Starting phenix.real_space_refine on Fri Jul 3 21:21:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l8s_23235/07_2026/7l8s_23235.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8s_23235/07_2026/7l8s_23235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7l8s_23235/07_2026/7l8s_23235.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l8s_23235/07_2026/7l8s_23235.cif" model { file = "/net/cci-nas-00/data/ceres_data/7l8s_23235/07_2026/7l8s_23235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8s_23235/07_2026/7l8s_23235.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l8s_23235/07_2026/7l8s_23235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8s_23235/07_2026/7l8s_23235.map" } resolution = 4.3 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= 0.000 sd= 0.003 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 105 5.16 5 C 9978 2.51 5 N 2694 2.21 5 O 3280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s 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: 16057 Number of models: 1 Model: "" Number of chains: 42 Chain: "C" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3482 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain breaks: 4 Chain: "D" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1027 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "E" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3487 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 4 Chain: "F" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1036 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "A" Number of atoms: 3517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3517 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Chain: "B" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1036 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "H" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 560 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'TRANS': 111} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 112 Planarities with less than four sites: {'UNK:plan-1': 112} Unresolved non-hydrogen planarities: 112 Chain: "L" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 500 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'UNK:plan-1': 100} Unresolved non-hydrogen planarities: 100 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: "P" 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: 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: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "S" 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: "T" 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: "U" 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: "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: 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: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 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: "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: 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: 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: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 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 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.52, per 1000 atoms: 0.22 Number of scatterers: 16057 At special positions: 0 Unit cell: (128.75, 126.69, 144.2, 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 105 16.00 O 3280 8.00 N 2694 7.00 C 9978 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.04 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS D 561 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.06 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS F 561 " distance=2.07 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 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=2.16 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 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=2.03 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 A 501 " - pdb=" SG CYS B 605 " distance=2.19 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA R 3 " - " MAN R 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA R 3 " - " MAN R 5 " " BMA Z 3 " - " MAN Z 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " 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 Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 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 i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A 601 " - " ASN A 276 " " NAG A 602 " - " ASN A 386 " " NAG A 603 " - " ASN A 363 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 289 " " NAG A 606 " - " ASN A 339 " " NAG A 607 " - " ASN A 355 " " NAG A 608 " - " ASN A 392 " " NAG A 609 " - " ASN A 137 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 601 " - " ASN C 276 " " NAG C 602 " - " ASN C 386 " " NAG C 603 " - " ASN C 363 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 133 " " NAG C 606 " - " ASN C 88 " " NAG C 607 " - " ASN C 289 " " NAG C 608 " - " ASN C 339 " " NAG C 609 " - " ASN C 355 " " NAG C 610 " - " ASN C 392 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 611 " " NAG E 601 " - " ASN E 276 " " NAG E 602 " - " ASN E 386 " " NAG E 603 " - " ASN E 363 " " NAG E 604 " - " ASN E 234 " " NAG E 605 " - " ASN E 133 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 88 " " NAG E 608 " - " ASN E 241 " " NAG E 609 " - " ASN E 289 " " NAG E 610 " - " ASN E 339 " " NAG E 611 " - " ASN E 355 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 611 " " NAG G 1 " - " ASN C 262 " " NAG I 1 " - " ASN C 448 " " NAG J 1 " - " ASN C 160 " " NAG K 1 " - " ASN C 295 " " NAG M 1 " - " ASN C 197 " " NAG N 1 " - " ASN C 156 " " NAG O 1 " - " ASN C 301 " " NAG P 1 " - " ASN C 241 " " NAG Q 1 " - " ASN C 332 " " NAG R 1 " - " ASN E 262 " " NAG S 1 " - " ASN E 448 " " NAG T 1 " - " ASN E 160 " " NAG U 1 " - " ASN E 295 " " NAG V 1 " - " ASN E 197 " " NAG W 1 " - " ASN E 156 " " NAG X 1 " - " ASN E 332 " " NAG Y 1 " - " ASN E 392 " " NAG Z 1 " - " ASN A 262 " " NAG a 1 " - " ASN A 448 " " NAG b 1 " - " ASN A 160 " " NAG c 1 " - " ASN A 295 " " NAG d 1 " - " ASN A 197 " " NAG e 1 " - " ASN A 156 " " NAG f 1 " - " ASN A 301 " " NAG g 1 " - " ASN A 88 " " NAG h 1 " - " ASN A 241 " " NAG i 1 " - " ASN A 332 " " NAG j 1 " - " ASN A 133 " Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 643.6 milliseconds 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3640 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 34 sheets defined 31.1% alpha, 38.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.024A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.822A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 377 through 381 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.427A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 483 removed outlier: 4.118A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.391A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 535 removed outlier: 4.013A pdb=" N MET D 535 " --> pdb=" O ALA D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 543 Processing helix chain 'D' and resid 562 through 566 Processing helix chain 'D' and resid 568 through 596 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.668A pdb=" N ILE D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'E' and resid 67 through 72 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.124A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.974A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 475 through 483 removed outlier: 3.569A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 removed outlier: 4.015A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 541 Processing helix chain 'F' and resid 560 through 562 No H-bonds generated for 'chain 'F' and resid 560 through 562' Processing helix chain 'F' and resid 563 through 568 Processing helix chain 'F' and resid 568 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 661 Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.175A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 150 through 153 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.518A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.842A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.362A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 562 through 568 Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'L' and resid 24 through 28 Processing helix chain 'L' and resid 48 through 51 Processing sheet with id=AA1, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'C' and resid 75 through 76 removed outlier: 4.160A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.668A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 394 through 395 removed outlier: 10.328A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.072A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 9.892A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.466A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.617A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 271 through 273 Processing sheet with id=AB1, first strand: chain 'C' and resid 315 through 323A removed outlier: 6.499A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.261A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.510A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 75 through 76 removed outlier: 4.499A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB6, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.819A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.623A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.503A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.198A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.503A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.198A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 301 through 308 removed outlier: 7.071A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY E 321 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 394 through 395 removed outlier: 6.358A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.716A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AC5, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AC6, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AC7, first strand: chain 'A' and resid 169 through 176 Processing sheet with id=AC8, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.635A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLN A 432 " --> pdb=" O MET A 426 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N MET A 426 " --> pdb=" O GLN A 432 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 394 through 396 removed outlier: 10.428A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.132A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.072A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.716A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.353A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.133A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 259 through 261 Processing sheet with id=AD2, first strand: chain 'A' and resid 271 through 273 Processing sheet with id=AD3, first strand: chain 'A' and resid 315 through 323A removed outlier: 7.264A pdb=" N TRP A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE A 309 " --> pdb=" O TRP A 316 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 34 through 35 Processing sheet with id=AD5, first strand: chain 'L' and resid 44 through 47 removed outlier: 6.603A pdb=" N UNK L 34 " --> pdb=" O UNK L 46 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N UNK L 35 " --> pdb=" O UNK L 84 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N UNK L 84 " --> pdb=" O UNK L 35 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N UNK L 82 " --> pdb=" O UNK L 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 44 through 47 removed outlier: 6.603A pdb=" N UNK L 34 " --> pdb=" O UNK L 46 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N UNK L 35 " --> pdb=" O UNK L 84 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N UNK L 84 " --> pdb=" O UNK L 35 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N UNK L 82 " --> pdb=" O UNK L 37 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N UNK L 99 " --> pdb=" O UNK L 83 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 62 through 63 removed outlier: 3.921A pdb=" N UNK L 63 " --> pdb=" O UNK L 70 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N UNK L 70 " --> pdb=" O UNK L 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 600 hydrogen bonds defined for protein. 1599 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: 2.96 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 3908 1.33 - 1.46: 4881 1.46 - 1.60: 7381 1.60 - 1.74: 28 1.74 - 1.87: 131 Bond restraints: 16329 Sorted by residual: bond pdb=" CB LEU F 661 " pdb=" CG LEU F 661 " ideal model delta sigma weight residual 1.530 1.666 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.65e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.413 0.084 1.40e-02 5.10e+03 3.59e+01 bond pdb=" CB LEU D 520 " pdb=" CG LEU D 520 " ideal model delta sigma weight residual 1.530 1.642 -0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" CB LEU B 520 " pdb=" CG LEU B 520 " ideal model delta sigma weight residual 1.530 1.630 -0.100 2.00e-02 2.50e+03 2.48e+01 ... (remaining 16324 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 19255 2.48 - 4.96: 2561 4.96 - 7.43: 347 7.43 - 9.91: 42 9.91 - 12.39: 3 Bond angle restraints: 22208 Sorted by residual: angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 128.07 -8.51 1.02e+00 9.61e-01 6.97e+01 angle pdb=" C GLU E 492 " pdb=" N PRO E 493 " pdb=" CA PRO E 493 " ideal model delta sigma weight residual 119.87 127.91 -8.04 1.04e+00 9.25e-01 5.98e+01 angle pdb=" C TYR C 319 " pdb=" N THR C 320 " pdb=" CA THR C 320 " ideal model delta sigma weight residual 120.63 133.02 -12.39 1.61e+00 3.86e-01 5.92e+01 angle pdb=" C VAL B 608 " pdb=" N PRO B 609 " pdb=" CA PRO B 609 " ideal model delta sigma weight residual 119.85 127.36 -7.51 1.01e+00 9.80e-01 5.53e+01 angle pdb=" C CYS E 205 " pdb=" N PRO E 206 " pdb=" CA PRO E 206 " ideal model delta sigma weight residual 119.56 127.04 -7.48 1.02e+00 9.61e-01 5.38e+01 ... (remaining 22203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 8662 17.45 - 34.90: 251 34.90 - 52.35: 71 52.35 - 69.80: 19 69.80 - 87.25: 10 Dihedral angle restraints: 9013 sinusoidal: 3425 harmonic: 5588 Sorted by residual: dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -141.52 55.52 1 1.00e+01 1.00e-02 4.16e+01 dihedral pdb=" CB CYS E 501 " pdb=" SG CYS E 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual 93.00 145.79 -52.79 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CA UNK H 11 " pdb=" C UNK H 11 " pdb=" N UNK H 12 " pdb=" CA UNK H 12 " ideal model delta harmonic sigma weight residual -180.00 -150.44 -29.56 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 9010 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1963 0.120 - 0.239: 527 0.239 - 0.359: 232 0.359 - 0.478: 120 0.478 - 0.598: 14 Chirality restraints: 2856 Sorted by residual: chirality pdb=" C1 NAG h 2 " pdb=" O4 NAG h 1 " pdb=" C2 NAG h 2 " pdb=" O5 NAG h 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.85e+02 chirality pdb=" C1 NAG j 2 " pdb=" O4 NAG j 1 " pdb=" C2 NAG j 2 " pdb=" O5 NAG j 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.56e+02 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.38e+02 ... (remaining 2853 not shown) Planarity restraints: 2772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 2 " -0.349 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG f 2 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG f 2 " -0.134 2.00e-02 2.50e+03 pdb=" N2 NAG f 2 " 0.534 2.00e-02 2.50e+03 pdb=" O7 NAG f 2 " -0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 701 " -0.346 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG B 701 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B 701 " -0.136 2.00e-02 2.50e+03 pdb=" N2 NAG B 701 " 0.530 2.00e-02 2.50e+03 pdb=" O7 NAG B 701 " -0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 2 " 0.328 2.00e-02 2.50e+03 2.79e-01 9.76e+02 pdb=" C7 NAG i 2 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG i 2 " 0.174 2.00e-02 2.50e+03 pdb=" N2 NAG i 2 " -0.490 2.00e-02 2.50e+03 pdb=" O7 NAG i 2 " 0.072 2.00e-02 2.50e+03 ... (remaining 2769 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3860 2.81 - 3.33: 15336 3.33 - 3.85: 26238 3.85 - 4.38: 31694 4.38 - 4.90: 48832 Nonbonded interactions: 125960 Sorted by model distance: nonbonded pdb=" O3 NAG b 2 " pdb=" O7 NAG b 2 " model vdw 2.287 3.040 nonbonded pdb=" OD1 ASN E 276 " pdb=" N ASN E 279 " model vdw 2.322 3.120 nonbonded pdb=" O HIS E 72 " pdb=" ND1 HIS E 72 " model vdw 2.351 3.120 nonbonded pdb=" N ASN A 425 " pdb=" O ASN A 425 " model vdw 2.379 2.496 nonbonded pdb=" N ILE C 213 " pdb=" O ILE C 213 " model vdw 2.405 2.496 ... (remaining 125955 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 186 or resid 189 through 397 or resid 411 throu \ gh 457 or resid 461 through 505 or resid 601 through 609)) selection = (chain 'C' and (resid 33 through 397 or resid 411 through 505 or resid 602 throu \ gh 610)) selection = (chain 'E' and (resid 33 through 457 or resid 461 through 505 or resid 601 throu \ gh 609)) } ncs_group { reference = (chain 'B' and (resid 520 through 661 or resid 702 through 703)) selection = chain 'D' selection = (chain 'F' and (resid 520 through 546 or resid 561 through 702)) } ncs_group { reference = chain 'G' selection = chain 'R' selection = chain 'Z' } ncs_group { reference = (chain 'H' and resid 15 through 114) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } 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: 2.260 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.090 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.023 0.157 16468 Z= 1.221 Angle : 1.786 20.114 22589 Z= 1.113 Chirality : 0.152 0.598 2856 Planarity : 0.014 0.300 2707 Dihedral : 9.935 87.252 5265 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.20), residues: 1673 helix: 0.66 (0.23), residues: 415 sheet: 0.99 (0.23), residues: 432 loop : 1.09 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 192 TYR 0.054 0.009 TYR B 638 PHE 0.031 0.006 PHE C 383 TRP 0.054 0.009 TRP F 571 HIS 0.011 0.003 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.02212 / 1.19 (16329) covalent geometry : angle 1.74136 / 1.11 (22208) SS BOND : bond 0.03571 / 2.53 ( 36) SS BOND : angle 2.63089 / 1.75 ( 72) hydrogen bonds : bond 0.17057 / 11.32 ( 588) hydrogen bonds : angle 7.87198 / 5.44 ( 1599) link_ALPHA1-3 : bond 0.08633 / 4.32 ( 3) link_ALPHA1-3 : angle 5.90086 / 4.82 ( 9) link_ALPHA1-6 : bond 0.05704 / 2.88 ( 3) link_ALPHA1-6 : angle 3.61124 / 2.37 ( 9) link_BETA1-4 : bond 0.07121 / 4.21 ( 32) link_BETA1-4 : angle 4.49639 / 3.20 ( 96) link_NAG-ASN : bond 0.07710 / 4.84 ( 65) link_NAG-ASN : angle 3.04538 / 2.11 ( 195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 474 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8271 (m-80) cc_final: 0.8026 (m-80) REVERT: D 584 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8866 (tm-30) REVERT: D 628 TRP cc_start: 0.7709 (m100) cc_final: 0.7434 (m100) REVERT: D 650 GLN cc_start: 0.8985 (tp40) cc_final: 0.8501 (tm-30) REVERT: D 654 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7560 (tm-30) REVERT: E 39 TYR cc_start: 0.8809 (m-80) cc_final: 0.8484 (m-80) REVERT: E 112 TRP cc_start: 0.8607 (t-100) cc_final: 0.8358 (t-100) REVERT: E 161 MET cc_start: 0.7460 (ppp) cc_final: 0.7027 (ppp) REVERT: E 210 PHE cc_start: 0.8605 (m-80) cc_final: 0.7661 (m-10) REVERT: E 309 ILE cc_start: 0.9395 (pt) cc_final: 0.9048 (tt) REVERT: F 536 THR cc_start: 0.9551 (p) cc_final: 0.9349 (p) REVERT: A 100 MET cc_start: 0.8791 (mtm) cc_final: 0.8553 (mtm) REVERT: A 122 LEU cc_start: 0.9514 (mt) cc_final: 0.9227 (mm) REVERT: A 382 PHE cc_start: 0.9267 (m-80) cc_final: 0.8994 (m-10) REVERT: B 522 PHE cc_start: 0.8449 (t80) cc_final: 0.8183 (t80) REVERT: B 622 ILE cc_start: 0.8721 (mt) cc_final: 0.7789 (mt) REVERT: B 639 THR cc_start: 0.9277 (m) cc_final: 0.8634 (p) REVERT: B 662 GLU cc_start: 0.4533 (mt-10) cc_final: 0.4162 (mt-10) outliers start: 0 outliers final: 0 residues processed: 474 average time/residue: 0.1295 time to fit residues: 88.9360 Evaluate side-chains 219 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 HIS C 300 ASN D 577 GLN D 653 GLN D 658 GLN E 105 HIS E 170 GLN E 328 GLN F 630 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN A 422 GLN B 575 GLN B 630 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.071021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.057465 restraints weight = 71281.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.059033 restraints weight = 43196.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.060114 restraints weight = 30939.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.060768 restraints weight = 24721.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.061287 restraints weight = 21377.033| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16468 Z= 0.199 Angle : 0.847 11.076 22589 Z= 0.410 Chirality : 0.049 0.303 2856 Planarity : 0.004 0.042 2707 Dihedral : 5.144 24.301 2020 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.49 % Favored : 98.45 % Rotamer: Outliers : 0.26 % Allowed : 2.67 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.20), residues: 1673 helix: 1.17 (0.25), residues: 416 sheet: 0.61 (0.22), residues: 474 loop : 0.49 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 542 TYR 0.030 0.002 TYR E 177 PHE 0.021 0.002 PHE D 522 TRP 0.026 0.002 TRP A 479 HIS 0.006 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 (16329) covalent geometry : angle 0.79199 / 0.40 (22208) SS BOND : bond 0.00418 / 0.26 ( 36) SS BOND : angle 1.26166 / 0.88 ( 72) hydrogen bonds : bond 0.06487 / 4.46 ( 588) hydrogen bonds : angle 6.33195 / 4.38 ( 1599) link_ALPHA1-3 : bond 0.00851 / 0.42 ( 3) link_ALPHA1-3 : angle 3.78918 / 3.45 ( 9) link_ALPHA1-6 : bond 0.00771 / 0.39 ( 3) link_ALPHA1-6 : angle 1.61253 / 1.21 ( 9) link_BETA1-4 : bond 0.00727 / 0.48 ( 32) link_BETA1-4 : angle 2.49617 / 1.77 ( 96) link_NAG-ASN : bond 0.00718 / 0.34 ( 65) link_NAG-ASN : angle 2.68765 / 1.91 ( 195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 305 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 ASN cc_start: 0.9157 (t0) cc_final: 0.8781 (t0) REVERT: C 104 MET cc_start: 0.8798 (ttt) cc_final: 0.8553 (ttp) REVERT: C 426 MET cc_start: 0.8617 (tpp) cc_final: 0.8377 (tpp) REVERT: D 522 PHE cc_start: 0.8425 (t80) cc_final: 0.8115 (t80) REVERT: D 530 MET cc_start: 0.7604 (mtp) cc_final: 0.7044 (mtp) REVERT: D 537 LEU cc_start: 0.8613 (mt) cc_final: 0.8165 (mt) REVERT: D 654 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7543 (tm-30) REVERT: E 85 HIS cc_start: 0.7901 (m90) cc_final: 0.7480 (m-70) REVERT: E 112 TRP cc_start: 0.8371 (t-100) cc_final: 0.8055 (t-100) REVERT: E 161 MET cc_start: 0.6874 (ppp) cc_final: 0.6397 (ppp) REVERT: E 210 PHE cc_start: 0.8335 (m-80) cc_final: 0.7806 (m-10) REVERT: E 303 THR cc_start: 0.8439 (p) cc_final: 0.8074 (p) REVERT: E 492 GLU cc_start: 0.8634 (tt0) cc_final: 0.8317 (pm20) REVERT: F 568 ASP cc_start: 0.7869 (t0) cc_final: 0.7597 (t0) REVERT: F 603 ILE cc_start: 0.9329 (mt) cc_final: 0.9009 (mt) REVERT: F 648 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8412 (mm-30) REVERT: A 95 MET cc_start: 0.8964 (ptt) cc_final: 0.7838 (ppp) REVERT: A 109 ILE cc_start: 0.9444 (mt) cc_final: 0.9153 (tt) REVERT: A 122 LEU cc_start: 0.9365 (mt) cc_final: 0.9139 (mm) REVERT: A 382 PHE cc_start: 0.9033 (m-80) cc_final: 0.8746 (m-10) REVERT: A 424 ILE cc_start: 0.9305 (mm) cc_final: 0.9029 (mm) REVERT: B 568 ASP cc_start: 0.7606 (t0) cc_final: 0.7148 (t0) REVERT: B 575 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8123 (tm-30) REVERT: B 596 TRP cc_start: 0.9097 (m-10) cc_final: 0.8738 (m-10) outliers start: 4 outliers final: 0 residues processed: 308 average time/residue: 0.1172 time to fit residues: 55.1618 Evaluate side-chains 187 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 166 optimal weight: 7.9990 chunk 40 optimal weight: 0.0060 chunk 108 optimal weight: 6.9990 chunk 188 optimal weight: 20.0000 chunk 161 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 186 optimal weight: 30.0000 chunk 123 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 overall best weight: 2.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 HIS D 577 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN E 300 ASN F 651 ASN A 85 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.069885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.056088 restraints weight = 72298.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.057622 restraints weight = 43414.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.058692 restraints weight = 30932.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.059343 restraints weight = 24689.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.059811 restraints weight = 21324.187| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16468 Z= 0.173 Angle : 0.717 9.332 22589 Z= 0.350 Chirality : 0.045 0.266 2856 Planarity : 0.004 0.052 2707 Dihedral : 4.881 34.301 2020 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.13 % Allowed : 2.41 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.91 (0.20), residues: 1673 helix: 1.41 (0.26), residues: 421 sheet: 0.60 (0.23), residues: 472 loop : 0.29 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 308 TYR 0.023 0.001 TYR F 638 PHE 0.021 0.002 PHE E 53 TRP 0.021 0.002 TRP F 623 HIS 0.005 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (16329) covalent geometry : angle 0.67582 / 0.34 (22208) SS BOND : bond 0.00360 / 0.23 ( 36) SS BOND : angle 1.16496 / 0.80 ( 72) hydrogen bonds : bond 0.05265 / 3.61 ( 588) hydrogen bonds : angle 5.90181 / 4.07 ( 1599) link_ALPHA1-3 : bond 0.00609 / 0.30 ( 3) link_ALPHA1-3 : angle 3.18746 / 2.98 ( 9) link_ALPHA1-6 : bond 0.00641 / 0.32 ( 3) link_ALPHA1-6 : angle 1.41709 / 1.04 ( 9) link_BETA1-4 : bond 0.00559 / 0.35 ( 32) link_BETA1-4 : angle 1.76153 / 1.26 ( 96) link_NAG-ASN : bond 0.00456 / 0.25 ( 65) link_NAG-ASN : angle 2.23502 / 1.59 ( 195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 247 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 ASN cc_start: 0.8918 (t0) cc_final: 0.8647 (t0) REVERT: C 104 MET cc_start: 0.8880 (ttt) cc_final: 0.8623 (ttp) REVERT: C 426 MET cc_start: 0.8807 (tpp) cc_final: 0.8491 (tpp) REVERT: C 427 TRP cc_start: 0.8363 (m100) cc_final: 0.8133 (m100) REVERT: D 522 PHE cc_start: 0.8567 (t80) cc_final: 0.8197 (t80) REVERT: D 537 LEU cc_start: 0.8746 (mt) cc_final: 0.8332 (mt) REVERT: D 647 GLU cc_start: 0.9096 (pp20) cc_final: 0.8795 (pp20) REVERT: D 654 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7628 (tm-30) REVERT: E 85 HIS cc_start: 0.7954 (m90) cc_final: 0.7545 (m-70) REVERT: E 104 MET cc_start: 0.9093 (ttt) cc_final: 0.8726 (ttm) REVERT: E 210 PHE cc_start: 0.8425 (m-80) cc_final: 0.7932 (m-10) REVERT: F 568 ASP cc_start: 0.7855 (t0) cc_final: 0.7493 (t0) REVERT: F 603 ILE cc_start: 0.9434 (mt) cc_final: 0.8977 (mp) REVERT: F 657 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8440 (tm-30) REVERT: A 100 MET cc_start: 0.8160 (mtm) cc_final: 0.7856 (mtt) REVERT: A 109 ILE cc_start: 0.9361 (mt) cc_final: 0.9066 (tt) REVERT: A 122 LEU cc_start: 0.9268 (mt) cc_final: 0.9040 (mm) REVERT: A 382 PHE cc_start: 0.9033 (m-80) cc_final: 0.8822 (m-10) REVERT: A 424 ILE cc_start: 0.9336 (mm) cc_final: 0.9080 (mm) REVERT: B 543 ASN cc_start: 0.9036 (t0) cc_final: 0.8761 (t0) REVERT: B 577 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8857 (tm-30) REVERT: B 596 TRP cc_start: 0.9003 (m-10) cc_final: 0.8776 (m-10) REVERT: B 631 TRP cc_start: 0.8972 (t-100) cc_final: 0.8761 (t-100) REVERT: B 646 LEU cc_start: 0.9414 (mt) cc_final: 0.9158 (mt) REVERT: B 647 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8792 (mt-10) outliers start: 2 outliers final: 1 residues processed: 249 average time/residue: 0.1120 time to fit residues: 42.7309 Evaluate side-chains 177 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 67 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 173 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 103 GLN D 577 GLN D 607 ASN D 658 GLN F 543 ASN A 82 GLN A 85 HIS B 651 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.070690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.056806 restraints weight = 72031.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.058353 restraints weight = 43459.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.059372 restraints weight = 31225.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.060108 restraints weight = 25065.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.060545 restraints weight = 21633.732| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16468 Z= 0.126 Angle : 0.653 9.931 22589 Z= 0.319 Chirality : 0.045 0.386 2856 Planarity : 0.003 0.051 2707 Dihedral : 4.735 31.128 2020 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.20 % Allowed : 1.95 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.83 (0.20), residues: 1673 helix: 1.52 (0.26), residues: 423 sheet: 0.59 (0.23), residues: 461 loop : 0.10 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 308 TYR 0.018 0.001 TYR A 217 PHE 0.020 0.002 PHE F 522 TRP 0.029 0.002 TRP E 479 HIS 0.011 0.001 HIS C 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (16329) covalent geometry : angle 0.61768 / 0.31 (22208) SS BOND : bond 0.00269 / 0.15 ( 36) SS BOND : angle 1.19173 / 0.78 ( 72) hydrogen bonds : bond 0.04613 / 3.18 ( 588) hydrogen bonds : angle 5.56553 / 3.83 ( 1599) link_ALPHA1-3 : bond 0.00691 / 0.34 ( 3) link_ALPHA1-3 : angle 3.03405 / 2.83 ( 9) link_ALPHA1-6 : bond 0.00603 / 0.30 ( 3) link_ALPHA1-6 : angle 1.36064 / 0.97 ( 9) link_BETA1-4 : bond 0.00524 / 0.32 ( 32) link_BETA1-4 : angle 1.46114 / 1.05 ( 96) link_NAG-ASN : bond 0.00353 / 0.21 ( 65) link_NAG-ASN : angle 1.96031 / 1.42 ( 195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 248 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.7519 (m-80) cc_final: 0.6949 (m-80) REVERT: C 98 ASN cc_start: 0.8916 (t0) cc_final: 0.8629 (t0) REVERT: C 104 MET cc_start: 0.8993 (ttt) cc_final: 0.8693 (ttp) REVERT: C 195 ASN cc_start: 0.8457 (t0) cc_final: 0.8242 (t0) REVERT: C 260 LEU cc_start: 0.9351 (mm) cc_final: 0.9021 (mm) REVERT: C 426 MET cc_start: 0.8855 (tpp) cc_final: 0.8563 (tpp) REVERT: D 537 LEU cc_start: 0.8648 (mt) cc_final: 0.8212 (mt) REVERT: D 542 ARG cc_start: 0.8501 (ptm160) cc_final: 0.8282 (ptm-80) REVERT: D 647 GLU cc_start: 0.9053 (pp20) cc_final: 0.8747 (pp20) REVERT: D 654 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7675 (tm-30) REVERT: E 85 HIS cc_start: 0.7967 (m90) cc_final: 0.7544 (m-70) REVERT: E 104 MET cc_start: 0.9038 (ttt) cc_final: 0.8790 (ttm) REVERT: E 210 PHE cc_start: 0.8258 (m-80) cc_final: 0.7902 (m-10) REVERT: F 530 MET cc_start: 0.7818 (mpp) cc_final: 0.7432 (mpp) REVERT: F 568 ASP cc_start: 0.7707 (t0) cc_final: 0.7237 (t0) REVERT: F 596 TRP cc_start: 0.8516 (m-10) cc_final: 0.8272 (m-10) REVERT: F 603 ILE cc_start: 0.9427 (mt) cc_final: 0.9058 (mp) REVERT: F 655 LYS cc_start: 0.8689 (pttm) cc_final: 0.8219 (pttm) REVERT: F 657 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8501 (tm-30) REVERT: A 109 ILE cc_start: 0.9379 (mt) cc_final: 0.8979 (tt) REVERT: A 122 LEU cc_start: 0.9241 (mt) cc_final: 0.9002 (mm) REVERT: B 577 GLN cc_start: 0.9042 (tm-30) cc_final: 0.8821 (tm-30) REVERT: B 649 SER cc_start: 0.9058 (t) cc_final: 0.8820 (p) outliers start: 3 outliers final: 1 residues processed: 250 average time/residue: 0.1084 time to fit residues: 42.1448 Evaluate side-chains 184 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 120 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 173 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 128 optimal weight: 0.0030 chunk 51 optimal weight: 2.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 HIS C 103 GLN D 577 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN E 195 ASN F 543 ASN F 651 ASN A 85 HIS A 411 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.070363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.056758 restraints weight = 72417.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.058171 restraints weight = 44810.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.059160 restraints weight = 32836.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.059763 restraints weight = 26713.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.060216 restraints weight = 23390.002| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16468 Z= 0.130 Angle : 0.630 9.382 22589 Z= 0.307 Chirality : 0.044 0.249 2856 Planarity : 0.003 0.038 2707 Dihedral : 4.588 32.119 2020 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.13 % Allowed : 1.56 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.69 (0.21), residues: 1673 helix: 1.54 (0.26), residues: 420 sheet: 0.44 (0.23), residues: 463 loop : -0.01 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 617 TYR 0.014 0.001 TYR C 484 PHE 0.018 0.002 PHE F 522 TRP 0.029 0.002 TRP F 628 HIS 0.003 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (16329) covalent geometry : angle 0.60016 / 0.30 (22208) SS BOND : bond 0.00476 / 0.23 ( 36) SS BOND : angle 1.23128 / 0.78 ( 72) hydrogen bonds : bond 0.04374 / 2.99 ( 588) hydrogen bonds : angle 5.43152 / 3.72 ( 1599) link_ALPHA1-3 : bond 0.00574 / 0.28 ( 3) link_ALPHA1-3 : angle 2.99596 / 2.79 ( 9) link_ALPHA1-6 : bond 0.00547 / 0.27 ( 3) link_ALPHA1-6 : angle 1.37674 / 0.99 ( 9) link_BETA1-4 : bond 0.00451 / 0.28 ( 32) link_BETA1-4 : angle 1.33683 / 0.96 ( 96) link_NAG-ASN : bond 0.00315 / 0.22 ( 65) link_NAG-ASN : angle 1.74407 / 1.24 ( 195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 244 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.7713 (m-80) cc_final: 0.7213 (m-80) REVERT: C 98 ASN cc_start: 0.8986 (t0) cc_final: 0.8736 (t0) REVERT: C 195 ASN cc_start: 0.8472 (t0) cc_final: 0.8204 (t0) REVERT: C 426 MET cc_start: 0.8860 (tpp) cc_final: 0.8515 (tpp) REVERT: D 537 LEU cc_start: 0.8856 (mt) cc_final: 0.8447 (mt) REVERT: D 584 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7955 (tm-30) REVERT: D 590 GLN cc_start: 0.9041 (mm110) cc_final: 0.8475 (tm-30) REVERT: D 647 GLU cc_start: 0.9027 (pp20) cc_final: 0.8715 (pp20) REVERT: D 654 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7694 (tm-30) REVERT: E 85 HIS cc_start: 0.7765 (m90) cc_final: 0.7505 (m-70) REVERT: E 95 MET cc_start: 0.9363 (ptm) cc_final: 0.8219 (ppp) REVERT: E 104 MET cc_start: 0.9001 (ttt) cc_final: 0.8792 (ttm) REVERT: E 210 PHE cc_start: 0.8246 (m-80) cc_final: 0.7911 (m-10) REVERT: F 530 MET cc_start: 0.7873 (mpp) cc_final: 0.7573 (mpp) REVERT: F 568 ASP cc_start: 0.7620 (t0) cc_final: 0.7103 (t0) REVERT: F 603 ILE cc_start: 0.9421 (mt) cc_final: 0.9069 (mp) REVERT: F 655 LYS cc_start: 0.8710 (pttm) cc_final: 0.8256 (pttm) REVERT: F 657 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8490 (tm-30) REVERT: A 109 ILE cc_start: 0.9366 (mt) cc_final: 0.9110 (tt) REVERT: A 122 LEU cc_start: 0.9219 (mt) cc_final: 0.8967 (mm) REVERT: B 577 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8846 (tm-30) REVERT: B 626 MET cc_start: 0.7507 (mpp) cc_final: 0.7103 (mpp) REVERT: B 631 TRP cc_start: 0.8863 (t-100) cc_final: 0.8447 (t-100) REVERT: B 646 LEU cc_start: 0.9452 (mt) cc_final: 0.9078 (mt) REVERT: B 649 SER cc_start: 0.9050 (t) cc_final: 0.8831 (p) REVERT: B 654 GLU cc_start: 0.9117 (tt0) cc_final: 0.8341 (tm-30) outliers start: 2 outliers final: 0 residues processed: 245 average time/residue: 0.1177 time to fit residues: 44.4306 Evaluate side-chains 178 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 69 optimal weight: 8.9990 chunk 146 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 HIS C 103 GLN D 577 GLN D 658 GLN E 425 ASN F 543 ASN A 85 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.069999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.056366 restraints weight = 71938.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.057827 restraints weight = 44124.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.058822 restraints weight = 32004.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.059515 restraints weight = 26034.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.059870 restraints weight = 22468.571| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16468 Z= 0.118 Angle : 0.606 8.897 22589 Z= 0.298 Chirality : 0.043 0.242 2856 Planarity : 0.003 0.037 2707 Dihedral : 4.517 29.497 2020 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.13 % Allowed : 1.24 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.21), residues: 1673 helix: 1.45 (0.26), residues: 422 sheet: 0.50 (0.23), residues: 467 loop : -0.07 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 542 TYR 0.014 0.001 TYR F 643 PHE 0.019 0.002 PHE E 53 TRP 0.046 0.002 TRP F 628 HIS 0.002 0.001 HIS D 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (16329) covalent geometry : angle 0.57849 / 0.29 (22208) SS BOND : bond 0.00422 / 0.21 ( 36) SS BOND : angle 1.20495 / 0.79 ( 72) hydrogen bonds : bond 0.04148 / 2.82 ( 588) hydrogen bonds : angle 5.31506 / 3.64 ( 1599) link_ALPHA1-3 : bond 0.00591 / 0.29 ( 3) link_ALPHA1-3 : angle 2.97295 / 2.78 ( 9) link_ALPHA1-6 : bond 0.00532 / 0.27 ( 3) link_ALPHA1-6 : angle 1.36132 / 0.96 ( 9) link_BETA1-4 : bond 0.00444 / 0.27 ( 32) link_BETA1-4 : angle 1.25546 / 0.90 ( 96) link_NAG-ASN : bond 0.00279 / 0.18 ( 65) link_NAG-ASN : angle 1.60245 / 1.15 ( 195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 244 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.7760 (m-80) cc_final: 0.7269 (m-80) REVERT: C 195 ASN cc_start: 0.8370 (t0) cc_final: 0.8143 (t0) REVERT: C 491 ILE cc_start: 0.9593 (mp) cc_final: 0.9180 (mm) REVERT: D 584 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7889 (tm-30) REVERT: D 590 GLN cc_start: 0.9046 (mm110) cc_final: 0.8488 (tm-30) REVERT: D 641 ILE cc_start: 0.9209 (mt) cc_final: 0.8842 (tt) REVERT: D 647 GLU cc_start: 0.9010 (pp20) cc_final: 0.8714 (pp20) REVERT: D 654 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7750 (tm-30) REVERT: E 85 HIS cc_start: 0.7803 (m90) cc_final: 0.7516 (m-70) REVERT: E 95 MET cc_start: 0.9315 (ptm) cc_final: 0.8282 (ppp) REVERT: E 104 MET cc_start: 0.9024 (ttt) cc_final: 0.8794 (ttm) REVERT: E 210 PHE cc_start: 0.8228 (m-80) cc_final: 0.7911 (m-10) REVERT: F 535 MET cc_start: 0.8365 (tmm) cc_final: 0.8143 (tmm) REVERT: F 543 ASN cc_start: 0.8759 (m110) cc_final: 0.8528 (p0) REVERT: F 568 ASP cc_start: 0.7539 (t0) cc_final: 0.7007 (t0) REVERT: F 603 ILE cc_start: 0.9398 (mt) cc_final: 0.9070 (mp) REVERT: F 655 LYS cc_start: 0.8709 (pttm) cc_final: 0.8242 (pttm) REVERT: F 657 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8479 (tm-30) REVERT: A 122 LEU cc_start: 0.9225 (mt) cc_final: 0.8964 (mm) REVERT: B 577 GLN cc_start: 0.8980 (tm-30) cc_final: 0.8706 (tm-30) REVERT: B 584 GLU cc_start: 0.8708 (pt0) cc_final: 0.8361 (tm-30) REVERT: B 601 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8446 (ttpt) REVERT: B 626 MET cc_start: 0.7471 (mpp) cc_final: 0.7232 (mpp) REVERT: B 646 LEU cc_start: 0.9441 (mt) cc_final: 0.9068 (mt) REVERT: B 649 SER cc_start: 0.9028 (t) cc_final: 0.8826 (p) REVERT: B 654 GLU cc_start: 0.9144 (tt0) cc_final: 0.8404 (tm-30) outliers start: 2 outliers final: 0 residues processed: 246 average time/residue: 0.1134 time to fit residues: 42.5043 Evaluate side-chains 179 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 28 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 176 optimal weight: 20.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 HIS C 103 GLN D 577 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS A 170 GLN B 625 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.067905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.054299 restraints weight = 73654.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.055656 restraints weight = 46325.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.056589 restraints weight = 34296.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.057147 restraints weight = 28025.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.057153 restraints weight = 24684.593| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16468 Z= 0.203 Angle : 0.693 10.546 22589 Z= 0.339 Chirality : 0.045 0.235 2856 Planarity : 0.004 0.042 2707 Dihedral : 4.710 32.504 2020 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.07 % Allowed : 1.17 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.45 (0.21), residues: 1673 helix: 1.34 (0.26), residues: 430 sheet: 0.25 (0.22), residues: 480 loop : -0.17 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 542 TYR 0.018 0.002 TYR D 638 PHE 0.025 0.002 PHE E 53 TRP 0.039 0.002 TRP E 479 HIS 0.006 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (16329) covalent geometry : angle 0.66507 / 0.33 (22208) SS BOND : bond 0.00498 / 0.28 ( 36) SS BOND : angle 1.36060 / 0.89 ( 72) hydrogen bonds : bond 0.04470 / 3.04 ( 588) hydrogen bonds : angle 5.51092 / 3.78 ( 1599) link_ALPHA1-3 : bond 0.00575 / 0.29 ( 3) link_ALPHA1-3 : angle 2.93082 / 2.69 ( 9) link_ALPHA1-6 : bond 0.00379 / 0.19 ( 3) link_ALPHA1-6 : angle 1.46218 / 1.06 ( 9) link_BETA1-4 : bond 0.00391 / 0.23 ( 32) link_BETA1-4 : angle 1.37129 / 0.99 ( 96) link_NAG-ASN : bond 0.00326 / 0.22 ( 65) link_NAG-ASN : angle 1.78686 / 1.28 ( 195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 195 ASN cc_start: 0.8557 (t0) cc_final: 0.8220 (t0) REVERT: D 537 LEU cc_start: 0.8844 (mt) cc_final: 0.8388 (mt) REVERT: D 584 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8042 (tm-30) REVERT: D 647 GLU cc_start: 0.9108 (pp20) cc_final: 0.8814 (pp20) REVERT: D 654 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7817 (tm-30) REVERT: E 85 HIS cc_start: 0.7861 (m90) cc_final: 0.7604 (m90) REVERT: E 95 MET cc_start: 0.9332 (ptm) cc_final: 0.8411 (ppp) REVERT: E 210 PHE cc_start: 0.8441 (m-80) cc_final: 0.8113 (m-10) REVERT: F 535 MET cc_start: 0.8566 (tmm) cc_final: 0.8318 (tmm) REVERT: F 568 ASP cc_start: 0.7588 (t0) cc_final: 0.6937 (t0) REVERT: F 655 LYS cc_start: 0.8653 (pttm) cc_final: 0.8312 (pttp) REVERT: F 657 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8477 (tm-30) REVERT: A 109 ILE cc_start: 0.9403 (mt) cc_final: 0.9051 (tt) REVERT: A 122 LEU cc_start: 0.9251 (mt) cc_final: 0.8953 (mm) REVERT: A 382 PHE cc_start: 0.9069 (m-80) cc_final: 0.8707 (m-10) REVERT: B 577 GLN cc_start: 0.9051 (tm-30) cc_final: 0.8787 (tm-30) REVERT: B 599 SER cc_start: 0.9489 (t) cc_final: 0.9193 (p) REVERT: B 646 LEU cc_start: 0.9475 (mt) cc_final: 0.9178 (mt) REVERT: B 649 SER cc_start: 0.9135 (t) cc_final: 0.8920 (p) REVERT: B 654 GLU cc_start: 0.9207 (tt0) cc_final: 0.8641 (tm-30) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.1237 time to fit residues: 42.6876 Evaluate side-chains 157 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 161 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 169 optimal weight: 40.0000 chunk 37 optimal weight: 5.9990 chunk 182 optimal weight: 30.0000 chunk 32 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 HIS C 103 GLN D 577 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN F 651 ASN A 85 HIS B 570 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.068349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.054647 restraints weight = 73590.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.056075 restraints weight = 45263.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.057031 restraints weight = 33096.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.057649 restraints weight = 26932.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.058112 restraints weight = 23473.570| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16468 Z= 0.147 Angle : 0.640 8.731 22589 Z= 0.313 Chirality : 0.044 0.227 2856 Planarity : 0.003 0.030 2707 Dihedral : 4.660 31.594 2020 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.07 % Allowed : 0.72 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.35 (0.21), residues: 1673 helix: 1.26 (0.26), residues: 430 sheet: 0.15 (0.22), residues: 490 loop : -0.20 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 542 TYR 0.020 0.002 TYR E 217 PHE 0.018 0.002 PHE E 53 TRP 0.035 0.002 TRP E 479 HIS 0.004 0.001 HIS C 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (16329) covalent geometry : angle 0.61223 / 0.31 (22208) SS BOND : bond 0.00385 / 0.20 ( 36) SS BOND : angle 1.48080 / 0.93 ( 72) hydrogen bonds : bond 0.04260 / 2.90 ( 588) hydrogen bonds : angle 5.40257 / 3.68 ( 1599) link_ALPHA1-3 : bond 0.00534 / 0.27 ( 3) link_ALPHA1-3 : angle 2.88628 / 2.67 ( 9) link_ALPHA1-6 : bond 0.00418 / 0.21 ( 3) link_ALPHA1-6 : angle 1.39317 / 0.97 ( 9) link_BETA1-4 : bond 0.00403 / 0.24 ( 32) link_BETA1-4 : angle 1.22060 / 0.88 ( 96) link_NAG-ASN : bond 0.00272 / 0.17 ( 65) link_NAG-ASN : angle 1.63843 / 1.17 ( 195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8580 (tm-30) REVERT: C 104 MET cc_start: 0.8823 (ttp) cc_final: 0.8506 (ttp) REVERT: C 150 MET cc_start: 0.7184 (mpp) cc_final: 0.6663 (mpp) REVERT: D 536 THR cc_start: 0.8590 (m) cc_final: 0.7943 (t) REVERT: D 647 GLU cc_start: 0.9051 (pp20) cc_final: 0.8789 (pp20) REVERT: D 654 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7822 (tm-30) REVERT: E 85 HIS cc_start: 0.7828 (m90) cc_final: 0.7617 (m-70) REVERT: E 95 MET cc_start: 0.9342 (ptm) cc_final: 0.8413 (ppp) REVERT: E 104 MET cc_start: 0.8926 (tpp) cc_final: 0.8695 (mmm) REVERT: E 210 PHE cc_start: 0.8514 (m-80) cc_final: 0.8078 (m-10) REVERT: E 217 TYR cc_start: 0.8751 (m-80) cc_final: 0.8277 (m-10) REVERT: E 381 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8252 (mt-10) REVERT: E 382 PHE cc_start: 0.8914 (m-80) cc_final: 0.8681 (m-80) REVERT: F 535 MET cc_start: 0.8447 (tmm) cc_final: 0.8198 (tmm) REVERT: F 568 ASP cc_start: 0.7484 (t0) cc_final: 0.6790 (t0) REVERT: F 655 LYS cc_start: 0.8743 (pttm) cc_final: 0.8390 (pttp) REVERT: F 657 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8403 (tm-30) REVERT: A 122 LEU cc_start: 0.9235 (mt) cc_final: 0.8926 (mm) REVERT: A 256 SER cc_start: 0.8875 (p) cc_final: 0.8602 (t) REVERT: A 356 ASN cc_start: 0.7595 (p0) cc_final: 0.7096 (m-40) REVERT: A 382 PHE cc_start: 0.9007 (m-80) cc_final: 0.8602 (m-10) REVERT: B 577 GLN cc_start: 0.8992 (tm-30) cc_final: 0.8722 (tm-30) REVERT: B 599 SER cc_start: 0.9494 (t) cc_final: 0.9189 (p) REVERT: B 626 MET cc_start: 0.7696 (mpp) cc_final: 0.7352 (mpp) REVERT: B 646 LEU cc_start: 0.9456 (mt) cc_final: 0.9089 (mt) REVERT: B 649 SER cc_start: 0.9089 (t) cc_final: 0.8867 (p) REVERT: B 654 GLU cc_start: 0.9152 (tt0) cc_final: 0.8616 (tm-30) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.1240 time to fit residues: 42.3782 Evaluate side-chains 175 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 179 optimal weight: 40.0000 chunk 178 optimal weight: 30.0000 chunk 102 optimal weight: 0.9990 chunk 148 optimal weight: 0.4980 chunk 118 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 HIS D 577 GLN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN A 85 HIS B 625 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.068128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.054470 restraints weight = 74127.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.055893 restraints weight = 46003.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.056850 restraints weight = 33489.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.057452 restraints weight = 27278.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.057452 restraints weight = 23827.106| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16468 Z= 0.174 Angle : 0.659 8.677 22589 Z= 0.323 Chirality : 0.044 0.220 2856 Planarity : 0.003 0.035 2707 Dihedral : 4.675 30.044 2020 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.30 (0.21), residues: 1673 helix: 1.24 (0.26), residues: 429 sheet: 0.14 (0.22), residues: 481 loop : -0.27 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 542 TYR 0.030 0.002 TYR E 217 PHE 0.026 0.002 PHE B 522 TRP 0.043 0.002 TRP E 479 HIS 0.004 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (16329) covalent geometry : angle 0.63262 / 0.32 (22208) SS BOND : bond 0.00408 / 0.22 ( 36) SS BOND : angle 1.38326 / 0.88 ( 72) hydrogen bonds : bond 0.04329 / 2.95 ( 588) hydrogen bonds : angle 5.44806 / 3.74 ( 1599) link_ALPHA1-3 : bond 0.00549 / 0.27 ( 3) link_ALPHA1-3 : angle 2.87315 / 2.65 ( 9) link_ALPHA1-6 : bond 0.00380 / 0.19 ( 3) link_ALPHA1-6 : angle 1.42176 / 1.01 ( 9) link_BETA1-4 : bond 0.00381 / 0.23 ( 32) link_BETA1-4 : angle 1.23641 / 0.89 ( 96) link_NAG-ASN : bond 0.00271 / 0.18 ( 65) link_NAG-ASN : angle 1.67658 / 1.20 ( 195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.8851 (ttp) cc_final: 0.8497 (ttp) REVERT: C 150 MET cc_start: 0.7197 (mpp) cc_final: 0.6655 (mpp) REVERT: C 195 ASN cc_start: 0.8279 (t0) cc_final: 0.8006 (t0) REVERT: D 535 MET cc_start: 0.6852 (mmm) cc_final: 0.6500 (mmp) REVERT: D 536 THR cc_start: 0.8569 (m) cc_final: 0.7929 (t) REVERT: D 584 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7977 (tm-30) REVERT: D 647 GLU cc_start: 0.9050 (pp20) cc_final: 0.8774 (pp20) REVERT: D 654 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7895 (tm-30) REVERT: E 85 HIS cc_start: 0.7905 (m90) cc_final: 0.7695 (m-70) REVERT: E 95 MET cc_start: 0.9377 (ptm) cc_final: 0.8402 (ppp) REVERT: E 210 PHE cc_start: 0.8529 (m-80) cc_final: 0.8101 (m-10) REVERT: E 217 TYR cc_start: 0.8667 (m-80) cc_final: 0.8179 (m-80) REVERT: E 381 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8389 (mt-10) REVERT: E 382 PHE cc_start: 0.8930 (m-80) cc_final: 0.8687 (m-80) REVERT: F 535 MET cc_start: 0.8615 (tmm) cc_final: 0.8374 (tmm) REVERT: F 568 ASP cc_start: 0.7529 (t0) cc_final: 0.6772 (t0) REVERT: F 654 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8724 (tm-30) REVERT: F 655 LYS cc_start: 0.8702 (pttm) cc_final: 0.8323 (pttp) REVERT: A 109 ILE cc_start: 0.9399 (mt) cc_final: 0.8988 (tt) REVERT: A 122 LEU cc_start: 0.9258 (mt) cc_final: 0.8950 (mm) REVERT: A 256 SER cc_start: 0.8877 (p) cc_final: 0.8604 (t) REVERT: A 382 PHE cc_start: 0.9063 (m-80) cc_final: 0.8508 (m-10) REVERT: B 584 GLU cc_start: 0.8707 (pm20) cc_final: 0.8278 (pm20) REVERT: B 599 SER cc_start: 0.9487 (t) cc_final: 0.9181 (p) REVERT: B 646 LEU cc_start: 0.9471 (mt) cc_final: 0.9196 (mt) REVERT: B 649 SER cc_start: 0.9125 (t) cc_final: 0.8881 (p) REVERT: B 654 GLU cc_start: 0.9168 (tt0) cc_final: 0.8629 (tm-30) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1241 time to fit residues: 41.2690 Evaluate side-chains 168 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 72 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 180 optimal weight: 40.0000 chunk 146 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 172 optimal weight: 20.0000 chunk 158 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 72 HIS C 85 HIS D 577 GLN D 658 GLN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 590 GLN F 651 ASN A 85 HIS ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.067020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.053767 restraints weight = 74361.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.055072 restraints weight = 46726.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.055927 restraints weight = 34453.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.056497 restraints weight = 28385.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.056960 restraints weight = 24945.374| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 16468 Z= 0.266 Angle : 0.773 8.642 22589 Z= 0.379 Chirality : 0.047 0.230 2856 Planarity : 0.004 0.047 2707 Dihedral : 4.985 33.032 2020 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.35 % Rotamer: Outliers : 0.07 % Allowed : 0.20 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.20), residues: 1673 helix: 0.77 (0.25), residues: 430 sheet: -0.16 (0.23), residues: 450 loop : -0.51 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 480 TYR 0.044 0.002 TYR F 643 PHE 0.026 0.002 PHE E 53 TRP 0.039 0.003 TRP E 479 HIS 0.007 0.002 HIS F 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.27 (16329) covalent geometry : angle 0.74553 / 0.37 (22208) SS BOND : bond 0.00493 / 0.29 ( 36) SS BOND : angle 1.50249 / 0.98 ( 72) hydrogen bonds : bond 0.04822 / 3.30 ( 588) hydrogen bonds : angle 5.79151 / 3.99 ( 1599) link_ALPHA1-3 : bond 0.00659 / 0.33 ( 3) link_ALPHA1-3 : angle 2.85792 / 2.57 ( 9) link_ALPHA1-6 : bond 0.00302 / 0.15 ( 3) link_ALPHA1-6 : angle 1.49136 / 1.08 ( 9) link_BETA1-4 : bond 0.00450 / 0.27 ( 32) link_BETA1-4 : angle 1.37945 / 1.00 ( 96) link_NAG-ASN : bond 0.00354 / 0.23 ( 65) link_NAG-ASN : angle 1.90851 / 1.37 ( 195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 GLN cc_start: 0.8400 (tm-30) cc_final: 0.7985 (tm-30) REVERT: C 104 MET cc_start: 0.9038 (ttp) cc_final: 0.8663 (ttp) REVERT: C 195 ASN cc_start: 0.8529 (t0) cc_final: 0.8281 (t0) REVERT: C 217 TYR cc_start: 0.8216 (m-10) cc_final: 0.7983 (m-10) REVERT: D 535 MET cc_start: 0.6958 (mmm) cc_final: 0.6571 (mmp) REVERT: D 536 THR cc_start: 0.8568 (m) cc_final: 0.7976 (t) REVERT: D 654 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8254 (tm-30) REVERT: E 85 HIS cc_start: 0.7975 (m90) cc_final: 0.7771 (m90) REVERT: E 95 MET cc_start: 0.9357 (ptm) cc_final: 0.9002 (ppp) REVERT: E 104 MET cc_start: 0.8899 (mmm) cc_final: 0.8618 (tpp) REVERT: E 210 PHE cc_start: 0.8635 (m-80) cc_final: 0.8229 (m-10) REVERT: E 217 TYR cc_start: 0.8596 (m-80) cc_final: 0.8102 (m-80) REVERT: E 381 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8425 (mt-10) REVERT: F 535 MET cc_start: 0.8643 (tmm) cc_final: 0.8419 (tmm) REVERT: F 536 THR cc_start: 0.9436 (p) cc_final: 0.9201 (p) REVERT: A 95 MET cc_start: 0.9188 (ptt) cc_final: 0.8783 (ppp) REVERT: A 109 ILE cc_start: 0.9411 (mt) cc_final: 0.9056 (tt) REVERT: A 122 LEU cc_start: 0.9227 (mt) cc_final: 0.8931 (mm) REVERT: A 382 PHE cc_start: 0.8984 (m-80) cc_final: 0.8508 (m-10) REVERT: B 568 ASP cc_start: 0.7527 (t0) cc_final: 0.6836 (t0) REVERT: B 584 GLU cc_start: 0.8651 (pm20) cc_final: 0.8219 (pm20) REVERT: B 599 SER cc_start: 0.9494 (t) cc_final: 0.9283 (t) REVERT: B 626 MET cc_start: 0.7438 (mpp) cc_final: 0.6888 (mpp) REVERT: B 654 GLU cc_start: 0.9066 (tt0) cc_final: 0.8846 (tm-30) outliers start: 1 outliers final: 0 residues processed: 199 average time/residue: 0.1264 time to fit residues: 38.3013 Evaluate side-chains 145 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 86 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 HIS ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN A 85 HIS ** A 300 ASN ** 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 = 0.3247 r_free = 0.3247 target = 0.066763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.053306 restraints weight = 74014.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.054678 restraints weight = 46352.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.055601 restraints weight = 34035.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.056205 restraints weight = 27746.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.056616 restraints weight = 24363.332| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.5816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16468 Z= 0.216 Angle : 0.722 8.555 22589 Z= 0.353 Chirality : 0.046 0.225 2856 Planarity : 0.004 0.051 2707 Dihedral : 4.947 32.052 2020 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.53 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.28 (0.20), residues: 1673 helix: 0.69 (0.25), residues: 430 sheet: -0.20 (0.23), residues: 450 loop : -0.56 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 542 TYR 0.021 0.002 TYR C 217 PHE 0.022 0.002 PHE E 53 TRP 0.031 0.002 TRP F 628 HIS 0.004 0.001 HIS D 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 (16329) covalent geometry : angle 0.69537 / 0.35 (22208) SS BOND : bond 0.00435 / 0.25 ( 36) SS BOND : angle 1.39667 / 0.93 ( 72) hydrogen bonds : bond 0.04684 / 3.17 ( 588) hydrogen bonds : angle 5.72568 / 3.94 ( 1599) link_ALPHA1-3 : bond 0.00536 / 0.27 ( 3) link_ALPHA1-3 : angle 2.81907 / 2.56 ( 9) link_ALPHA1-6 : bond 0.00328 / 0.16 ( 3) link_ALPHA1-6 : angle 1.43982 / 1.03 ( 9) link_BETA1-4 : bond 0.00413 / 0.25 ( 32) link_BETA1-4 : angle 1.29928 / 0.94 ( 96) link_NAG-ASN : bond 0.00282 / 0.19 ( 65) link_NAG-ASN : angle 1.81054 / 1.30 ( 195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2327.42 seconds wall clock time: 41 minutes 20.54 seconds (2480.54 seconds total)