Starting phenix.real_space_refine on Sun Jul 5 13:16:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ymx_33946/07_2026/7ymx_33946.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ymx_33946/07_2026/7ymx_33946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ymx_33946/07_2026/7ymx_33946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ymx_33946/07_2026/7ymx_33946.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ymx_33946/07_2026/7ymx_33946.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ymx_33946/07_2026/7ymx_33946.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ymx_33946/07_2026/7ymx_33946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ymx_33946/07_2026/7ymx_33946.map" } resolution = 4.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.117 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 153 5.16 5 C 17602 2.51 5 N 4511 2.21 5 O 5509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27775 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "B" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "C" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 7 Time building chain proxies: 5.70, per 1000 atoms: 0.21 Number of scatterers: 27775 At special positions: 0 Unit cell: (151.8, 170.5, 179.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 153 16.00 O 5509 8.00 N 4511 7.00 C 17602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.03 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.02 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.03 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.03 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.05 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.02 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.04 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.03 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.03 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.03 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.03 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.03 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.03 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.03 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.03 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.05 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA I 3 " - " MAN I 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA I 3 " - " MAN I 5 " " BMA O 3 " - " MAN O 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A1401 " - " ASN A 222 " " NAG A1402 " - " ASN A 236 " " NAG A1403 " - " ASN A 244 " " NAG A1404 " - " ASN A 619 " " NAG A1405 " - " ASN A 719 " " NAG A1406 " - " ASN A 774 " " NAG A1407 " - " ASN A 785 " " NAG B1401 " - " ASN B 619 " " NAG B1402 " - " ASN B 774 " " NAG B1403 " - " ASN B 785 " " NAG B1404 " - " ASN B 244 " " NAG B1405 " - " ASN B 66 " " NAG B1406 " - " ASN B 719 " " NAG C1401 " - " ASN C 719 " " NAG C1402 " - " ASN C 870 " " NAG C1403 " - " ASN C 785 " " NAG C1404 " - " ASN C 166 " " NAG C1405 " - " ASN C 244 " " NAG C1406 " - " ASN C 619 " " NAG C1407 " - " ASN C 66 " " NAG D 1 " - " ASN A 66 " " NAG E 1 " - " ASN A 125 " " NAG F 1 " - " ASN A 166 " " NAG G 1 " - " ASN A 870 " " NAG H 1 " - " ASN A1213 " " NAG I 1 " - " ASN B 125 " " NAG J 1 " - " ASN B1213 " " NAG K 1 " - " ASN B 870 " " NAG L 1 " - " ASN B 222 " " NAG M 1 " - " ASN C1213 " " NAG N 1 " - " ASN C 222 " " NAG O 1 " - " ASN C 125 " Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 1.1 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: 1.06 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: 7.28 Time building geometry restraints manager: 2.88 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 - 17.99: 14796 17.99 - 35.98: 1395 35.98 - 53.97: 239 53.97 - 71.97: 65 71.97 - 89.96: 35 Dihedral angle restraints: 16530 sinusoidal: 6339 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 16527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 4380 0.136 - 0.271: 93 0.271 - 0.407: 2 0.407 - 0.542: 1 0.542 - 0.678: 1 Chirality restraints: 4477 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN B 222 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" CA ASN B 222 " pdb=" N ASN B 222 " pdb=" C ASN B 222 " pdb=" CB ASN B 222 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.41e+00 chirality pdb=" CB VAL A 86 " pdb=" CA VAL A 86 " pdb=" CG1 VAL A 86 " pdb=" CG2 VAL A 86 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 4474 not shown) Planarity restraints: 4972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 212 " -0.023 2.00e-02 2.50e+03 4.78e-02 2.28e+01 pdb=" C THR B 212 " 0.083 2.00e-02 2.50e+03 pdb=" O THR B 212 " -0.031 2.00e-02 2.50e+03 pdb=" N ASP B 213 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 928 " 0.014 2.00e-02 2.50e+03 2.68e-02 1.43e+01 pdb=" CG TYR C 928 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR C 928 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR C 928 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR C 928 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 928 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR C 928 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 928 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 84 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.27e+00 pdb=" C MET A 84 " -0.053 2.00e-02 2.50e+03 pdb=" O MET A 84 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR A 85 " 0.018 2.00e-02 2.50e+03 ... (remaining 4969 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5461 2.77 - 3.30: 26658 3.30 - 3.84: 48568 3.84 - 4.37: 53419 4.37 - 4.90: 89487 Nonbonded interactions: 223593 Sorted by model distance: nonbonded pdb=" O SER A 350 " pdb=" OG SER B 829 " model vdw 2.240 3.040 nonbonded pdb=" OD1 ASN B 421 " pdb=" OG1 THR B 483 " model vdw 2.245 3.040 nonbonded pdb=" OD2 ASP C 664 " pdb=" OG1 THR C 667 " model vdw 2.250 3.040 nonbonded pdb=" O GLN B 346 " pdb=" OG SER B 350 " model vdw 2.252 3.040 nonbonded pdb=" OD2 ASP B 664 " pdb=" OG1 THR B 667 " model vdw 2.260 3.040 ... (remaining 223588 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 19 through 1406) selection = chain 'B' selection = (chain 'C' and resid 19 through 1406) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.040 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.550 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 : 14.727 89.956 9876 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.08 % Rotamer: Outliers : 0.33 % Allowed : 0.60 % Favored : 99.07 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.13), residues: 3462 helix: 0.24 (0.19), residues: 686 sheet: -0.18 (0.20), residues: 584 loop : -1.36 (0.12), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 505 TYR 0.062 0.002 TYR C 928 PHE 0.027 0.002 PHE B1136 TRP 0.020 0.002 TRP A 553 HIS 0.005 0.001 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.22 (28405) covalent geometry : angle 0.82513 / 0.43 (38642) SS BOND : bond 0.00452 / 0.36 ( 48) SS BOND : angle 1.92449 / 1.26 ( 96) hydrogen bonds : bond 0.14277 / 9.59 ( 997) hydrogen bonds : angle 7.02211 / 4.86 ( 2715) link_ALPHA1-3 : bond 0.00553 / 0.21 ( 3) link_ALPHA1-3 : angle 1.58567 / 0.88 ( 9) link_ALPHA1-6 : bond 0.00295 / 0.12 ( 3) link_ALPHA1-6 : angle 1.69481 / 0.82 ( 9) link_BETA1-4 : bond 0.00718 / 0.47 ( 15) link_BETA1-4 : angle 2.85447 / 2.03 ( 45) link_NAG-ASN : bond 0.00702 / 0.40 ( 32) link_NAG-ASN : angle 2.61247 / 1.64 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 ASN cc_start: 0.9770 (t0) cc_final: 0.9502 (p0) REVERT: A 452 MET cc_start: 0.1376 (ttp) cc_final: 0.0946 (ptt) REVERT: B 673 LEU cc_start: 0.9082 (mp) cc_final: 0.8841 (tp) REVERT: B 943 MET cc_start: 0.8514 (mmm) cc_final: 0.7951 (tmm) REVERT: C 169 LEU cc_start: 0.9397 (tp) cc_final: 0.9113 (mt) REVERT: C 563 MET cc_start: 0.8087 (mmt) cc_final: 0.7525 (mmp) REVERT: C 569 MET cc_start: 0.9270 (pmm) cc_final: 0.8672 (pmm) REVERT: C 943 MET cc_start: 0.8368 (ppp) cc_final: 0.7955 (ppp) outliers start: 10 outliers final: 2 residues processed: 112 average time/residue: 0.1659 time to fit residues: 31.3541 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 : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 50.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 C 808 GLN C1028 ASN C1029 ASN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1145 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.023361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2270 r_free = 0.2270 target = 0.014616 restraints weight = 541670.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2293 r_free = 0.2293 target = 0.015061 restraints weight = 355746.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2308 r_free = 0.2308 target = 0.015401 restraints weight = 271493.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2319 r_free = 0.2319 target = 0.015593 restraints weight = 225163.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2325 r_free = 0.2325 target = 0.015792 restraints weight = 197830.403| |-----------------------------------------------------------------------------| r_work (final): 0.2323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 28506 Z= 0.201 Angle : 0.620 11.856 38897 Z= 0.320 Chirality : 0.042 0.424 4477 Planarity : 0.005 0.064 4940 Dihedral : 4.972 25.624 3786 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.34 % Favored : 94.63 % Rotamer: Outliers : 0.13 % Allowed : 4.89 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.14), residues: 3462 helix: 1.22 (0.20), residues: 708 sheet: -0.63 (0.19), residues: 696 loop : -1.11 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 822 TYR 0.026 0.002 TYR B 219 PHE 0.017 0.002 PHE B 850 TRP 0.014 0.002 TRP B 960 HIS 0.007 0.001 HIS C 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.20 (28405) covalent geometry : angle 0.60473 / 0.32 (38642) SS BOND : bond 0.00324 / 0.23 ( 48) SS BOND : angle 1.03199 / 0.71 ( 96) hydrogen bonds : bond 0.03932 / 2.65 ( 997) hydrogen bonds : angle 5.92767 / 4.12 ( 2715) link_ALPHA1-3 : bond 0.00691 / 0.28 ( 3) link_ALPHA1-3 : angle 2.43504 / 1.36 ( 9) link_ALPHA1-6 : bond 0.00295 / 0.15 ( 3) link_ALPHA1-6 : angle 1.89368 / 1.03 ( 9) link_BETA1-4 : bond 0.00321 / 0.20 ( 15) link_BETA1-4 : angle 1.92029 / 1.38 ( 45) link_NAG-ASN : bond 0.00311 / 0.20 ( 32) link_NAG-ASN : angle 2.24382 / 1.48 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 939 MET cc_start: 0.6859 (mtp) cc_final: 0.5755 (ttm) REVERT: C 147 PHE cc_start: 0.9831 (m-80) cc_final: 0.9569 (m-80) REVERT: C 757 MET cc_start: 0.8795 (mtt) cc_final: 0.8308 (tpp) REVERT: C 939 MET cc_start: 0.8413 (mmp) cc_final: 0.8166 (mmp) outliers start: 4 outliers final: 3 residues processed: 84 average time/residue: 0.1530 time to fit residues: 23.0976 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 : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 158 optimal weight: 30.0000 chunk 320 optimal weight: 0.0870 chunk 264 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 18 optimal weight: 40.0000 chunk 6 optimal weight: 30.0000 chunk 261 optimal weight: 10.0000 chunk 174 optimal weight: 20.0000 chunk 87 optimal weight: 40.0000 chunk 67 optimal weight: 30.0000 chunk 45 optimal weight: 0.6980 overall best weight: 7.5568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 GLN A1085 GLN B 808 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 ASN ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.022960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2254 r_free = 0.2254 target = 0.014283 restraints weight = 552314.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2277 r_free = 0.2277 target = 0.014757 restraints weight = 355177.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2293 r_free = 0.2293 target = 0.015102 restraints weight = 267496.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2305 r_free = 0.2305 target = 0.015311 restraints weight = 220119.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2311 r_free = 0.2311 target = 0.015502 restraints weight = 193512.114| |-----------------------------------------------------------------------------| r_work (final): 0.2318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28506 Z= 0.186 Angle : 0.610 11.634 38897 Z= 0.311 Chirality : 0.042 0.387 4477 Planarity : 0.004 0.064 4940 Dihedral : 4.888 26.042 3786 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.82 % Rotamer: Outliers : 0.03 % Allowed : 4.59 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 3462 helix: 0.82 (0.19), residues: 781 sheet: -0.67 (0.19), residues: 705 loop : -1.19 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.022 0.002 TYR C 909 PHE 0.015 0.001 PHE A 850 TRP 0.029 0.002 TRP A 44 HIS 0.006 0.001 HIS B1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 (28405) covalent geometry : angle 0.59565 / 0.31 (38642) SS BOND : bond 0.00333 / 0.20 ( 48) SS BOND : angle 1.05176 / 0.70 ( 96) hydrogen bonds : bond 0.03717 / 2.49 ( 997) hydrogen bonds : angle 5.83814 / 4.05 ( 2715) link_ALPHA1-3 : bond 0.00550 / 0.21 ( 3) link_ALPHA1-3 : angle 1.83923 / 1.05 ( 9) link_ALPHA1-6 : bond 0.00219 / 0.11 ( 3) link_ALPHA1-6 : angle 1.79003 / 0.96 ( 9) link_BETA1-4 : bond 0.00320 / 0.20 ( 15) link_BETA1-4 : angle 1.84551 / 1.30 ( 45) link_NAG-ASN : bond 0.00387 / 0.21 ( 32) link_NAG-ASN : angle 2.11644 / 1.45 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 939 MET cc_start: 0.6467 (mtp) cc_final: 0.5757 (mtp) REVERT: B 943 MET cc_start: 0.8821 (tpt) cc_final: 0.8478 (tmm) REVERT: C 147 PHE cc_start: 0.9773 (m-80) cc_final: 0.9492 (m-80) REVERT: C 757 MET cc_start: 0.8645 (mtt) cc_final: 0.8158 (tpp) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.1656 time to fit residues: 23.5764 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 : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 79 optimal weight: 5.9990 chunk 236 optimal weight: 0.8980 chunk 173 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 243 optimal weight: 0.9990 chunk 145 optimal weight: 30.0000 chunk 264 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 346 optimal weight: 9.9990 chunk 130 optimal weight: 0.6980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 681 HIS ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1066 GLN ** A1084 GLN ** 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 842 GLN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1122 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.023324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2275 r_free = 0.2275 target = 0.014570 restraints weight = 532241.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2297 r_free = 0.2297 target = 0.015008 restraints weight = 338712.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2312 r_free = 0.2312 target = 0.015363 restraints weight = 255820.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2325 r_free = 0.2325 target = 0.015580 restraints weight = 210026.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2332 r_free = 0.2332 target = 0.015787 restraints weight = 182766.877| |-----------------------------------------------------------------------------| r_work (final): 0.2339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 28506 Z= 0.111 Angle : 0.563 10.742 38897 Z= 0.283 Chirality : 0.043 0.383 4477 Planarity : 0.004 0.061 4940 Dihedral : 4.673 23.013 3786 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.49 % Favored : 94.48 % Rotamer: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3462 helix: 1.16 (0.20), residues: 739 sheet: -0.63 (0.19), residues: 702 loop : -1.15 (0.14), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1088 TYR 0.014 0.001 TYR A 314 PHE 0.029 0.001 PHE A 164 TRP 0.017 0.001 TRP A 44 HIS 0.003 0.001 HIS A1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (28405) covalent geometry : angle 0.55110 / 0.28 (38642) SS BOND : bond 0.00260 / 0.16 ( 48) SS BOND : angle 1.11414 / 0.72 ( 96) hydrogen bonds : bond 0.03245 / 2.20 ( 997) hydrogen bonds : angle 5.56253 / 3.86 ( 2715) link_ALPHA1-3 : bond 0.00804 / 0.30 ( 3) link_ALPHA1-3 : angle 1.60065 / 0.89 ( 9) link_ALPHA1-6 : bond 0.00242 / 0.10 ( 3) link_ALPHA1-6 : angle 1.58155 / 0.84 ( 9) link_BETA1-4 : bond 0.00384 / 0.24 ( 15) link_BETA1-4 : angle 1.57231 / 1.14 ( 45) link_NAG-ASN : bond 0.00288 / 0.17 ( 32) link_NAG-ASN : angle 1.83214 / 1.22 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 939 MET cc_start: 0.6451 (mtp) cc_final: 0.5233 (mtp) REVERT: B 943 MET cc_start: 0.8856 (tpt) cc_final: 0.8405 (tmm) REVERT: C 569 MET cc_start: 0.9124 (pmm) cc_final: 0.8592 (pmm) REVERT: C 757 MET cc_start: 0.8642 (mtt) cc_final: 0.8124 (tpp) outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 0.1693 time to fit residues: 23.7800 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 : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 66 optimal weight: 40.0000 chunk 270 optimal weight: 50.0000 chunk 63 optimal weight: 20.0000 chunk 305 optimal weight: 1.9990 chunk 310 optimal weight: 20.0000 chunk 141 optimal weight: 30.0000 chunk 345 optimal weight: 6.9990 chunk 179 optimal weight: 30.0000 chunk 14 optimal weight: 40.0000 chunk 241 optimal weight: 30.0000 chunk 162 optimal weight: 50.0000 overall best weight: 15.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 ASN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 HIS ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 HIS B 421 ASN B 568 GLN B 769 GLN ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1028 ASN ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1208 GLN ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 769 GLN C 772 GLN C 833 GLN ** C 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.021693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2234 r_free = 0.2234 target = 0.013512 restraints weight = 603841.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2254 r_free = 0.2254 target = 0.013946 restraints weight = 390040.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.2269 r_free = 0.2269 target = 0.014280 restraints weight = 294721.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2278 r_free = 0.2278 target = 0.014429 restraints weight = 243356.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2288 r_free = 0.2288 target = 0.014629 restraints weight = 217228.887| |-----------------------------------------------------------------------------| r_work (final): 0.2293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.149 28506 Z= 0.378 Angle : 0.850 15.828 38897 Z= 0.441 Chirality : 0.046 0.459 4477 Planarity : 0.006 0.060 4940 Dihedral : 5.589 31.479 3786 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 28.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.68 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.14), residues: 3462 helix: 0.32 (0.18), residues: 751 sheet: -1.14 (0.18), residues: 732 loop : -1.47 (0.14), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 758 TYR 0.033 0.003 TYR B 689 PHE 0.035 0.003 PHE A 164 TRP 0.021 0.003 TRP B 960 HIS 0.012 0.003 HIS B1146 Details of bonding type rmsd/Z covalent geometry : bond 0.00744 / 0.38 (28405) covalent geometry : angle 0.83225 / 0.44 (38642) SS BOND : bond 0.01172 / 0.74 ( 48) SS BOND : angle 1.76483 / 1.17 ( 96) hydrogen bonds : bond 0.05117 / 3.40 ( 997) hydrogen bonds : angle 6.57024 / 4.55 ( 2715) link_ALPHA1-3 : bond 0.00333 / 0.17 ( 3) link_ALPHA1-3 : angle 2.63789 / 1.50 ( 9) link_ALPHA1-6 : bond 0.00454 / 0.23 ( 3) link_ALPHA1-6 : angle 2.47705 / 1.37 ( 9) link_BETA1-4 : bond 0.00430 / 0.25 ( 15) link_BETA1-4 : angle 2.11010 / 1.45 ( 45) link_NAG-ASN : bond 0.00824 / 0.53 ( 32) link_NAG-ASN : angle 2.72116 / 1.86 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: B 943 MET cc_start: 0.8876 (tpt) cc_final: 0.8582 (tpp) REVERT: C 147 PHE cc_start: 0.9811 (m-10) cc_final: 0.9585 (m-80) REVERT: C 939 MET cc_start: 0.8804 (mmm) cc_final: 0.8319 (mmm) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1774 time to fit residues: 22.8392 Evaluate side-chains 61 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 188 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 170 optimal weight: 50.0000 chunk 72 optimal weight: 4.9990 chunk 294 optimal weight: 8.9990 chunk 256 optimal weight: 7.9990 chunk 267 optimal weight: 30.0000 chunk 212 optimal weight: 10.0000 chunk 76 optimal weight: 30.0000 chunk 236 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN B 568 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 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** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 772 GLN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1097 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.022219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2245 r_free = 0.2245 target = 0.013881 restraints weight = 574304.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2268 r_free = 0.2268 target = 0.014347 restraints weight = 368577.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2284 r_free = 0.2284 target = 0.014675 restraints weight = 276688.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2295 r_free = 0.2295 target = 0.014862 restraints weight = 227087.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2302 r_free = 0.2302 target = 0.015069 restraints weight = 198556.468| |-----------------------------------------------------------------------------| r_work (final): 0.2306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28506 Z= 0.181 Angle : 0.628 12.728 38897 Z= 0.321 Chirality : 0.043 0.429 4477 Planarity : 0.004 0.075 4940 Dihedral : 5.234 28.401 3786 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.12 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.14), residues: 3462 helix: 0.86 (0.20), residues: 738 sheet: -1.05 (0.18), residues: 719 loop : -1.26 (0.14), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 758 TYR 0.035 0.002 TYR B 219 PHE 0.024 0.002 PHE A 164 TRP 0.019 0.002 TRP A 535 HIS 0.006 0.001 HIS B1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (28405) covalent geometry : angle 0.61344 / 0.32 (38642) SS BOND : bond 0.00361 / 0.24 ( 48) SS BOND : angle 1.34080 / 0.86 ( 96) hydrogen bonds : bond 0.03678 / 2.47 ( 997) hydrogen bonds : angle 6.09254 / 4.24 ( 2715) link_ALPHA1-3 : bond 0.00679 / 0.27 ( 3) link_ALPHA1-3 : angle 1.74554 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00332 / 0.17 ( 3) link_ALPHA1-6 : angle 1.82524 / 0.98 ( 9) link_BETA1-4 : bond 0.00304 / 0.18 ( 15) link_BETA1-4 : angle 1.61998 / 1.15 ( 45) link_NAG-ASN : bond 0.00346 / 0.20 ( 32) link_NAG-ASN : angle 2.21360 / 1.61 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.096 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1692 time to fit residues: 22.5773 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 : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 131 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 chunk 168 optimal weight: 50.0000 chunk 175 optimal weight: 20.0000 chunk 303 optimal weight: 20.0000 chunk 205 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 214 optimal weight: 6.9990 chunk 220 optimal weight: 20.0000 chunk 136 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN A1208 GLN B 277 ASN ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 772 GLN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.022110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2244 r_free = 0.2244 target = 0.013663 restraints weight = 572102.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2268 r_free = 0.2268 target = 0.014123 restraints weight = 368383.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2285 r_free = 0.2285 target = 0.014394 restraints weight = 277465.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2300 r_free = 0.2300 target = 0.014656 restraints weight = 229895.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.2302 r_free = 0.2302 target = 0.014839 restraints weight = 200672.297| |-----------------------------------------------------------------------------| r_work (final): 0.2306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28506 Z= 0.194 Angle : 0.629 12.764 38897 Z= 0.322 Chirality : 0.043 0.400 4477 Planarity : 0.004 0.065 4940 Dihedral : 5.163 27.597 3786 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.82 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.14), residues: 3462 helix: 0.90 (0.19), residues: 750 sheet: -1.12 (0.18), residues: 711 loop : -1.26 (0.14), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 190 TYR 0.025 0.002 TYR B 219 PHE 0.021 0.002 PHE A 164 TRP 0.018 0.002 TRP A 535 HIS 0.006 0.001 HIS C1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 (28405) covalent geometry : angle 0.61555 / 0.32 (38642) SS BOND : bond 0.00347 / 0.22 ( 48) SS BOND : angle 1.38358 / 0.93 ( 96) hydrogen bonds : bond 0.03716 / 2.49 ( 997) hydrogen bonds : angle 6.07532 / 4.23 ( 2715) link_ALPHA1-3 : bond 0.00470 / 0.19 ( 3) link_ALPHA1-3 : angle 1.73239 / 0.99 ( 9) link_ALPHA1-6 : bond 0.00346 / 0.18 ( 3) link_ALPHA1-6 : angle 1.80238 / 0.97 ( 9) link_BETA1-4 : bond 0.00268 / 0.18 ( 15) link_BETA1-4 : angle 1.56551 / 1.10 ( 45) link_NAG-ASN : bond 0.00351 / 0.21 ( 32) link_NAG-ASN : angle 2.05735 / 1.40 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: B 939 MET cc_start: 0.8918 (mmp) cc_final: 0.8406 (mtp) REVERT: C 147 PHE cc_start: 0.9749 (m-10) cc_final: 0.9478 (m-80) REVERT: C 569 MET cc_start: 0.9234 (pmm) cc_final: 0.8674 (pmm) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1689 time to fit residues: 22.0474 Evaluate side-chains 64 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 34 optimal weight: 30.0000 chunk 48 optimal weight: 8.9990 chunk 310 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 166 optimal weight: 4.9990 chunk 147 optimal weight: 20.0000 chunk 253 optimal weight: 9.9990 chunk 248 optimal weight: 30.0000 chunk 252 optimal weight: 7.9990 chunk 179 optimal weight: 30.0000 overall best weight: 10.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 GLN A 566 GLN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 772 GLN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1122 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.021735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2229 r_free = 0.2229 target = 0.013623 restraints weight = 586454.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2253 r_free = 0.2253 target = 0.013940 restraints weight = 374585.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2272 r_free = 0.2272 target = 0.014231 restraints weight = 280766.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2285 r_free = 0.2285 target = 0.014478 restraints weight = 231680.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2291 r_free = 0.2291 target = 0.014639 restraints weight = 203101.868| |-----------------------------------------------------------------------------| r_work (final): 0.2298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 28506 Z= 0.249 Angle : 0.692 13.900 38897 Z= 0.356 Chirality : 0.043 0.398 4477 Planarity : 0.005 0.075 4940 Dihedral : 5.381 28.682 3786 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.39 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.14), residues: 3462 helix: 0.75 (0.19), residues: 750 sheet: -1.28 (0.18), residues: 723 loop : -1.35 (0.14), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 190 TYR 0.023 0.002 TYR B 219 PHE 0.025 0.002 PHE A 164 TRP 0.019 0.002 TRP A 535 HIS 0.012 0.002 HIS B 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.25 (28405) covalent geometry : angle 0.67586 / 0.35 (38642) SS BOND : bond 0.00397 / 0.25 ( 48) SS BOND : angle 1.52563 / 1.03 ( 96) hydrogen bonds : bond 0.04083 / 2.73 ( 997) hydrogen bonds : angle 6.33012 / 4.41 ( 2715) link_ALPHA1-3 : bond 0.00480 / 0.19 ( 3) link_ALPHA1-3 : angle 1.89234 / 1.09 ( 9) link_ALPHA1-6 : bond 0.00472 / 0.23 ( 3) link_ALPHA1-6 : angle 1.96233 / 1.06 ( 9) link_BETA1-4 : bond 0.00289 / 0.18 ( 15) link_BETA1-4 : angle 1.62871 / 1.12 ( 45) link_NAG-ASN : bond 0.00457 / 0.30 ( 32) link_NAG-ASN : angle 2.40493 / 1.70 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 939 MET cc_start: 0.8873 (mmp) cc_final: 0.8341 (mtp) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1710 time to fit residues: 21.5509 Evaluate side-chains 61 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 178 optimal weight: 7.9990 chunk 272 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 215 optimal weight: 30.0000 chunk 311 optimal weight: 9.9990 chunk 273 optimal weight: 50.0000 chunk 162 optimal weight: 8.9990 chunk 315 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 129 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 568 GLN ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 772 GLN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.021847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2237 r_free = 0.2237 target = 0.013552 restraints weight = 584477.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.2262 r_free = 0.2262 target = 0.014017 restraints weight = 372539.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2276 r_free = 0.2276 target = 0.014233 restraints weight = 278841.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.2286 r_free = 0.2286 target = 0.014562 restraints weight = 234717.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2296 r_free = 0.2296 target = 0.014730 restraints weight = 202195.332| |-----------------------------------------------------------------------------| r_work (final): 0.2301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28506 Z= 0.196 Angle : 0.648 13.917 38897 Z= 0.330 Chirality : 0.043 0.398 4477 Planarity : 0.004 0.068 4940 Dihedral : 5.291 27.312 3786 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.14), residues: 3462 helix: 0.82 (0.19), residues: 752 sheet: -1.18 (0.19), residues: 712 loop : -1.37 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 190 TYR 0.022 0.002 TYR B 219 PHE 0.025 0.002 PHE A 895 TRP 0.021 0.002 TRP A 535 HIS 0.006 0.001 HIS B1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.20 (28405) covalent geometry : angle 0.63360 / 0.33 (38642) SS BOND : bond 0.00331 / 0.21 ( 48) SS BOND : angle 1.36993 / 0.91 ( 96) hydrogen bonds : bond 0.03764 / 2.53 ( 997) hydrogen bonds : angle 6.22313 / 4.34 ( 2715) link_ALPHA1-3 : bond 0.00496 / 0.19 ( 3) link_ALPHA1-3 : angle 1.66071 / 0.95 ( 9) link_ALPHA1-6 : bond 0.00289 / 0.15 ( 3) link_ALPHA1-6 : angle 1.85307 / 1.00 ( 9) link_BETA1-4 : bond 0.00313 / 0.18 ( 15) link_BETA1-4 : angle 1.51886 / 1.07 ( 45) link_NAG-ASN : bond 0.00405 / 0.28 ( 32) link_NAG-ASN : angle 2.28416 / 1.63 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: B 757 MET cc_start: 0.9114 (tpp) cc_final: 0.8862 (tpp) REVERT: B 939 MET cc_start: 0.8697 (mmp) cc_final: 0.8321 (mtp) REVERT: C 569 MET cc_start: 0.9200 (pmm) cc_final: 0.8649 (pmm) REVERT: C 696 MET cc_start: 0.7854 (tpp) cc_final: 0.7529 (tpt) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1690 time to fit residues: 21.3876 Evaluate side-chains 61 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 285 optimal weight: 50.0000 chunk 202 optimal weight: 20.0000 chunk 28 optimal weight: 30.0000 chunk 92 optimal weight: 7.9990 chunk 174 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 218 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 266 optimal weight: 20.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN C 772 GLN ** 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 = 0.2610 r_free = 0.2610 target = 0.021762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2236 r_free = 0.2236 target = 0.013622 restraints weight = 582982.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2261 r_free = 0.2261 target = 0.013997 restraints weight = 370124.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2278 r_free = 0.2278 target = 0.014312 restraints weight = 274352.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2289 r_free = 0.2289 target = 0.014512 restraints weight = 226361.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2294 r_free = 0.2294 target = 0.014708 restraints weight = 198474.347| |-----------------------------------------------------------------------------| r_work (final): 0.2301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28506 Z= 0.194 Angle : 0.646 13.538 38897 Z= 0.329 Chirality : 0.043 0.394 4477 Planarity : 0.004 0.063 4940 Dihedral : 5.262 25.966 3786 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.14), residues: 3462 helix: 0.84 (0.20), residues: 752 sheet: -1.20 (0.19), residues: 714 loop : -1.36 (0.14), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 190 TYR 0.021 0.002 TYR B 219 PHE 0.029 0.002 PHE B 467 TRP 0.022 0.002 TRP A 535 HIS 0.006 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 (28405) covalent geometry : angle 0.63114 / 0.33 (38642) SS BOND : bond 0.00330 / 0.21 ( 48) SS BOND : angle 1.39523 / 0.92 ( 96) hydrogen bonds : bond 0.03741 / 2.51 ( 997) hydrogen bonds : angle 6.18977 / 4.31 ( 2715) link_ALPHA1-3 : bond 0.00571 / 0.24 ( 3) link_ALPHA1-3 : angle 1.56707 / 0.90 ( 9) link_ALPHA1-6 : bond 0.00284 / 0.15 ( 3) link_ALPHA1-6 : angle 1.83997 / 0.99 ( 9) link_BETA1-4 : bond 0.00316 / 0.19 ( 15) link_BETA1-4 : angle 1.52036 / 1.07 ( 45) link_NAG-ASN : bond 0.00362 / 0.24 ( 32) link_NAG-ASN : angle 2.27670 / 1.63 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 939 MET cc_start: 0.8737 (mmp) cc_final: 0.8236 (mtp) REVERT: C 569 MET cc_start: 0.9189 (pmm) cc_final: 0.8599 (pmm) REVERT: C 696 MET cc_start: 0.7848 (tpp) cc_final: 0.7536 (tpt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1757 time to fit residues: 22.2026 Evaluate side-chains 61 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 283 optimal weight: 40.0000 chunk 190 optimal weight: 30.0000 chunk 219 optimal weight: 5.9990 chunk 265 optimal weight: 7.9990 chunk 150 optimal weight: 40.0000 chunk 202 optimal weight: 20.0000 chunk 208 optimal weight: 0.9980 chunk 259 optimal weight: 9.9990 chunk 204 optimal weight: 0.0970 chunk 50 optimal weight: 20.0000 chunk 338 optimal weight: 0.0370 overall best weight: 3.0260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 GLN A 486 HIS A 566 GLN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.024162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.017514 restraints weight = 598960.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.017840 restraints weight = 377366.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.018127 restraints weight = 278028.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.018359 restraints weight = 227833.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.018493 restraints weight = 197945.411| |-----------------------------------------------------------------------------| r_work (final): 0.2388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28506 Z= 0.120 Angle : 0.608 12.198 38897 Z= 0.304 Chirality : 0.044 0.377 4477 Planarity : 0.004 0.058 4940 Dihedral : 4.990 22.195 3786 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.14), residues: 3462 helix: 1.01 (0.20), residues: 752 sheet: -0.97 (0.19), residues: 669 loop : -1.31 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 505 TYR 0.030 0.001 TYR A 85 PHE 0.022 0.001 PHE B 467 TRP 0.022 0.002 TRP A 535 HIS 0.004 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (28405) covalent geometry : angle 0.59487 / 0.30 (38642) SS BOND : bond 0.00240 / 0.15 ( 48) SS BOND : angle 1.31218 / 0.85 ( 96) hydrogen bonds : bond 0.03298 / 2.22 ( 997) hydrogen bonds : angle 5.89907 / 4.11 ( 2715) link_ALPHA1-3 : bond 0.00623 / 0.24 ( 3) link_ALPHA1-3 : angle 1.34172 / 0.75 ( 9) link_ALPHA1-6 : bond 0.00115 / 0.05 ( 3) link_ALPHA1-6 : angle 1.54863 / 0.83 ( 9) link_BETA1-4 : bond 0.00473 / 0.29 ( 15) link_BETA1-4 : angle 1.38648 / 0.99 ( 45) link_NAG-ASN : bond 0.00309 / 0.22 ( 32) link_NAG-ASN : angle 2.11825 / 1.52 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5116.14 seconds wall clock time: 89 minutes 57.21 seconds (5397.21 seconds total)