle 1.75869 ( 9) link_BETA1-4 : bond 0.00273 ( 15) link_BETA1-4 : angle 2.02594 ( 45) link_NAG-ASN : bond 0.00472 ( 32) link_NAG-ASN : angle 2.37599 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 943 MET cc_start: 0.8981 (tpt) cc_final: 0.8770 (tpt) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1403 time to fit residues: 16.8066 Evaluate side-chains 61 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 178 optimal weight: 20.0000 chunk 272 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 chunk 311 optimal weight: 10.0000 chunk 273 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 315 optimal weight: 20.0000 chunk 126 optimal weight: 30.0000 chunk 14 optimal weight: 20.0000 chunk 129 optimal weight: 9.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.021846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2246 r_free = 0.2246 target = 0.013672 restraints weight = 576598.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2268 r_free = 0.2268 target = 0.014015 restraints weight = 368662.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2287 r_free = 0.2287 target = 0.014351 restraints weight = 276594.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2295 r_free = 0.2295 target = 0.014586 restraints weight = 228003.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2304 r_free = 0.2304 target = 0.014749 restraints weight = 198752.924| |-----------------------------------------------------------------------------| r_work (final): 0.2342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28506 Z= 0.198 Angle : 0.643 13.385 38897 Z= 0.326 Chirality : 0.044 0.440 4477 Planarity : 0.004 0.070 4940 Dihedral : 7.195 113.743 4881 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.14), residues: 3462 helix: 0.90 (0.20), residues: 746 sheet: -1.18 (0.19), residues: 715 loop : -1.31 (0.14), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 62 TYR 0.022 0.002 TYR B 947 PHE 0.022 0.002 PHE A 164 TRP 0.021 0.002 TRP A 535 HIS 0.006 0.001 HIS B1138 Details of bonding type rmsd covalent geometry : bond 0.00402 (28405) covalent geometry : angle 0.62697 (38642) SS BOND : bond 0.00329 ( 48) SS BOND : angle 1.32908 ( 96) hydrogen bonds : bond 0.03783 ( 997) hydrogen bonds : angle 6.15969 ( 2715) link_ALPHA1-3 : bond 0.00949 ( 3) link_ALPHA1-3 : angle 3.02464 ( 9) link_ALPHA1-6 : bond 0.00568 ( 3) link_ALPHA1-6 : angle 1.64056 ( 9) link_BETA1-4 : bond 0.00291 ( 15) link_BETA1-4 : angle 1.91704 ( 45) link_NAG-ASN : bond 0.00339 ( 32) link_NAG-ASN : angle 2.22523 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: C 696 MET cc_start: 0.7981 (tpp) cc_final: 0.7682 (tpt) REVERT: C 757 MET cc_start: 0.8595 (mtt) cc_final: 0.7726 (mmm) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1374 time to fit residues: 16.4486 Evaluate side-chains 62 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 285 optimal weight: 40.0000 chunk 202 optimal weight: 0.0000 chunk 28 optimal weight: 20.0000 chunk 92 optimal weight: 0.9980 chunk 174 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 218 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 266 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 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 = 0.2627 r_free = 0.2627 target = 0.022055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2252 r_free = 0.2252 target = 0.013774 restraints weight = 562838.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2274 r_free = 0.2274 target = 0.014145 restraints weight = 358724.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2291 r_free = 0.2291 target = 0.014404 restraints weight = 268517.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2305 r_free = 0.2305 target = 0.014713 restraints weight = 221367.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2309 r_free = 0.2309 target = 0.014876 restraints weight = 193680.168| |-----------------------------------------------------------------------------| r_work (final): 0.2342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28506 Z= 0.139 Angle : 0.619 12.488 38897 Z= 0.308 Chirality : 0.044 0.424 4477 Planarity : 0.004 0.062 4940 Dihedral : 6.944 111.472 4881 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.14), residues: 3462 helix: 1.10 (0.20), residues: 734 sheet: -1.00 (0.19), residues: 676 loop : -1.29 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 221 TYR 0.026 0.001 TYR B 947 PHE 0.020 0.001 PHE A 164 TRP 0.021 0.002 TRP A 535 HIS 0.005 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00297 (28405) covalent geometry : angle 0.60108 (38642) SS BOND : bond 0.00256 ( 48) SS BOND : angle 1.23830 ( 96) hydrogen bonds : bond 0.03416 ( 997) hydrogen bonds : angle 5.95470 ( 2715) link_ALPHA1-3 : bond 0.00960 ( 3) link_ALPHA1-3 : angle 2.58884 ( 9) link_ALPHA1-6 : bond 0.00636 ( 3) link_ALPHA1-6 : angle 1.54558 ( 9) link_BETA1-4 : bond 0.00363 ( 15) link_BETA1-4 : angle 1.88819 ( 45) link_NAG-ASN : bond 0.00405 ( 32) link_NAG-ASN : angle 2.34946 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: B 943 MET cc_start: 0.8770 (tpt) cc_final: 0.8558 (tpt) REVERT: C 171 LEU cc_start: 0.9704 (tp) cc_final: 0.9487 (pp) REVERT: C 569 MET cc_start: 0.9189 (pmm) cc_final: 0.8603 (pmm) REVERT: C 696 MET cc_start: 0.7820 (tpp) cc_final: 0.7494 (tpt) REVERT: C 757 MET cc_start: 0.8868 (mtt) cc_final: 0.8073 (tpp) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1451 time to fit residues: 17.3593 Evaluate side-chains 63 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 283 optimal weight: 40.0000 chunk 190 optimal weight: 40.0000 chunk 219 optimal weight: 6.9990 chunk 265 optimal weight: 0.0980 chunk 150 optimal weight: 30.0000 chunk 202 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 chunk 259 optimal weight: 7.9990 chunk 204 optimal weight: 8.9990 chunk 50 optimal weight: 50.0000 chunk 338 optimal weight: 30.0000 overall best weight: 5.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 826 GLN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 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 = 0.2622 r_free = 0.2622 target = 0.021934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2245 r_free = 0.2245 target = 0.013753 restraints weight = 567494.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2267 r_free = 0.2267 target = 0.014056 restraints weight = 366690.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2283 r_free = 0.2283 target = 0.014298 restraints weight = 273307.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2298 r_free = 0.2298 target = 0.014586 restraints weight = 227549.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2306 r_free = 0.2306 target = 0.014719 restraints weight = 199702.811| |-----------------------------------------------------------------------------| r_work (final): 0.2311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28506 Z= 0.159 Angle : 0.624 12.030 38897 Z= 0.312 Chirality : 0.043 0.414 4477 Planarity : 0.004 0.057 4940 Dihedral : 6.737 110.769 4881 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.14), residues: 3462 helix: 1.08 (0.20), residues: 746 sheet: -1.05 (0.19), residues: 693 loop : -1.26 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 221 TYR 0.027 0.002 TYR B 947 PHE 0.019 0.002 PHE A 164 TRP 0.019 0.002 TRP A 535 HIS 0.005 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00333 (28405) covalent geometry : angle 0.60658 (38642) SS BOND : bond 0.00286 ( 48) SS BOND : angle 1.26189 ( 96) hydrogen bonds : bond 0.03486 ( 997) hydrogen bonds : angle 5.95153 ( 2715) link_ALPHA1-3 : bond 0.01032 ( 3) link_ALPHA1-3 : angle 2.82785 ( 9) link_ALPHA1-6 : bond 0.00613 ( 3) link_ALPHA1-6 : angle 1.56377 ( 9) link_BETA1-4 : bond 0.00328 ( 15) link_BETA1-4 : angle 1.93222 ( 45) link_NAG-ASN : bond 0.00408 ( 32) link_NAG-ASN : angle 2.30396 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4476.73 seconds wall clock time: 78 minutes 39.31 seconds (4719.31 seconds total)