Starting phenix.real_space_refine on Tue Jun 24 06:50:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ymx_33946/06_2025/7ymx_33946.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ymx_33946/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ymx_33946/06_2025/7ymx_33946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ymx_33946/06_2025/7ymx_33946.map" model { file = "/net/cci-nas-00/data/ceres_data/7ymx_33946/06_2025/7ymx_33946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ymx_33946/06_2025/7ymx_33946.cif" } resolution = 4.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 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): 0.47s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.62, per 1000 atoms: 0.63 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: 7.42 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 4.02 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: 12.53 Time building geometry restraints manager: 8.71 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 1223 or resid 1401 through 1406)) selection = chain 'B' selection = (chain 'C' and (resid 19 through 1223 or resid 1401 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: 0.720 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: 1.160 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 66.520 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.170 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.560 ------------------------------------------------------------------------------- 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 : 7.67 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.020 0.002 TRP A 553 HIS 0.005 0.001 HIS A 264 PHE 0.027 0.002 PHE B1136 TYR 0.062 0.002 TYR C 928 ARG 0.008 0.000 ARG C 505 Details of bonding type rmsd link_NAG-ASN : bond 0.00702 ( 32) link_NAG-ASN : angle 2.61247 ( 96) 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_ALPHA1-3 : bond 0.00553 ( 3) link_ALPHA1-3 : angle 1.58567 ( 9) hydrogen bonds : bond 0.14277 ( 997) hydrogen bonds : angle 7.02211 ( 2715) SS BOND : bond 0.00452 ( 48) SS BOND : angle 1.92449 ( 96) covalent geometry : bond 0.00446 (28405) covalent geometry : angle 0.82513 (38642) *********************** 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 : 3.862 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: 0.8840 (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: 0.7526 (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: 0.7956 (ppp) outliers start: 10 outliers final: 2 residues processed: 112 average time/residue: 0.4014 time to fit residues: 76.2505 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 : 2.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 10.0000 chunk 263 optimal weight: 20.0000 chunk 146 optimal weight: 30.0000 chunk 90 optimal weight: 0.8980 chunk 177 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 272 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 165 optimal weight: 0.0980 chunk 203 optimal weight: 50.0000 chunk 316 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** A1084 GLN A1085 GLN 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 C1029 ASN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1122 HIS C1145 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.023690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2286 r_free = 0.2286 target = 0.014794 restraints weight = 529287.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2310 r_free = 0.2310 target = 0.015251 restraints weight = 346932.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2324 r_free = 0.2324 target = 0.015595 restraints weight = 265041.353| |-----------------------------------------------------------------------------| r_work (final): 0.2317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28506 Z= 0.159 Angle : 0.605 12.258 38897 Z= 0.307 Chirality : 0.043 0.474 4477 Planarity : 0.004 0.064 4940 Dihedral : 9.343 110.398 4881 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.37 % Favored : 94.60 % Rotamer: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.14), residues: 3462 helix: 1.34 (0.20), residues: 684 sheet: -0.50 (0.19), residues: 686 loop : -1.10 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 960 HIS 0.005 0.001 HIS C 670 PHE 0.017 0.001 PHE B 850 TYR 0.017 0.001 TYR B 219 ARG 0.004 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 32) link_NAG-ASN : angle 2.30231 ( 96) link_ALPHA1-6 : bond 0.00352 ( 3) link_ALPHA1-6 : angle 1.86658 ( 9) link_BETA1-4 : bond 0.00378 ( 15) link_BETA1-4 : angle 2.16361 ( 45) link_ALPHA1-3 : bond 0.00932 ( 3) link_ALPHA1-3 : angle 3.63931 ( 9) hydrogen bonds : bond 0.03766 ( 997) hydrogen bonds : angle 5.80590 ( 2715) SS BOND : bond 0.00263 ( 48) SS BOND : angle 1.02218 ( 96) covalent geometry : bond 0.00324 (28405) covalent geometry : angle 0.58614 (38642) *********************** 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 85 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 3.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 939 MET cc_start: 0.6824 (mtp) cc_final: 0.5740 (ttm) REVERT: C 147 PHE cc_start: 0.9815 (m-80) cc_final: 0.9544 (m-80) REVERT: C 757 MET cc_start: 0.8741 (mtt) cc_final: 0.8301 (tpp) REVERT: C 939 MET cc_start: 0.8406 (mmp) cc_final: 0.8160 (mmp) outliers start: 4 outliers final: 3 residues processed: 85 average time/residue: 0.3515 time to fit residues: 52.8443 Evaluate side-chains 71 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 1 optimal weight: 40.0000 chunk 4 optimal weight: 8.9990 chunk 296 optimal weight: 10.0000 chunk 87 optimal weight: 40.0000 chunk 3 optimal weight: 5.9990 chunk 104 optimal weight: 30.0000 chunk 325 optimal weight: 7.9990 chunk 191 optimal weight: 30.0000 chunk 273 optimal weight: 30.0000 chunk 317 optimal weight: 0.0980 chunk 345 optimal weight: 8.9990 overall best weight: 6.4188 ------------------------------------------------------------------------------- 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** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 ASN ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 GLN C 842 GLN C1028 ASN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.023328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2275 r_free = 0.2275 target = 0.014601 restraints weight = 545396.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2294 r_free = 0.2294 target = 0.015011 restraints weight = 347703.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2310 r_free = 0.2310 target = 0.015351 restraints weight = 263477.913| |-----------------------------------------------------------------------------| r_work (final): 0.2311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1776 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= 0.166 Angle : 0.604 11.745 38897 Z= 0.304 Chirality : 0.043 0.435 4477 Planarity : 0.004 0.064 4940 Dihedral : 8.471 111.130 4881 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.86 % Favored : 94.11 % Rotamer: Outliers : 0.03 % Allowed : 3.66 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3462 helix: 1.09 (0.20), residues: 737 sheet: -0.61 (0.19), residues: 684 loop : -1.09 (0.14), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 44 HIS 0.008 0.001 HIS B1122 PHE 0.014 0.001 PHE A 895 TYR 0.026 0.002 TYR C 909 ARG 0.004 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 32) link_NAG-ASN : angle 2.22033 ( 96) link_ALPHA1-6 : bond 0.00425 ( 3) link_ALPHA1-6 : angle 1.69073 ( 9) link_BETA1-4 : bond 0.00524 ( 15) link_BETA1-4 : angle 2.11310 ( 45) link_ALPHA1-3 : bond 0.00856 ( 3) link_ALPHA1-3 : angle 2.83368 ( 9) hydrogen bonds : bond 0.03616 ( 997) hydrogen bonds : angle 5.71799 ( 2715) SS BOND : bond 0.00359 ( 48) SS BOND : angle 1.01817 ( 96) covalent geometry : bond 0.00338 (28405) covalent geometry : angle 0.58708 (38642) *********************** 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 80 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 3.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 939 MET cc_start: 0.6385 (mtp) cc_final: 0.5183 (mtp) REVERT: B 943 MET cc_start: 0.8789 (tpt) cc_final: 0.8345 (tmm) REVERT: C 147 PHE cc_start: 0.9781 (m-80) cc_final: 0.9522 (m-80) REVERT: C 757 MET cc_start: 0.8650 (mtt) cc_final: 0.8151 (tpp) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.3732 time to fit residues: 52.6583 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 : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 211 optimal weight: 6.9990 chunk 315 optimal weight: 7.9990 chunk 73 optimal weight: 0.0870 chunk 148 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 chunk 275 optimal weight: 4.9990 chunk 247 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 229 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 overall best weight: 3.8166 ------------------------------------------------------------------------------- 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** B 792 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** 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 = 0.2665 r_free = 0.2665 target = 0.023471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2278 r_free = 0.2278 target = 0.014625 restraints weight = 535815.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2302 r_free = 0.2302 target = 0.015096 restraints weight = 344144.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2316 r_free = 0.2316 target = 0.015452 restraints weight = 260179.038| |-----------------------------------------------------------------------------| r_work (final): 0.2315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28506 Z= 0.120 Angle : 0.568 11.713 38897 Z= 0.283 Chirality : 0.043 0.436 4477 Planarity : 0.004 0.064 4940 Dihedral : 7.903 110.562 4881 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.52 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3462 helix: 1.37 (0.20), residues: 717 sheet: -0.52 (0.19), residues: 682 loop : -1.09 (0.14), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 44 HIS 0.003 0.001 HIS B1146 PHE 0.029 0.001 PHE C 164 TYR 0.022 0.001 TYR B 689 ARG 0.004 0.000 ARG A 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 32) link_NAG-ASN : angle 2.05042 ( 96) link_ALPHA1-6 : bond 0.00581 ( 3) link_ALPHA1-6 : angle 1.60487 ( 9) link_BETA1-4 : bond 0.00410 ( 15) link_BETA1-4 : angle 1.96366 ( 45) link_ALPHA1-3 : bond 0.01119 ( 3) link_ALPHA1-3 : angle 2.80818 ( 9) hydrogen bonds : bond 0.03285 ( 997) hydrogen bonds : angle 5.57202 ( 2715) SS BOND : bond 0.00351 ( 48) SS BOND : angle 1.14495 ( 96) covalent geometry : bond 0.00259 (28405) covalent geometry : angle 0.55144 (38642) *********************** 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 78 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 3.524 Fit side-chains revert: symmetry clash REVERT: B 939 MET cc_start: 0.6521 (mtp) cc_final: 0.5299 (mtp) REVERT: B 943 MET cc_start: 0.8905 (tpt) cc_final: 0.8440 (tmm) REVERT: C 757 MET cc_start: 0.8697 (mtt) cc_final: 0.8156 (tpp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.3797 time to fit residues: 53.4922 Evaluate side-chains 67 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 3.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 290 optimal weight: 5.9990 chunk 214 optimal weight: 30.0000 chunk 45 optimal weight: 40.0000 chunk 108 optimal weight: 6.9990 chunk 220 optimal weight: 20.0000 chunk 131 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 256 optimal weight: 6.9990 chunk 126 optimal weight: 30.0000 chunk 130 optimal weight: 20.0000 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1085 GLN B 808 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** 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 = 0.2662 r_free = 0.2662 target = 0.023350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2280 r_free = 0.2280 target = 0.014625 restraints weight = 535835.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2299 r_free = 0.2299 target = 0.015018 restraints weight = 347099.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2316 r_free = 0.2316 target = 0.015351 restraints weight = 263094.798| |-----------------------------------------------------------------------------| r_work (final): 0.2310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28506 Z= 0.127 Angle : 0.569 12.468 38897 Z= 0.284 Chirality : 0.043 0.479 4477 Planarity : 0.004 0.060 4940 Dihedral : 7.318 110.245 4881 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.72 % Favored : 94.25 % Rotamer: Outliers : 0.03 % Allowed : 2.06 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3462 helix: 1.24 (0.20), residues: 736 sheet: -0.55 (0.19), residues: 688 loop : -1.09 (0.14), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 535 HIS 0.003 0.001 HIS B1146 PHE 0.019 0.001 PHE C 850 TYR 0.018 0.001 TYR B 689 ARG 0.003 0.000 ARG A1057 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 32) link_NAG-ASN : angle 2.13584 ( 96) link_ALPHA1-6 : bond 0.00704 ( 3) link_ALPHA1-6 : angle 1.50271 ( 9) link_BETA1-4 : bond 0.00400 ( 15) link_BETA1-4 : angle 1.91154 ( 45) link_ALPHA1-3 : bond 0.01103 ( 3) link_ALPHA1-3 : angle 2.90549 ( 9) hydrogen bonds : bond 0.03216 ( 997) hydrogen bonds : angle 5.49583 ( 2715) SS BOND : bond 0.00211 ( 48) SS BOND : angle 1.13576 ( 96) covalent geometry : bond 0.00271 (28405) covalent geometry : angle 0.55192 (38642) *********************** 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 75 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 3.232 Fit side-chains revert: symmetry clash REVERT: B 943 MET cc_start: 0.8964 (tpt) cc_final: 0.8633 (tpp) REVERT: C 147 PHE cc_start: 0.9833 (m-80) cc_final: 0.9452 (m-80) REVERT: C 569 MET cc_start: 0.9176 (pmm) cc_final: 0.8609 (pmm) REVERT: C 757 MET cc_start: 0.8729 (mtt) cc_final: 0.8161 (tpp) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.3580 time to fit residues: 48.5042 Evaluate side-chains 67 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 278 optimal weight: 3.9990 chunk 125 optimal weight: 30.0000 chunk 95 optimal weight: 4.9990 chunk 209 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 140 optimal weight: 30.0000 chunk 6 optimal weight: 7.9990 chunk 159 optimal weight: 40.0000 chunk 195 optimal weight: 10.0000 chunk 307 optimal weight: 7.9990 chunk 156 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 HIS ** 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 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** C 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1122 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.023039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2270 r_free = 0.2270 target = 0.014366 restraints weight = 549278.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2292 r_free = 0.2292 target = 0.014779 restraints weight = 352041.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2308 r_free = 0.2308 target = 0.015064 restraints weight = 264799.652| |-----------------------------------------------------------------------------| r_work (final): 0.2309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28506 Z= 0.146 Angle : 0.577 11.432 38897 Z= 0.289 Chirality : 0.043 0.446 4477 Planarity : 0.004 0.070 4940 Dihedral : 6.989 110.366 4881 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.86 % Favored : 94.11 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3462 helix: 1.29 (0.20), residues: 738 sheet: -0.55 (0.19), residues: 671 loop : -1.03 (0.14), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 535 HIS 0.005 0.001 HIS C1122 PHE 0.022 0.001 PHE C 850 TYR 0.013 0.001 TYR C 351 ARG 0.007 0.000 ARG A 221 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 32) link_NAG-ASN : angle 2.15631 ( 96) link_ALPHA1-6 : bond 0.00670 ( 3) link_ALPHA1-6 : angle 1.47115 ( 9) link_BETA1-4 : bond 0.00304 ( 15) link_BETA1-4 : angle 1.99570 ( 45) link_ALPHA1-3 : bond 0.01018 ( 3) link_ALPHA1-3 : angle 3.02005 ( 9) hydrogen bonds : bond 0.03288 ( 997) hydrogen bonds : angle 5.48554 ( 2715) SS BOND : bond 0.00238 ( 48) SS BOND : angle 1.08492 ( 96) covalent geometry : bond 0.00304 (28405) covalent geometry : angle 0.55938 (38642) *********************** 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 : 3.068 Fit side-chains REVERT: C 757 MET cc_start: 0.8709 (mtt) cc_final: 0.7996 (mmm) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.3498 time to fit residues: 46.5704 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 : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 298 optimal weight: 40.0000 chunk 155 optimal weight: 3.9990 chunk 337 optimal weight: 9.9990 chunk 259 optimal weight: 7.9990 chunk 129 optimal weight: 8.9990 chunk 127 optimal weight: 30.0000 chunk 330 optimal weight: 8.9990 chunk 63 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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** ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 772 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 = 0.2639 r_free = 0.2639 target = 0.022601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2263 r_free = 0.2263 target = 0.014128 restraints weight = 559180.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2282 r_free = 0.2282 target = 0.014517 restraints weight = 357135.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2298 r_free = 0.2298 target = 0.014851 restraints weight = 268636.305| |-----------------------------------------------------------------------------| r_work (final): 0.2298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2916 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= 0.187 Angle : 0.614 12.093 38897 Z= 0.310 Chirality : 0.043 0.475 4477 Planarity : 0.004 0.062 4940 Dihedral : 6.912 111.532 4881 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.35 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3462 helix: 1.20 (0.20), residues: 750 sheet: -0.67 (0.19), residues: 678 loop : -1.12 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 535 HIS 0.006 0.001 HIS C1122 PHE 0.049 0.002 PHE A 164 TYR 0.030 0.002 TYR B 219 ARG 0.004 0.000 ARG B 758 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 32) link_NAG-ASN : angle 2.26813 ( 96) link_ALPHA1-6 : bond 0.00655 ( 3) link_ALPHA1-6 : angle 1.59140 ( 9) link_BETA1-4 : bond 0.00259 ( 15) link_BETA1-4 : angle 1.91019 ( 45) link_ALPHA1-3 : bond 0.01047 ( 3) link_ALPHA1-3 : angle 3.25437 ( 9) hydrogen bonds : bond 0.03515 ( 997) hydrogen bonds : angle 5.65361 ( 2715) SS BOND : bond 0.00290 ( 48) SS BOND : angle 1.12262 ( 96) covalent geometry : bond 0.00378 (28405) covalent geometry : angle 0.59687 (38642) *********************** 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 73 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 3.026 Fit side-chains REVERT: B 939 MET cc_start: 0.8888 (mmp) cc_final: 0.8033 (mtp) REVERT: B 943 MET cc_start: 0.8844 (tpt) cc_final: 0.8278 (tpt) REVERT: C 147 PHE cc_start: 0.9803 (m-80) cc_final: 0.9421 (m-80) REVERT: C 569 MET cc_start: 0.9221 (pmm) cc_final: 0.8717 (pmm) REVERT: C 757 MET cc_start: 0.8551 (mtt) cc_final: 0.7827 (tpp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3491 time to fit residues: 46.2127 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 : 3.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 107 optimal weight: 8.9990 chunk 164 optimal weight: 30.0000 chunk 330 optimal weight: 7.9990 chunk 209 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 252 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 overall best weight: 5.9788 ------------------------------------------------------------------------------- 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 72 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 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.022632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2256 r_free = 0.2256 target = 0.014078 restraints weight = 560689.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2279 r_free = 0.2279 target = 0.014567 restraints weight = 357658.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2297 r_free = 0.2297 target = 0.014861 restraints weight = 267519.276| |-----------------------------------------------------------------------------| r_work (final): 0.2302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28506 Z= 0.156 Angle : 0.595 12.097 38897 Z= 0.300 Chirality : 0.043 0.464 4477 Planarity : 0.004 0.059 4940 Dihedral : 6.821 111.439 4881 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.09 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3462 helix: 1.16 (0.20), residues: 750 sheet: -0.70 (0.19), residues: 683 loop : -1.14 (0.14), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 535 HIS 0.005 0.001 HIS B1138 PHE 0.025 0.001 PHE A 164 TYR 0.026 0.001 TYR B 219 ARG 0.004 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 32) link_NAG-ASN : angle 2.12876 ( 96) link_ALPHA1-6 : bond 0.00650 ( 3) link_ALPHA1-6 : angle 1.56332 ( 9) link_BETA1-4 : bond 0.00307 ( 15) link_BETA1-4 : angle 1.87440 ( 45) link_ALPHA1-3 : bond 0.00916 ( 3) link_ALPHA1-3 : angle 2.92786 ( 9) hydrogen bonds : bond 0.03357 ( 997) hydrogen bonds : angle 5.63725 ( 2715) SS BOND : bond 0.00297 ( 48) SS BOND : angle 1.28820 ( 96) covalent geometry : bond 0.00324 (28405) covalent geometry : angle 0.57799 (38642) *********************** 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 76 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 3.317 Fit side-chains revert: symmetry clash REVERT: C 569 MET cc_start: 0.9266 (pmm) cc_final: 0.8781 (pmm) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.3918 time to fit residues: 52.3737 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 : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 339 optimal weight: 2.9990 chunk 210 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 145 optimal weight: 5.9990 chunk 252 optimal weight: 30.0000 chunk 24 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 246 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 155 optimal weight: 0.7980 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 GLN ** 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 = 0.2642 r_free = 0.2642 target = 0.022638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2258 r_free = 0.2258 target = 0.013991 restraints weight = 550818.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2284 r_free = 0.2284 target = 0.014472 restraints weight = 352995.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2303 r_free = 0.2303 target = 0.014812 restraints weight = 265239.290| |-----------------------------------------------------------------------------| r_work (final): 0.2305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3165 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= 0.140 Angle : 0.594 12.125 38897 Z= 0.297 Chirality : 0.043 0.460 4477 Planarity : 0.004 0.059 4940 Dihedral : 6.660 110.200 4881 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3462 helix: 1.23 (0.20), residues: 745 sheet: -0.76 (0.20), residues: 651 loop : -1.16 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 535 HIS 0.005 0.001 HIS B1138 PHE 0.027 0.001 PHE A 164 TYR 0.018 0.001 TYR B 219 ARG 0.005 0.000 ARG B 505 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 32) link_NAG-ASN : angle 2.06788 ( 96) link_ALPHA1-6 : bond 0.00719 ( 3) link_ALPHA1-6 : angle 1.54061 ( 9) link_BETA1-4 : bond 0.00329 ( 15) link_BETA1-4 : angle 1.88579 ( 45) link_ALPHA1-3 : bond 0.00876 ( 3) link_ALPHA1-3 : angle 2.73114 ( 9) hydrogen bonds : bond 0.03259 ( 997) hydrogen bonds : angle 5.63332 ( 2715) SS BOND : bond 0.00374 ( 48) SS BOND : angle 1.46217 ( 96) covalent geometry : bond 0.00297 (28405) covalent geometry : angle 0.57639 (38642) *********************** 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 73 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 3.135 Fit side-chains REVERT: A 757 MET cc_start: 0.8986 (mmm) cc_final: 0.8748 (tpp) REVERT: C 147 PHE cc_start: 0.9785 (m-80) cc_final: 0.9391 (m-80) REVERT: C 569 MET cc_start: 0.9252 (pmm) cc_final: 0.8763 (pmm) REVERT: C 696 MET cc_start: 0.8211 (tpp) cc_final: 0.7789 (tpt) REVERT: C 757 MET cc_start: 0.8383 (mtt) cc_final: 0.7522 (mmm) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3626 time to fit residues: 47.2704 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 : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 40 optimal weight: 50.0000 chunk 56 optimal weight: 7.9990 chunk 241 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 312 optimal weight: 9.9990 chunk 267 optimal weight: 40.0000 chunk 17 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 278 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 209 optimal weight: 0.4980 overall best weight: 4.8988 ------------------------------------------------------------------------------- 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 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.022588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2261 r_free = 0.2261 target = 0.014060 restraints weight = 554041.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2285 r_free = 0.2285 target = 0.014519 restraints weight = 352277.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2301 r_free = 0.2301 target = 0.014859 restraints weight = 264436.490| |-----------------------------------------------------------------------------| r_work (final): 0.2304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3278 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= 0.140 Angle : 0.592 12.409 38897 Z= 0.296 Chirality : 0.043 0.457 4477 Planarity : 0.004 0.058 4940 Dihedral : 6.515 109.775 4881 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.12 % Favored : 93.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3462 helix: 1.25 (0.20), residues: 744 sheet: -0.76 (0.19), residues: 663 loop : -1.15 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 535 HIS 0.004 0.001 HIS B1138 PHE 0.025 0.001 PHE A 164 TYR 0.018 0.001 TYR B 219 ARG 0.004 0.000 ARG A 505 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 32) link_NAG-ASN : angle 2.06823 ( 96) link_ALPHA1-6 : bond 0.00703 ( 3) link_ALPHA1-6 : angle 1.51167 ( 9) link_BETA1-4 : bond 0.00325 ( 15) link_BETA1-4 : angle 1.91293 ( 45) link_ALPHA1-3 : bond 0.01000 ( 3) link_ALPHA1-3 : angle 2.77289 ( 9) hydrogen bonds : bond 0.03246 ( 997) hydrogen bonds : angle 5.61661 ( 2715) SS BOND : bond 0.00324 ( 48) SS BOND : angle 1.37754 ( 96) covalent geometry : bond 0.00299 (28405) covalent geometry : angle 0.57526 (38642) ********************** 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 73 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 3.270 Fit side-chains REVERT: B 939 MET cc_start: 0.8825 (mmp) cc_final: 0.8604 (mmm) REVERT: B 943 MET cc_start: 0.8661 (tpt) cc_final: 0.8389 (tpp) REVERT: C 569 MET cc_start: 0.9253 (pmm) cc_final: 0.8760 (pmm) REVERT: C 696 MET cc_start: 0.8096 (tpp) cc_final: 0.7663 (tpt) REVERT: C 757 MET cc_start: 0.8409 (mtt) cc_final: 0.7520 (mmm) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3594 time to fit residues: 47.3849 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 : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 129 optimal weight: 50.0000 chunk 109 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 16 optimal weight: 40.0000 chunk 215 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 199 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 271 optimal weight: 0.0870 chunk 27 optimal weight: 9.9990 overall best weight: 2.8164 ------------------------------------------------------------------------------- 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 B 72 GLN ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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 = 0.2653 r_free = 0.2653 target = 0.022861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2273 r_free = 0.2273 target = 0.014277 restraints weight = 545562.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2296 r_free = 0.2296 target = 0.014727 restraints weight = 346684.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2314 r_free = 0.2314 target = 0.015015 restraints weight = 261317.264| |-----------------------------------------------------------------------------| r_work (final): 0.2310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28506 Z= 0.109 Angle : 0.583 11.490 38897 Z= 0.288 Chirality : 0.043 0.446 4477 Planarity : 0.004 0.059 4940 Dihedral : 6.303 108.202 4881 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3462 helix: 1.23 (0.20), residues: 749 sheet: -0.75 (0.19), residues: 691 loop : -1.10 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 535 HIS 0.003 0.001 HIS B1138 PHE 0.023 0.001 PHE B 366 TYR 0.012 0.001 TYR B 219 ARG 0.005 0.000 ARG A 758 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 32) link_NAG-ASN : angle 1.98551 ( 96) link_ALPHA1-6 : bond 0.00760 ( 3) link_ALPHA1-6 : angle 1.44421 ( 9) link_BETA1-4 : bond 0.00399 ( 15) link_BETA1-4 : angle 1.87320 ( 45) link_ALPHA1-3 : bond 0.01075 ( 3) link_ALPHA1-3 : angle 2.38821 ( 9) hydrogen bonds : bond 0.03081 ( 997) hydrogen bonds : angle 5.47105 ( 2715) SS BOND : bond 0.00239 ( 48) SS BOND : angle 1.26254 ( 96) covalent geometry : bond 0.00242 (28405) covalent geometry : angle 0.56787 (38642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8791.74 seconds wall clock time: 154 minutes 15.34 seconds (9255.34 seconds total)