Starting phenix.real_space_refine on Sat Jul 4 15:27:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t9b_25755/07_2026/7t9b_25755.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t9b_25755/07_2026/7t9b_25755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t9b_25755/07_2026/7t9b_25755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t9b_25755/07_2026/7t9b_25755.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7t9b_25755/07_2026/7t9b_25755.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t9b_25755/07_2026/7t9b_25755.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t9b_25755/07_2026/7t9b_25755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t9b_25755/07_2026/7t9b_25755.map" } resolution = 3.72 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= 0.002 sd= 0.039 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 131 5.16 5 C 13523 2.51 5 N 3572 2.21 5 O 4366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 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: 21592 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3433 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 3 Chain: "B" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "J" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "K" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "C" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3425 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 410} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "M" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "N" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "E" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3387 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 23, 'TRANS': 405} Chain breaks: 4 Chain: "F" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "O" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "P" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "H" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1051 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} 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: "I" 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: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "T" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "V" 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: "W" 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: "X" 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: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "Z" 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: "a" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 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 Time building chain proxies: 5.47, per 1000 atoms: 0.25 Number of scatterers: 21592 At special positions: 0 Unit cell: (124.2, 127.65, 188.6, 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 131 16.00 O 4366 8.00 N 3572 7.00 C 13523 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.00 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.10 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.06 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.15 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 Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 7 " " MAN S 4 " - " MAN S 5 " " BMA Y 3 " - " MAN Y 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA S 3 " - " MAN S 4 " " MAN S 4 " - " MAN S 6 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 2 " - " BMA S 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG j 1 " - " NAG j 2 " BETA1-6 " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " FUC T 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG U 1 " - " FUC U 3 " " NAG a 1 " - " FUC a 2 " " NAG b 1 " - " FUC b 3 " " NAG i 1 " - " FUC i 2 " " NAG j 1 " - " FUC j 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 137 " " NAG A 604 " - " ASN A 355 " " NAG A 605 " - " ASN A 276 " " NAG A 606 " - " ASN A 392 " " NAG A 607 " - " ASN A 339 " " NAG A 608 " - " ASN A 295 " " NAG A 609 " - " ASN A 448 " " NAG A 610 " - " ASN A 301 " " NAG A 611 " - " ASN A 197 " " NAG A 612 " - " ASN A 133 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 625 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 137 " " NAG C 604 " - " ASN C 355 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 448 " " NAG C 610 " - " ASN C 301 " " NAG C 611 " - " ASN C 197 " " NAG C 612 " - " ASN C 133 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 625 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 137 " " NAG E 604 " - " ASN E 355 " " NAG E 605 " - " ASN E 276 " " NAG E 606 " - " ASN E 392 " " NAG E 607 " - " ASN E 339 " " NAG E 608 " - " ASN E 295 " " NAG E 609 " - " ASN E 448 " " NAG E 610 " - " ASN E 301 " " NAG E 611 " - " ASN E 133 " " NAG F 701 " - " ASN F 625 " " NAG F 702 " - " ASN F 637 " " NAG G 1 " - " ASN A 386 " " NAG I 1 " - " ASN A 332 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 156 " " NAG S 1 " - " ASN A 160 " " NAG T 1 " - " ASN B 618 " " NAG U 1 " - " ASN B 611 " " NAG V 1 " - " ASN C 160 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 332 " " NAG Y 1 " - " ASN C 262 " " NAG Z 1 " - " ASN C 156 " " NAG a 1 " - " ASN D 618 " " NAG b 1 " - " ASN D 611 " " NAG c 1 " - " ASN E 386 " " NAG d 1 " - " ASN E 332 " " NAG e 1 " - " ASN E 262 " " NAG f 1 " - " ASN E 197 " " NAG g 1 " - " ASN E 156 " " NAG h 1 " - " ASN E 160 " " NAG i 1 " - " ASN F 618 " " NAG j 1 " - " ASN F 611 " Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 862.9 milliseconds 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 38 sheets defined 18.7% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 99 through 115 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.515A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.525A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 removed outlier: 4.355A pdb=" N GLY B 525 " --> pdb=" O GLY B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 534 through 540 Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.600A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.610A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.519A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 526 removed outlier: 4.278A pdb=" N GLY D 525 " --> pdb=" O GLY D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 532 Processing helix chain 'D' and resid 534 through 540 Processing helix chain 'D' and resid 572 through 596 removed outlier: 3.671A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 661 removed outlier: 3.715A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.755A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.581A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.846A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 526 removed outlier: 4.403A pdb=" N GLY F 525 " --> pdb=" O GLY F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 532 Processing helix chain 'F' and resid 534 through 540 Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 636 through 638 No H-bonds generated for 'chain 'F' and resid 636 through 638' Processing helix chain 'F' and resid 639 through 662 Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.381A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.489A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 3.988A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 5.974A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 466 through 470 Processing sheet with id=AA8, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'J' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 11 through 12 current: chain 'J' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100H through 103 Processing sheet with id=AB1, first strand: chain 'K' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 12 through 13 current: chain 'K' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 45 through 48 current: chain 'K' and resid 96 through 98 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 19 through 24 Processing sheet with id=AB3, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.376A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB8, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.490A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 6.663A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323A current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 466 through 470 Processing sheet with id=AC1, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'M' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 11 through 12 current: chain 'M' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 57 through 59 current: chain 'M' and resid 100H through 103 Processing sheet with id=AC3, first strand: chain 'N' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 12 through 13 current: chain 'N' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 96 through 98 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AC5, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.414A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.515A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AC8, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC9, first strand: chain 'E' and resid 130 through 133 Processing sheet with id=AD1, first strand: chain 'E' and resid 181 through 182 Processing sheet with id=AD2, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.457A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 6.722A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323A current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 466 through 470 Processing sheet with id=AD4, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AD5, first strand: chain 'O' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 11 through 12 current: chain 'O' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 57 through 59 current: chain 'O' and resid 100H through 103 Processing sheet with id=AD6, first strand: chain 'P' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 12 through 13 current: chain 'P' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 45 through 48 current: chain 'P' and resid 96 through 98 No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'P' and resid 19 through 24 Processing sheet with id=AD8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'H' and resid 34 through 39 removed outlier: 6.966A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100J through 103 Processing sheet with id=AE1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 12 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 96 through 98 555 hydrogen bonds defined for protein. 1455 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: 4.03 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4674 1.32 - 1.46: 7079 1.46 - 1.59: 10059 1.59 - 1.73: 46 1.73 - 1.87: 175 Bond restraints: 22033 Sorted by residual: bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.396 -0.070 1.10e-02 8.26e+03 4.00e+01 bond pdb=" CB ASP N 27B" pdb=" CG ASP N 27B" ideal model delta sigma weight residual 1.516 1.361 0.155 2.50e-02 1.60e+03 3.84e+01 bond pdb=" NE ARG C 503 " pdb=" CZ ARG C 503 " ideal model delta sigma weight residual 1.326 1.393 -0.067 1.10e-02 8.26e+03 3.75e+01 bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.392 -0.066 1.10e-02 8.26e+03 3.61e+01 bond pdb=" CB LEU N 107 " pdb=" CG LEU N 107 " ideal model delta sigma weight residual 1.530 1.649 -0.119 2.00e-02 2.50e+03 3.56e+01 ... (remaining 22028 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.60: 29874 7.60 - 15.21: 43 15.21 - 22.81: 0 22.81 - 30.42: 0 30.42 - 38.02: 3 Bond angle restraints: 29920 Sorted by residual: angle pdb=" C2 NAG d 1 " pdb=" N2 NAG d 1 " pdb=" C7 NAG d 1 " ideal model delta sigma weight residual 124.56 162.58 -38.02 3.00e+00 1.11e-01 1.61e+02 angle pdb=" C2 NAG I 1 " pdb=" N2 NAG I 1 " pdb=" C7 NAG I 1 " ideal model delta sigma weight residual 124.56 161.38 -36.82 3.00e+00 1.11e-01 1.51e+02 angle pdb=" C2 NAG X 1 " pdb=" N2 NAG X 1 " pdb=" C7 NAG X 1 " ideal model delta sigma weight residual 124.56 160.89 -36.33 3.00e+00 1.11e-01 1.47e+02 angle pdb=" N HIS C 85 " pdb=" CA HIS C 85 " pdb=" C HIS C 85 " ideal model delta sigma weight residual 111.82 120.98 -9.16 1.16e+00 7.43e-01 6.23e+01 angle pdb=" N GLU C 83 " pdb=" CA GLU C 83 " pdb=" C GLU C 83 " ideal model delta sigma weight residual 109.96 121.71 -11.75 1.50e+00 4.44e-01 6.14e+01 ... (remaining 29915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 11733 17.15 - 34.31: 384 34.31 - 51.46: 122 51.46 - 68.62: 52 68.62 - 85.77: 21 Dihedral angle restraints: 12312 sinusoidal: 4886 harmonic: 7426 Sorted by residual: dihedral pdb=" CA ASN C 197 " pdb=" C ASN C 197 " pdb=" N THR C 198 " pdb=" CA THR C 198 " ideal model delta harmonic sigma weight residual 180.00 147.63 32.37 0 5.00e+00 4.00e-02 4.19e+01 dihedral pdb=" CA VAL C 68 " pdb=" C VAL C 68 " pdb=" N TRP C 69 " pdb=" CA TRP C 69 " ideal model delta harmonic sigma weight residual -180.00 -151.99 -28.01 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA THR A 198 " pdb=" C THR A 198 " pdb=" N SER A 199 " pdb=" CA SER A 199 " ideal model delta harmonic sigma weight residual -180.00 -153.18 -26.82 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 12309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.218: 3289 0.218 - 0.435: 316 0.435 - 0.653: 24 0.653 - 0.871: 0 0.871 - 1.088: 1 Chirality restraints: 3630 Sorted by residual: chirality pdb=" C1 FUC i 2 " pdb=" O6 NAG i 1 " pdb=" C2 FUC i 2 " pdb=" O5 FUC i 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.31 -1.09 2.00e-02 2.50e+03 2.96e+03 chirality pdb=" C1 NAG S 2 " pdb=" O6 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-02 2.50e+03 6.46e+02 chirality pdb=" C1 MAN S 6 " pdb=" O6 MAN S 4 " pdb=" C2 MAN S 6 " pdb=" O5 MAN S 6 " both_signs ideal model delta sigma weight residual False 2.40 1.93 0.47 2.00e-02 2.50e+03 5.41e+02 ... (remaining 3627 not shown) Planarity restraints: 3736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " 0.348 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG S 2 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " 0.184 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " -0.513 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 2 " 0.318 2.00e-02 2.50e+03 2.78e-01 9.64e+02 pdb=" C7 NAG j 2 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG j 2 " 0.103 2.00e-02 2.50e+03 pdb=" N2 NAG j 2 " -0.498 2.00e-02 2.50e+03 pdb=" O7 NAG j 2 " 0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 701 " -0.324 2.00e-02 2.50e+03 2.75e-01 9.47e+02 pdb=" C7 NAG F 701 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG F 701 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG F 701 " 0.480 2.00e-02 2.50e+03 pdb=" O7 NAG F 701 " -0.055 2.00e-02 2.50e+03 ... (remaining 3733 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5451 2.81 - 3.33: 19130 3.33 - 3.86: 36326 3.86 - 4.38: 43973 4.38 - 4.90: 70120 Nonbonded interactions: 175000 Sorted by model distance: nonbonded pdb=" O5 NAG j 1 " pdb=" O6 NAG j 1 " model vdw 2.289 2.432 nonbonded pdb=" N ASP J 84 " pdb=" OD1 ASP J 84 " model vdw 2.370 3.120 nonbonded pdb=" N ASP O 84 " pdb=" OD1 ASP O 84 " model vdw 2.370 3.120 nonbonded pdb=" N ASP M 84 " pdb=" OD1 ASP M 84 " model vdw 2.370 3.120 nonbonded pdb=" OD1 ASP A 107 " pdb=" NZ LYS B 574 " model vdw 2.411 3.120 ... (remaining 174995 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 33 through 57 or resid 72 through 611)) selection = (chain 'C' and (resid 33 through 57 or resid 72 through 611)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'i' and resid 1) } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'K' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'Y' selection = chain 'e' } ncs_group { reference = (chain 'R' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) } 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 21.030 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 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 : 0.021 0.155 22174 Z= 1.146 Angle : 1.797 38.021 30303 Z= 1.146 Chirality : 0.133 1.088 3630 Planarity : 0.015 0.294 3673 Dihedral : 11.098 85.771 7434 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.67 % Allowed : 3.71 % Favored : 95.62 % Rotamer: Outliers : 0.98 % Allowed : 0.76 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.40 (0.16), residues: 2535 helix: -0.34 (0.24), residues: 385 sheet: 0.93 (0.18), residues: 817 loop : 0.13 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 71 TYR 0.070 0.007 TYR L 87 PHE 0.044 0.006 PHE L 98 TRP 0.063 0.008 TRP A 96 HIS 0.009 0.002 HIS J 82A Details of bonding type rmsd/Z covalent geometry : bond 0.02105 / 1.13 (22033) covalent geometry : angle 1.77494 / 1.15 (29920) SS BOND : bond 0.02375 / 1.78 ( 40) SS BOND : angle 2.43405 / 1.75 ( 80) hydrogen bonds : bond 0.16830 / 11.21 ( 555) hydrogen bonds : angle 6.86540 / 4.85 ( 1455) link_ALPHA1-3 : bond 0.06139 / 3.56 ( 5) link_ALPHA1-3 : angle 3.43561 / 1.88 ( 15) link_ALPHA1-6 : bond 0.00449 / 0.24 ( 2) link_ALPHA1-6 : angle 2.71457 / 1.92 ( 6) link_BETA1-4 : bond 0.05873 / 3.92 ( 24) link_BETA1-4 : angle 4.02949 / 2.91 ( 72) link_BETA1-6 : bond 0.02558 / 1.22 ( 7) link_BETA1-6 : angle 4.60429 / 2.58 ( 21) link_NAG-ASN : bond 0.06922 / 4.36 ( 63) link_NAG-ASN : angle 2.62635 / 1.85 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 395 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.8555 (m-80) cc_final: 0.8237 (m-10) REVERT: A 475 MET cc_start: 0.8713 (mmm) cc_final: 0.8353 (mmm) REVERT: A 482 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7968 (mm-30) REVERT: J 2 VAL cc_start: 0.9262 (t) cc_final: 0.8702 (t) REVERT: K 11 VAL cc_start: 0.8529 (t) cc_final: 0.8195 (p) REVERT: K 47 MET cc_start: 0.8336 (mmm) cc_final: 0.8060 (mmt) REVERT: K 94 ARG cc_start: 0.6115 (mpt180) cc_final: 0.5238 (mmt180) REVERT: K 104 LEU cc_start: 0.8447 (tp) cc_final: 0.7758 (tt) REVERT: C 72 HIS cc_start: 0.6914 (OUTLIER) cc_final: 0.6650 (p90) REVERT: C 107 ASP cc_start: 0.8076 (m-30) cc_final: 0.7733 (t0) REVERT: C 153 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8298 (tt0) REVERT: C 449 ILE cc_start: 0.9419 (mt) cc_final: 0.9217 (mm) REVERT: D 616 ASN cc_start: 0.9247 (p0) cc_final: 0.8815 (p0) REVERT: D 624 ASP cc_start: 0.8310 (p0) cc_final: 0.7722 (p0) REVERT: D 626 MET cc_start: 0.8826 (ttm) cc_final: 0.8612 (ttm) REVERT: M 78 LEU cc_start: 0.9138 (tp) cc_final: 0.8921 (tp) REVERT: N 47 MET cc_start: 0.8484 (mmm) cc_final: 0.8238 (mmp) REVERT: N 58 VAL cc_start: 0.8613 (m) cc_final: 0.8390 (p) REVERT: N 94 ARG cc_start: 0.6713 (mpt180) cc_final: 0.6141 (tpt170) REVERT: N 102 THR cc_start: 0.8431 (m) cc_final: 0.8120 (p) REVERT: E 104 MET cc_start: 0.8272 (ttm) cc_final: 0.8009 (ttt) REVERT: F 571 TRP cc_start: 0.5920 (t-100) cc_final: 0.5584 (p-90) REVERT: F 581 LEU cc_start: 0.8928 (pp) cc_final: 0.8712 (tp) REVERT: O 52 ASN cc_start: 0.8951 (t0) cc_final: 0.8700 (t0) REVERT: P 42 LYS cc_start: 0.8307 (mmtt) cc_final: 0.8034 (ttpt) REVERT: P 94 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7679 (tpt170) REVERT: H 27 PHE cc_start: 0.5955 (t80) cc_final: 0.5593 (t80) REVERT: H 80 LEU cc_start: 0.7504 (tp) cc_final: 0.7102 (tp) REVERT: H 98 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.8066 (p) REVERT: L 42 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8154 (mp10) REVERT: L 71 PHE cc_start: 0.4742 (m-80) cc_final: 0.3290 (m-80) REVERT: L 75 ILE cc_start: 0.7447 (mt) cc_final: 0.6938 (mt) REVERT: L 77 ARG cc_start: 0.7874 (mmt-90) cc_final: 0.7515 (tmm-80) REVERT: L 89 GLN cc_start: 0.8572 (tt0) cc_final: 0.8092 (tm-30) outliers start: 22 outliers final: 2 residues processed: 412 average time/residue: 0.1851 time to fit residues: 112.2778 Evaluate side-chains 196 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 191 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain H residue 98 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 302 ASN A 425 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN C 195 ASN C 246 GLN C 425 ASN D 653 GLN E 130 GLN E 195 ASN E 246 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.075593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.057395 restraints weight = 63027.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.058796 restraints weight = 38477.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.059328 restraints weight = 27277.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.059566 restraints weight = 26471.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.059647 restraints weight = 23677.197| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22174 Z= 0.177 Angle : 0.752 16.038 30303 Z= 0.367 Chirality : 0.046 0.327 3630 Planarity : 0.004 0.067 3673 Dihedral : 5.547 59.733 2795 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.55 % Favored : 96.25 % Rotamer: Outliers : 1.56 % Allowed : 6.02 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.42 (0.16), residues: 2535 helix: 1.54 (0.27), residues: 375 sheet: 0.75 (0.18), residues: 779 loop : -0.31 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 588 TYR 0.017 0.001 TYR C 173 PHE 0.025 0.002 PHE H 29 TRP 0.026 0.001 TRP E 479 HIS 0.006 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 (22033) covalent geometry : angle 0.71719 / 0.36 (29920) SS BOND : bond 0.00280 / 0.20 ( 40) SS BOND : angle 0.80740 / 0.60 ( 80) hydrogen bonds : bond 0.05515 / 3.69 ( 555) hydrogen bonds : angle 5.32102 / 3.79 ( 1455) link_ALPHA1-3 : bond 0.00936 / 0.54 ( 5) link_ALPHA1-3 : angle 1.58663 / 1.01 ( 15) link_ALPHA1-6 : bond 0.01100 / 0.53 ( 2) link_ALPHA1-6 : angle 1.77793 / 1.33 ( 6) link_BETA1-4 : bond 0.00559 / 0.33 ( 24) link_BETA1-4 : angle 2.36216 / 1.58 ( 72) link_BETA1-6 : bond 0.00381 / 0.17 ( 7) link_BETA1-6 : angle 2.44935 / 1.52 ( 21) link_NAG-ASN : bond 0.00557 / 0.34 ( 63) link_NAG-ASN : angle 2.43104 / 1.77 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 226 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.8154 (m-80) cc_final: 0.7707 (m-80) REVERT: K 27 ASP cc_start: 0.8818 (t70) cc_final: 0.8572 (t70) REVERT: K 94 ARG cc_start: 0.5390 (mpt180) cc_final: 0.4790 (mmt180) REVERT: D 616 ASN cc_start: 0.8988 (p0) cc_final: 0.8715 (p0) REVERT: M 86 ASP cc_start: 0.8354 (m-30) cc_final: 0.8057 (m-30) REVERT: N 95 THR cc_start: 0.8727 (p) cc_final: 0.8519 (p) REVERT: E 104 MET cc_start: 0.7744 (ttm) cc_final: 0.7483 (ttt) REVERT: F 586 TYR cc_start: 0.9347 (t80) cc_final: 0.9147 (t80) REVERT: O 52 ASN cc_start: 0.8880 (t0) cc_final: 0.8649 (t0) REVERT: P 27 ASP cc_start: 0.8817 (OUTLIER) cc_final: 0.8459 (t70) REVERT: P 94 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7633 (tpt170) REVERT: H 4 LEU cc_start: 0.7484 (mp) cc_final: 0.7254 (mp) REVERT: H 27 PHE cc_start: 0.5326 (t80) cc_final: 0.5082 (t80) REVERT: H 80 LEU cc_start: 0.7205 (tp) cc_final: 0.6952 (tp) REVERT: H 101 ASP cc_start: 0.8366 (t0) cc_final: 0.7822 (t0) REVERT: L 46 LEU cc_start: 0.9158 (tt) cc_final: 0.8790 (mt) outliers start: 35 outliers final: 16 residues processed: 253 average time/residue: 0.1630 time to fit residues: 63.5847 Evaluate side-chains 191 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 114 optimal weight: 0.0050 chunk 180 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 250 optimal weight: 30.0000 chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 195 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN C 195 ASN N 53 GLN E 99 ASN L 42 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.075141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.055824 restraints weight = 63107.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.057566 restraints weight = 37311.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.058766 restraints weight = 26789.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.059534 restraints weight = 21518.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.060052 restraints weight = 18634.228| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22174 Z= 0.137 Angle : 0.660 15.834 30303 Z= 0.318 Chirality : 0.043 0.322 3630 Planarity : 0.004 0.043 3673 Dihedral : 4.947 51.302 2790 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.79 % Favored : 96.09 % Rotamer: Outliers : 1.43 % Allowed : 7.18 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.39 (0.17), residues: 2535 helix: 1.64 (0.27), residues: 384 sheet: 0.73 (0.18), residues: 769 loop : -0.39 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 103 TYR 0.012 0.001 TYR C 173 PHE 0.014 0.001 PHE L 98 TRP 0.017 0.001 TRP E 479 HIS 0.006 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (22033) covalent geometry : angle 0.63008 / 0.31 (29920) SS BOND : bond 0.00226 / 0.15 ( 40) SS BOND : angle 0.75914 / 0.54 ( 80) hydrogen bonds : bond 0.04424 / 2.99 ( 555) hydrogen bonds : angle 4.83313 / 3.47 ( 1455) link_ALPHA1-3 : bond 0.00742 / 0.42 ( 5) link_ALPHA1-3 : angle 1.50793 / 0.94 ( 15) link_ALPHA1-6 : bond 0.00769 / 0.37 ( 2) link_ALPHA1-6 : angle 1.50617 / 1.15 ( 6) link_BETA1-4 : bond 0.00474 / 0.29 ( 24) link_BETA1-4 : angle 1.73315 / 1.16 ( 72) link_BETA1-6 : bond 0.00689 / 0.29 ( 7) link_BETA1-6 : angle 1.93342 / 1.21 ( 21) link_NAG-ASN : bond 0.00543 / 0.36 ( 63) link_NAG-ASN : angle 2.23728 / 1.68 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.8153 (m-80) cc_final: 0.7665 (m-80) REVERT: K 27 ASP cc_start: 0.8865 (OUTLIER) cc_final: 0.8579 (t70) REVERT: K 94 ARG cc_start: 0.5451 (mpt180) cc_final: 0.4689 (mmt180) REVERT: C 434 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7816 (tpp) REVERT: D 616 ASN cc_start: 0.9002 (p0) cc_final: 0.8738 (p0) REVERT: D 634 GLU cc_start: 0.8091 (tp30) cc_final: 0.7864 (tp30) REVERT: E 104 MET cc_start: 0.7851 (ttm) cc_final: 0.7578 (ttt) REVERT: E 475 MET cc_start: 0.8218 (mmp) cc_final: 0.7929 (mmm) REVERT: P 27 ASP cc_start: 0.8891 (OUTLIER) cc_final: 0.8588 (m-30) REVERT: P 94 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7598 (tpt170) REVERT: H 27 PHE cc_start: 0.5186 (t80) cc_final: 0.4923 (t80) REVERT: H 101 ASP cc_start: 0.8150 (t0) cc_final: 0.7525 (t0) outliers start: 32 outliers final: 17 residues processed: 211 average time/residue: 0.1632 time to fit residues: 53.5907 Evaluate side-chains 183 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 5 optimal weight: 2.9990 chunk 218 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 231 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 246 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN F 570 HIS L 37 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.072695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.053288 restraints weight = 64235.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.054972 restraints weight = 38382.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.056085 restraints weight = 27647.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.056730 restraints weight = 22442.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.057242 restraints weight = 19723.468| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 22174 Z= 0.220 Angle : 0.675 11.090 30303 Z= 0.329 Chirality : 0.045 0.304 3630 Planarity : 0.004 0.047 3673 Dihedral : 4.919 50.755 2790 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.22 % Favored : 95.70 % Rotamer: Outliers : 1.65 % Allowed : 7.41 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.22 (0.17), residues: 2535 helix: 1.66 (0.27), residues: 384 sheet: 0.57 (0.18), residues: 765 loop : -0.51 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 45 TYR 0.021 0.001 TYR A 484 PHE 0.016 0.002 PHE H 29 TRP 0.026 0.002 TRP L 35 HIS 0.007 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 (22033) covalent geometry : angle 0.64528 / 0.32 (29920) SS BOND : bond 0.00327 / 0.24 ( 40) SS BOND : angle 0.74773 / 0.53 ( 80) hydrogen bonds : bond 0.04531 / 3.07 ( 555) hydrogen bonds : angle 4.85315 / 3.49 ( 1455) link_ALPHA1-3 : bond 0.00659 / 0.39 ( 5) link_ALPHA1-3 : angle 1.55492 / 1.06 ( 15) link_ALPHA1-6 : bond 0.00715 / 0.35 ( 2) link_ALPHA1-6 : angle 1.60518 / 1.22 ( 6) link_BETA1-4 : bond 0.00307 / 0.18 ( 24) link_BETA1-4 : angle 1.68102 / 1.13 ( 72) link_BETA1-6 : bond 0.00569 / 0.24 ( 7) link_BETA1-6 : angle 1.85380 / 1.18 ( 21) link_NAG-ASN : bond 0.00522 / 0.33 ( 63) link_NAG-ASN : angle 2.28184 / 1.75 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.9433 (t) cc_final: 0.9157 (m) REVERT: A 475 MET cc_start: 0.8662 (mmm) cc_final: 0.8311 (tpp) REVERT: K 27 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8668 (t70) REVERT: K 94 ARG cc_start: 0.5739 (mpt180) cc_final: 0.4867 (mmt180) REVERT: D 616 ASN cc_start: 0.9076 (p0) cc_final: 0.8802 (p0) REVERT: E 95 MET cc_start: 0.8446 (ptm) cc_final: 0.8195 (ptp) REVERT: E 173 TYR cc_start: 0.7321 (p90) cc_final: 0.6965 (p90) REVERT: E 475 MET cc_start: 0.8394 (mmp) cc_final: 0.8088 (mmm) REVERT: F 586 TYR cc_start: 0.9321 (t80) cc_final: 0.9050 (t80) REVERT: O 75 LYS cc_start: 0.8917 (mttm) cc_final: 0.8587 (mttp) REVERT: P 27 ASP cc_start: 0.8960 (OUTLIER) cc_final: 0.8632 (m-30) REVERT: P 94 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.7634 (tpt170) REVERT: H 3 GLN cc_start: 0.8068 (tm-30) cc_final: 0.7509 (tm-30) REVERT: H 20 LEU cc_start: 0.6319 (mt) cc_final: 0.5925 (mt) REVERT: H 27 PHE cc_start: 0.4939 (t80) cc_final: 0.4653 (t80) REVERT: L 70 ASP cc_start: 0.7241 (p0) cc_final: 0.6987 (m-30) outliers start: 37 outliers final: 24 residues processed: 194 average time/residue: 0.1582 time to fit residues: 48.4573 Evaluate side-chains 180 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 223 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 211 optimal weight: 4.9990 chunk 183 optimal weight: 0.0070 chunk 82 optimal weight: 0.3980 chunk 9 optimal weight: 7.9990 chunk 178 optimal weight: 10.0000 chunk 209 optimal weight: 9.9990 chunk 251 optimal weight: 5.9990 chunk 199 optimal weight: 3.9990 overall best weight: 2.2804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN A 302 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN E 82 GLN ** L 89 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 = 0.3285 r_free = 0.3285 target = 0.072484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.053117 restraints weight = 63801.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.054779 restraints weight = 38047.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.055894 restraints weight = 27556.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.056600 restraints weight = 22335.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.057062 restraints weight = 19539.845| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22174 Z= 0.179 Angle : 0.622 11.250 30303 Z= 0.302 Chirality : 0.044 0.282 3630 Planarity : 0.004 0.048 3673 Dihedral : 4.772 51.036 2790 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.26 % Favored : 95.66 % Rotamer: Outliers : 2.01 % Allowed : 7.54 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.16 (0.17), residues: 2535 helix: 1.95 (0.28), residues: 371 sheet: 0.41 (0.18), residues: 771 loop : -0.56 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 24 TYR 0.020 0.001 TYR B 586 PHE 0.011 0.001 PHE A 53 TRP 0.022 0.001 TRP L 35 HIS 0.006 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (22033) covalent geometry : angle 0.59421 / 0.30 (29920) SS BOND : bond 0.00268 / 0.19 ( 40) SS BOND : angle 0.71200 / 0.51 ( 80) hydrogen bonds : bond 0.04204 / 2.85 ( 555) hydrogen bonds : angle 4.70788 / 3.40 ( 1455) link_ALPHA1-3 : bond 0.00667 / 0.38 ( 5) link_ALPHA1-3 : angle 1.50640 / 0.99 ( 15) link_ALPHA1-6 : bond 0.00699 / 0.34 ( 2) link_ALPHA1-6 : angle 1.50813 / 1.17 ( 6) link_BETA1-4 : bond 0.00315 / 0.18 ( 24) link_BETA1-4 : angle 1.50106 / 1.00 ( 72) link_BETA1-6 : bond 0.00555 / 0.23 ( 7) link_BETA1-6 : angle 1.72795 / 1.12 ( 21) link_NAG-ASN : bond 0.00429 / 0.27 ( 63) link_NAG-ASN : angle 2.13351 / 1.64 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 161 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.9449 (t) cc_final: 0.9179 (m) REVERT: J 83 ARG cc_start: 0.7780 (tpp80) cc_final: 0.7368 (tpp80) REVERT: K 94 ARG cc_start: 0.5829 (mpt180) cc_final: 0.4813 (mmt180) REVERT: C 72 HIS cc_start: 0.7616 (OUTLIER) cc_final: 0.7276 (p90) REVERT: D 616 ASN cc_start: 0.9069 (p0) cc_final: 0.8780 (p0) REVERT: E 173 TYR cc_start: 0.7329 (p90) cc_final: 0.6995 (p90) REVERT: E 475 MET cc_start: 0.8482 (mmp) cc_final: 0.8120 (mmm) REVERT: F 586 TYR cc_start: 0.9273 (t80) cc_final: 0.9011 (t80) REVERT: O 75 LYS cc_start: 0.8948 (mttm) cc_final: 0.8621 (mttp) REVERT: P 27 ASP cc_start: 0.8963 (OUTLIER) cc_final: 0.8635 (m-30) REVERT: P 94 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7707 (tpt170) REVERT: H 3 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7615 (tm-30) REVERT: H 27 PHE cc_start: 0.4905 (t80) cc_final: 0.4592 (t80) REVERT: L 70 ASP cc_start: 0.7468 (p0) cc_final: 0.7103 (m-30) outliers start: 45 outliers final: 29 residues processed: 195 average time/residue: 0.1629 time to fit residues: 49.3520 Evaluate side-chains 180 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 236 optimal weight: 20.0000 chunk 174 optimal weight: 20.0000 chunk 187 optimal weight: 6.9990 chunk 193 optimal weight: 0.4980 chunk 209 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 196 optimal weight: 0.5980 chunk 238 optimal weight: 30.0000 chunk 11 optimal weight: 7.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 HIS ** L 89 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 = 0.3271 r_free = 0.3271 target = 0.071924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.052592 restraints weight = 64345.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.054218 restraints weight = 38597.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.055338 restraints weight = 27978.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.056057 restraints weight = 22608.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.056474 restraints weight = 19707.366| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22174 Z= 0.198 Angle : 0.635 11.247 30303 Z= 0.307 Chirality : 0.044 0.283 3630 Planarity : 0.004 0.050 3673 Dihedral : 4.754 50.517 2790 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.58 % Favored : 95.35 % Rotamer: Outliers : 1.92 % Allowed : 8.17 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: 0.06 (0.17), residues: 2535 helix: 1.74 (0.28), residues: 380 sheet: 0.33 (0.18), residues: 760 loop : -0.58 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 588 TYR 0.032 0.001 TYR H 100L PHE 0.013 0.002 PHE H 29 TRP 0.018 0.001 TRP E 479 HIS 0.006 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (22033) covalent geometry : angle 0.60709 / 0.30 (29920) SS BOND : bond 0.00285 / 0.20 ( 40) SS BOND : angle 0.74489 / 0.55 ( 80) hydrogen bonds : bond 0.04247 / 2.88 ( 555) hydrogen bonds : angle 4.73041 / 3.41 ( 1455) link_ALPHA1-3 : bond 0.00683 / 0.39 ( 5) link_ALPHA1-3 : angle 1.55756 / 1.01 ( 15) link_ALPHA1-6 : bond 0.00674 / 0.33 ( 2) link_ALPHA1-6 : angle 1.55046 / 1.19 ( 6) link_BETA1-4 : bond 0.00289 / 0.17 ( 24) link_BETA1-4 : angle 1.50609 / 1.00 ( 72) link_BETA1-6 : bond 0.00488 / 0.21 ( 7) link_BETA1-6 : angle 1.73321 / 1.11 ( 21) link_NAG-ASN : bond 0.00450 / 0.30 ( 63) link_NAG-ASN : angle 2.15222 / 1.65 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 157 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.9479 (t) cc_final: 0.9190 (m) REVERT: A 452 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.7888 (mt) REVERT: B 586 TYR cc_start: 0.8972 (t80) cc_final: 0.8633 (t80) REVERT: J 83 ARG cc_start: 0.7854 (tpp80) cc_final: 0.7402 (tpp80) REVERT: K 94 ARG cc_start: 0.6163 (mpt180) cc_final: 0.5017 (mmt180) REVERT: D 616 ASN cc_start: 0.9092 (p0) cc_final: 0.8815 (p0) REVERT: E 173 TYR cc_start: 0.7295 (p90) cc_final: 0.6978 (p90) REVERT: F 586 TYR cc_start: 0.9319 (t80) cc_final: 0.9068 (t80) REVERT: O 43 LYS cc_start: 0.8367 (mmtm) cc_final: 0.8158 (mmmt) REVERT: O 75 LYS cc_start: 0.8944 (mttm) cc_final: 0.8630 (mttp) REVERT: P 27 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8642 (m-30) REVERT: H 3 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7734 (tm-30) REVERT: H 20 LEU cc_start: 0.6194 (mp) cc_final: 0.5930 (mm) REVERT: H 27 PHE cc_start: 0.5078 (t80) cc_final: 0.4651 (t80) REVERT: L 70 ASP cc_start: 0.7319 (p0) cc_final: 0.6890 (m-30) outliers start: 43 outliers final: 32 residues processed: 186 average time/residue: 0.1598 time to fit residues: 46.8210 Evaluate side-chains 185 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 102 optimal weight: 6.9990 chunk 118 optimal weight: 0.7980 chunk 188 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 208 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 chunk 230 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 211 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.071704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.052394 restraints weight = 64501.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.054040 restraints weight = 38821.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.055142 restraints weight = 28017.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.055859 restraints weight = 22683.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.056309 restraints weight = 19765.088| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 22174 Z= 0.186 Angle : 0.627 12.775 30303 Z= 0.304 Chirality : 0.044 0.280 3630 Planarity : 0.004 0.043 3673 Dihedral : 4.575 28.985 2786 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.54 % Favored : 95.35 % Rotamer: Outliers : 1.83 % Allowed : 9.10 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: 0.00 (0.17), residues: 2535 helix: 1.94 (0.28), residues: 368 sheet: 0.30 (0.19), residues: 751 loop : -0.68 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 588 TYR 0.021 0.001 TYR H 100L PHE 0.020 0.001 PHE H 29 TRP 0.015 0.001 TRP E 479 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (22033) covalent geometry : angle 0.59952 / 0.30 (29920) SS BOND : bond 0.00343 / 0.26 ( 40) SS BOND : angle 0.96764 / 0.75 ( 80) hydrogen bonds : bond 0.04161 / 2.82 ( 555) hydrogen bonds : angle 4.69950 / 3.39 ( 1455) link_ALPHA1-3 : bond 0.00656 / 0.37 ( 5) link_ALPHA1-3 : angle 1.50828 / 0.98 ( 15) link_ALPHA1-6 : bond 0.00679 / 0.33 ( 2) link_ALPHA1-6 : angle 1.51656 / 1.16 ( 6) link_BETA1-4 : bond 0.00281 / 0.16 ( 24) link_BETA1-4 : angle 1.47103 / 0.98 ( 72) link_BETA1-6 : bond 0.00544 / 0.23 ( 7) link_BETA1-6 : angle 1.74641 / 1.12 ( 21) link_NAG-ASN : bond 0.00597 / 0.45 ( 63) link_NAG-ASN : angle 2.08840 / 1.61 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.9470 (t) cc_final: 0.9174 (m) REVERT: A 452 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.7870 (mt) REVERT: B 586 TYR cc_start: 0.8984 (t80) cc_final: 0.8657 (t80) REVERT: J 83 ARG cc_start: 0.7668 (tpp80) cc_final: 0.7378 (tpp80) REVERT: K 27 ASP cc_start: 0.8799 (t70) cc_final: 0.8586 (t0) REVERT: K 94 ARG cc_start: 0.6091 (mpt180) cc_final: 0.4848 (mmt180) REVERT: C 72 HIS cc_start: 0.7965 (OUTLIER) cc_final: 0.7525 (p90) REVERT: D 616 ASN cc_start: 0.9095 (p0) cc_final: 0.8824 (p0) REVERT: E 138 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8184 (tt) REVERT: E 173 TYR cc_start: 0.7305 (p90) cc_final: 0.6996 (p90) REVERT: E 475 MET cc_start: 0.8474 (mmp) cc_final: 0.8111 (mmm) REVERT: F 586 TYR cc_start: 0.9301 (t80) cc_final: 0.9049 (t80) REVERT: O 43 LYS cc_start: 0.8511 (mmtm) cc_final: 0.8305 (mmmt) REVERT: O 75 LYS cc_start: 0.8931 (mttm) cc_final: 0.8621 (mttp) REVERT: P 27 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8635 (m-30) REVERT: P 94 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7806 (tpt170) REVERT: H 3 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7803 (tm-30) REVERT: H 27 PHE cc_start: 0.4960 (t80) cc_final: 0.4575 (t80) REVERT: H 75 LYS cc_start: 0.8019 (mmmt) cc_final: 0.7809 (ptpp) REVERT: L 70 ASP cc_start: 0.7265 (p0) cc_final: 0.6885 (m-30) outliers start: 41 outliers final: 33 residues processed: 185 average time/residue: 0.1534 time to fit residues: 44.8234 Evaluate side-chains 190 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 173 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 227 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 126 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 189 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN E 82 GLN ** L 89 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 = 0.3316 r_free = 0.3316 target = 0.073746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.054634 restraints weight = 63747.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.056417 restraints weight = 37147.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.057641 restraints weight = 26383.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.058444 restraints weight = 21062.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.058950 restraints weight = 18124.468| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22174 Z= 0.149 Angle : 0.604 11.651 30303 Z= 0.291 Chirality : 0.043 0.275 3630 Planarity : 0.004 0.043 3673 Dihedral : 4.442 28.241 2786 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.73 % Favored : 95.15 % Rotamer: Outliers : 1.74 % Allowed : 9.55 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: 0.06 (0.17), residues: 2535 helix: 2.05 (0.28), residues: 368 sheet: 0.38 (0.19), residues: 747 loop : -0.69 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 588 TYR 0.020 0.001 TYR H 100L PHE 0.019 0.001 PHE H 29 TRP 0.014 0.001 TRP E 479 HIS 0.006 0.001 HIS E 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (22033) covalent geometry : angle 0.57736 / 0.29 (29920) SS BOND : bond 0.00371 / 0.29 ( 40) SS BOND : angle 0.89687 / 0.69 ( 80) hydrogen bonds : bond 0.03931 / 2.66 ( 555) hydrogen bonds : angle 4.58382 / 3.31 ( 1455) link_ALPHA1-3 : bond 0.00647 / 0.37 ( 5) link_ALPHA1-3 : angle 1.47056 / 0.94 ( 15) link_ALPHA1-6 : bond 0.00689 / 0.34 ( 2) link_ALPHA1-6 : angle 1.46595 / 1.11 ( 6) link_BETA1-4 : bond 0.00290 / 0.17 ( 24) link_BETA1-4 : angle 1.41322 / 0.94 ( 72) link_BETA1-6 : bond 0.00526 / 0.22 ( 7) link_BETA1-6 : angle 1.73113 / 1.11 ( 21) link_NAG-ASN : bond 0.00498 / 0.36 ( 63) link_NAG-ASN : angle 2.01809 / 1.56 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7790 (mt) REVERT: B 586 TYR cc_start: 0.8965 (t80) cc_final: 0.8645 (t80) REVERT: J 83 ARG cc_start: 0.7560 (tpp80) cc_final: 0.7316 (tpp80) REVERT: K 27 ASP cc_start: 0.8790 (t70) cc_final: 0.8551 (t0) REVERT: K 94 ARG cc_start: 0.6068 (mpt180) cc_final: 0.4797 (mmt180) REVERT: C 72 HIS cc_start: 0.7876 (OUTLIER) cc_final: 0.7362 (p90) REVERT: D 616 ASN cc_start: 0.9163 (p0) cc_final: 0.8915 (p0) REVERT: E 138 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8187 (tt) REVERT: E 173 TYR cc_start: 0.7259 (p90) cc_final: 0.6994 (p90) REVERT: E 475 MET cc_start: 0.8515 (mmp) cc_final: 0.8110 (mmm) REVERT: F 586 TYR cc_start: 0.9291 (t80) cc_final: 0.9045 (t80) REVERT: O 75 LYS cc_start: 0.8952 (mttm) cc_final: 0.8626 (mttp) REVERT: P 27 ASP cc_start: 0.8983 (OUTLIER) cc_final: 0.8662 (m-30) REVERT: P 94 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.7784 (tpt170) REVERT: H 3 GLN cc_start: 0.8362 (tm-30) cc_final: 0.7923 (tm-30) REVERT: H 20 LEU cc_start: 0.6010 (mp) cc_final: 0.5315 (mt) REVERT: H 27 PHE cc_start: 0.4873 (t80) cc_final: 0.4470 (t80) REVERT: L 70 ASP cc_start: 0.7209 (p0) cc_final: 0.6866 (m-30) outliers start: 39 outliers final: 28 residues processed: 184 average time/residue: 0.1525 time to fit residues: 44.1996 Evaluate side-chains 181 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 210 optimal weight: 0.0980 chunk 102 optimal weight: 0.8980 chunk 198 optimal weight: 0.9980 chunk 146 optimal weight: 8.9990 chunk 236 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 118 optimal weight: 0.9990 chunk 213 optimal weight: 9.9990 chunk 175 optimal weight: 0.4980 chunk 132 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS N 17 GLN E 82 GLN ** L 89 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 = 0.3344 r_free = 0.3344 target = 0.075039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.056075 restraints weight = 63379.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.057927 restraints weight = 36489.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.059152 restraints weight = 25732.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.059955 restraints weight = 20521.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.060449 restraints weight = 17671.074| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 22174 Z= 0.103 Angle : 0.576 12.089 30303 Z= 0.278 Chirality : 0.042 0.265 3630 Planarity : 0.004 0.042 3673 Dihedral : 4.209 26.650 2786 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.26 % Favored : 95.58 % Rotamer: Outliers : 1.29 % Allowed : 9.82 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: 0.19 (0.17), residues: 2535 helix: 2.24 (0.28), residues: 368 sheet: 0.52 (0.18), residues: 775 loop : -0.68 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 588 TYR 0.020 0.001 TYR H 100L PHE 0.028 0.001 PHE H 29 TRP 0.015 0.001 TRP E 188 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (22033) covalent geometry : angle 0.54979 / 0.27 (29920) SS BOND : bond 0.00322 / 0.25 ( 40) SS BOND : angle 0.80254 / 0.60 ( 80) hydrogen bonds : bond 0.03424 / 2.31 ( 555) hydrogen bonds : angle 4.38119 / 3.16 ( 1455) link_ALPHA1-3 : bond 0.00677 / 0.37 ( 5) link_ALPHA1-3 : angle 1.42687 / 0.90 ( 15) link_ALPHA1-6 : bond 0.00681 / 0.33 ( 2) link_ALPHA1-6 : angle 1.39291 / 1.03 ( 6) link_BETA1-4 : bond 0.00365 / 0.21 ( 24) link_BETA1-4 : angle 1.38295 / 0.90 ( 72) link_BETA1-6 : bond 0.00470 / 0.20 ( 7) link_BETA1-6 : angle 1.67847 / 1.05 ( 21) link_NAG-ASN : bond 0.00427 / 0.30 ( 63) link_NAG-ASN : angle 1.94727 / 1.52 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 586 TYR cc_start: 0.8909 (t80) cc_final: 0.8588 (t80) REVERT: J 83 ARG cc_start: 0.7485 (tpp80) cc_final: 0.7260 (tpp80) REVERT: K 94 ARG cc_start: 0.5966 (mpt180) cc_final: 0.5144 (tpp-160) REVERT: C 72 HIS cc_start: 0.7827 (OUTLIER) cc_final: 0.7284 (p90) REVERT: D 616 ASN cc_start: 0.9139 (p0) cc_final: 0.8859 (p0) REVERT: E 138 ILE cc_start: 0.8459 (mp) cc_final: 0.8174 (tt) REVERT: E 475 MET cc_start: 0.8391 (mmp) cc_final: 0.7937 (mmm) REVERT: F 528 MET cc_start: 0.8477 (mtt) cc_final: 0.8156 (mtt) REVERT: F 586 TYR cc_start: 0.9255 (t80) cc_final: 0.9024 (t80) REVERT: O 75 LYS cc_start: 0.8911 (mttm) cc_final: 0.8610 (mttp) REVERT: P 27 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8752 (m-30) REVERT: H 3 GLN cc_start: 0.8370 (tm-30) cc_final: 0.7922 (tm-30) REVERT: H 27 PHE cc_start: 0.4906 (t80) cc_final: 0.4607 (t80) REVERT: L 70 ASP cc_start: 0.7404 (p0) cc_final: 0.6985 (m-30) outliers start: 29 outliers final: 25 residues processed: 190 average time/residue: 0.1641 time to fit residues: 49.0131 Evaluate side-chains 178 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 180 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 213 optimal weight: 0.7980 chunk 235 optimal weight: 9.9990 chunk 231 optimal weight: 0.7980 chunk 72 optimal weight: 0.0010 chunk 154 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.074938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.055903 restraints weight = 63592.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.057778 restraints weight = 36777.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.059009 restraints weight = 25914.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.059783 restraints weight = 20630.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.060325 restraints weight = 17841.862| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.157 22174 Z= 0.145 Angle : 0.838 59.199 30303 Z= 0.474 Chirality : 0.043 0.415 3630 Planarity : 0.004 0.042 3673 Dihedral : 4.206 26.593 2786 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.18 % Favored : 95.66 % Rotamer: Outliers : 1.25 % Allowed : 10.08 % Favored : 88.67 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.94 % 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: 0.20 (0.17), residues: 2535 helix: 2.13 (0.28), residues: 374 sheet: 0.54 (0.18), residues: 775 loop : -0.67 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 588 TYR 0.019 0.001 TYR H 100L PHE 0.025 0.001 PHE H 29 TRP 0.014 0.001 TRP A 69 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (22033) covalent geometry : angle 0.82360 / 0.47 (29920) SS BOND : bond 0.00328 / 0.25 ( 40) SS BOND : angle 0.81305 / 0.60 ( 80) hydrogen bonds : bond 0.03434 / 2.32 ( 555) hydrogen bonds : angle 4.37915 / 3.16 ( 1455) link_ALPHA1-3 : bond 0.00506 / 0.30 ( 5) link_ALPHA1-3 : angle 1.44771 / 0.90 ( 15) link_ALPHA1-6 : bond 0.00675 / 0.33 ( 2) link_ALPHA1-6 : angle 1.39415 / 1.03 ( 6) link_BETA1-4 : bond 0.00359 / 0.21 ( 24) link_BETA1-4 : angle 1.38918 / 0.90 ( 72) link_BETA1-6 : bond 0.00457 / 0.20 ( 7) link_BETA1-6 : angle 1.68314 / 1.05 ( 21) link_NAG-ASN : bond 0.00429 / 0.30 ( 63) link_NAG-ASN : angle 1.94499 / 1.52 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 586 TYR cc_start: 0.8903 (t80) cc_final: 0.8589 (t80) REVERT: J 83 ARG cc_start: 0.7488 (tpp80) cc_final: 0.7270 (tpp80) REVERT: K 94 ARG cc_start: 0.5971 (mpt180) cc_final: 0.5156 (tpp-160) REVERT: C 72 HIS cc_start: 0.7827 (OUTLIER) cc_final: 0.7286 (p90) REVERT: D 616 ASN cc_start: 0.9122 (p0) cc_final: 0.8838 (p0) REVERT: E 138 ILE cc_start: 0.8469 (mp) cc_final: 0.8176 (tt) REVERT: E 475 MET cc_start: 0.8379 (mmp) cc_final: 0.7932 (mmm) REVERT: F 528 MET cc_start: 0.8485 (mtt) cc_final: 0.8162 (mtt) REVERT: F 586 TYR cc_start: 0.9255 (t80) cc_final: 0.9024 (t80) REVERT: O 75 LYS cc_start: 0.8913 (mttm) cc_final: 0.8610 (mttp) REVERT: P 27 ASP cc_start: 0.8981 (OUTLIER) cc_final: 0.8753 (m-30) REVERT: H 3 GLN cc_start: 0.8376 (tm-30) cc_final: 0.7935 (tm-30) REVERT: L 70 ASP cc_start: 0.7391 (p0) cc_final: 0.6966 (m-30) outliers start: 28 outliers final: 25 residues processed: 174 average time/residue: 0.1537 time to fit residues: 42.3810 Evaluate side-chains 177 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 149 optimal weight: 7.9990 chunk 197 optimal weight: 8.9990 chunk 133 optimal weight: 9.9990 chunk 201 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.074973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.055966 restraints weight = 63623.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.057832 restraints weight = 36702.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.059046 restraints weight = 25859.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.059826 restraints weight = 20624.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.060367 restraints weight = 17806.486| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.157 22174 Z= 0.145 Angle : 0.838 59.199 30303 Z= 0.474 Chirality : 0.043 0.415 3630 Planarity : 0.004 0.042 3673 Dihedral : 4.206 26.593 2786 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.18 % Favored : 95.66 % Rotamer: Outliers : 1.25 % Allowed : 10.08 % Favored : 88.67 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.94 % 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: 0.20 (0.17), residues: 2535 helix: 2.13 (0.28), residues: 374 sheet: 0.54 (0.18), residues: 775 loop : -0.67 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 588 TYR 0.019 0.001 TYR H 100L PHE 0.025 0.001 PHE H 29 TRP 0.014 0.001 TRP A 69 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (22033) covalent geometry : angle 0.82360 / 0.47 (29920) SS BOND : bond 0.00328 / 0.25 ( 40) SS BOND : angle 0.81305 / 0.60 ( 80) hydrogen bonds : bond 0.03434 / 2.32 ( 555) hydrogen bonds : angle 4.37915 / 3.16 ( 1455) link_ALPHA1-3 : bond 0.00506 / 0.30 ( 5) link_ALPHA1-3 : angle 1.44771 / 0.90 ( 15) link_ALPHA1-6 : bond 0.00675 / 0.33 ( 2) link_ALPHA1-6 : angle 1.39415 / 1.03 ( 6) link_BETA1-4 : bond 0.00359 / 0.21 ( 24) link_BETA1-4 : angle 1.38918 / 0.90 ( 72) link_BETA1-6 : bond 0.00457 / 0.20 ( 7) link_BETA1-6 : angle 1.68314 / 1.05 ( 21) link_NAG-ASN : bond 0.00429 / 0.30 ( 63) link_NAG-ASN : angle 1.94499 / 1.52 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3384.57 seconds wall clock time: 59 minutes 52.17 seconds (3592.17 seconds total)