Starting phenix.real_space_refine on Sun Aug 24 00:32:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l8b_23228/08_2025/7l8b_23228.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8b_23228/08_2025/7l8b_23228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l8b_23228/08_2025/7l8b_23228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8b_23228/08_2025/7l8b_23228.map" model { file = "/net/cci-nas-00/data/ceres_data/7l8b_23228/08_2025/7l8b_23228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8b_23228/08_2025/7l8b_23228.cif" } resolution = 3.7 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= 0.004 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 99 5.16 5 C 9776 2.51 5 N 2634 2.21 5 O 3195 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15704 Number of models: 1 Model: "" Number of chains: 42 Chain: "C" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Chain: "D" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "A" Number of atoms: 3463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3463 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "B" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "E" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3424 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 4 Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "H" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 590 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'TRANS': 117} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 118 Planarities with less than four sites: {'UNK:plan-1': 118} Unresolved non-hydrogen planarities: 118 Chain: "L" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 540 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'TRANS': 107} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 108 Planarities with less than four sites: {'UNK:plan-1': 108} Unresolved non-hydrogen planarities: 108 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "F" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.20, per 1000 atoms: 0.20 Number of scatterers: 15704 At special positions: 0 Unit cell: (141.11, 125.66, 120.51, 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 99 16.00 O 3195 8.00 N 2634 7.00 C 9776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.05 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.06 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=2.02 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 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 J 3 " - " MAN J 4 " " BMA U 3 " - " MAN U 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA J 3 " - " MAN J 5 " " BMA U 3 " - " MAN U 5 " " BMA e 3 " - " MAN e 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " 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 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 160 " " NAG A 602 " - " ASN A 301 " " NAG A 603 " - " ASN A 339 " " NAG A 604 " - " ASN A 448 " " NAG A 605 " - " ASN A 137 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 160 " " NAG C 603 " - " ASN C 234 " " NAG C 604 " - " ASN C 295 " " NAG C 605 " - " ASN C 339 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 88 " " NAG C 608 " - " ASN C 137 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 301 " " NAG E 604 " - " ASN E 339 " " NAG E 605 " - " ASN E 392 " " NAG E 606 " - " ASN E 88 " " NAG E 607 " - " ASN E 137 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 1 " - " ASN C 156 " " NAG I 1 " - " ASN C 197 " " NAG J 1 " - " ASN C 262 " " NAG K 1 " - " ASN C 276 " " NAG M 1 " - " ASN C 301 " " NAG N 1 " - " ASN C 332 " " NAG O 1 " - " ASN C 386 " " NAG P 1 " - " ASN C 448 " " NAG Q 1 " - " ASN A 133 " " NAG R 1 " - " ASN A 156 " " NAG S 1 " - " ASN A 197 " " NAG T 1 " - " ASN A 234 " " NAG U 1 " - " ASN A 262 " " NAG V 1 " - " ASN A 276 " " NAG W 1 " - " ASN A 295 " " NAG X 1 " - " ASN A 332 " " NAG Y 1 " - " ASN A 386 " " NAG Z 1 " - " ASN A 392 " " NAG a 1 " - " ASN A 88 " " NAG b 1 " - " ASN E 156 " " NAG c 1 " - " ASN E 197 " " NAG d 1 " - " ASN E 234 " " NAG e 1 " - " ASN E 262 " " NAG f 1 " - " ASN E 276 " " NAG g 1 " - " ASN E 295 " " NAG h 1 " - " ASN E 332 " " NAG i 1 " - " ASN E 386 " " NAG j 1 " - " ASN E 448 " Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 504.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3604 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 0 sheets defined 28.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.191A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.590A pdb=" N VAL C 127 " --> pdb=" O PRO C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.131A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.933A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.755A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 572 through 596 Processing helix chain 'D' and resid 618 through 625 removed outlier: 3.520A pdb=" N ASN D 625 " --> pdb=" O GLU D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 664 Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 354 removed outlier: 4.001A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.567A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 537 removed outlier: 3.533A pdb=" N LEU B 537 " --> pdb=" O SER B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 664 Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 94 through 98 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.173A 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 390 Processing helix chain 'E' and resid 475 through 483 removed outlier: 3.763A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 544 Processing helix chain 'F' and resid 570 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 664 Processing helix chain 'H' and resid 64 through 67 Processing helix chain 'L' and resid 30 through 34 301 hydrogen bonds defined for protein. 819 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: 1.71 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3634 1.32 - 1.46: 4954 1.46 - 1.60: 7236 1.60 - 1.74: 23 1.74 - 1.87: 126 Bond restraints: 15973 Sorted by residual: bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.408 -0.082 1.10e-02 8.26e+03 5.51e+01 bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.399 -0.073 1.10e-02 8.26e+03 4.39e+01 bond pdb=" NE ARG C 503 " pdb=" CZ ARG C 503 " ideal model delta sigma weight residual 1.326 1.395 -0.069 1.10e-02 8.26e+03 3.95e+01 bond pdb=" CG GLN B 540 " pdb=" CD GLN B 540 " ideal model delta sigma weight residual 1.516 1.361 0.155 2.50e-02 1.60e+03 3.83e+01 bond pdb=" CB ILE E 396 " pdb=" CG1 ILE E 396 " ideal model delta sigma weight residual 1.530 1.650 -0.120 2.00e-02 2.50e+03 3.60e+01 ... (remaining 15968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 20322 3.27 - 6.54: 1330 6.54 - 9.82: 73 9.82 - 13.09: 4 13.09 - 16.36: 3 Bond angle restraints: 21732 Sorted by residual: angle pdb=" N GLY C 471 " pdb=" CA GLY C 471 " pdb=" C GLY C 471 " ideal model delta sigma weight residual 110.38 94.02 16.36 1.48e+00 4.57e-01 1.22e+02 angle pdb=" N ILE A 396 " pdb=" CA ILE A 396 " pdb=" C ILE A 396 " ideal model delta sigma weight residual 112.43 120.46 -8.03 9.20e-01 1.18e+00 7.62e+01 angle pdb=" C CYS C 239 " pdb=" N PRO C 240 " pdb=" CA PRO C 240 " ideal model delta sigma weight residual 119.56 128.03 -8.47 1.02e+00 9.61e-01 6.89e+01 angle pdb=" N SER A 56 " pdb=" CA SER A 56 " pdb=" C SER A 56 " ideal model delta sigma weight residual 111.28 120.18 -8.90 1.09e+00 8.42e-01 6.67e+01 angle pdb=" C CYS E 205 " pdb=" N PRO E 206 " pdb=" CA PRO E 206 " ideal model delta sigma weight residual 119.56 127.32 -7.76 1.02e+00 9.61e-01 5.78e+01 ... (remaining 21727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.23: 10482 21.23 - 42.46: 230 42.46 - 63.70: 77 63.70 - 84.93: 28 84.93 - 106.16: 14 Dihedral angle restraints: 10831 sinusoidal: 5296 harmonic: 5535 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.71 -60.71 1 1.00e+01 1.00e-02 4.90e+01 dihedral pdb=" N ASP A 57 " pdb=" C ASP A 57 " pdb=" CA ASP A 57 " pdb=" CB ASP A 57 " ideal model delta harmonic sigma weight residual 122.80 140.18 -17.38 0 2.50e+00 1.60e-01 4.83e+01 dihedral pdb=" C ASP A 57 " pdb=" N ASP A 57 " pdb=" CA ASP A 57 " pdb=" CB ASP A 57 " ideal model delta harmonic sigma weight residual -122.60 -139.90 17.30 0 2.50e+00 1.60e-01 4.79e+01 ... (remaining 10828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.217: 2400 0.217 - 0.435: 343 0.435 - 0.652: 36 0.652 - 0.870: 1 0.870 - 1.087: 1 Chirality restraints: 2781 Sorted by residual: chirality pdb=" C1 NAG i 2 " pdb=" O4 NAG i 1 " pdb=" C2 NAG i 2 " pdb=" O5 NAG i 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.83e+02 chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.58e+02 chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.39e+02 ... (remaining 2778 not shown) Planarity restraints: 2719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 2 " 0.355 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG Z 2 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG Z 2 " 0.111 2.00e-02 2.50e+03 pdb=" N2 NAG Z 2 " -0.544 2.00e-02 2.50e+03 pdb=" O7 NAG Z 2 " 0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " -0.357 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG I 2 " 0.090 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " -0.162 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " 0.539 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " -0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 703 " -0.330 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG D 703 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG D 703 " -0.046 2.00e-02 2.50e+03 pdb=" N2 NAG D 703 " 0.502 2.00e-02 2.50e+03 pdb=" O7 NAG D 703 " -0.201 2.00e-02 2.50e+03 ... (remaining 2716 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.95: 2 1.95 - 2.69: 862 2.69 - 3.43: 20468 3.43 - 4.16: 37907 4.16 - 4.90: 61624 Nonbonded interactions: 120863 Sorted by model distance: nonbonded pdb=" OG SER E 393 " pdb=" CZ3 TRP E 395 " model vdw 1.218 3.340 nonbonded pdb=" OG SER E 393 " pdb=" CH2 TRP E 395 " model vdw 1.814 3.340 nonbonded pdb=" O3 NAG I 1 " pdb=" O7 NAG I 1 " model vdw 2.052 3.040 nonbonded pdb=" CB SER E 393 " pdb=" CZ3 TRP E 395 " model vdw 2.170 3.740 nonbonded pdb=" O ILE C 453 " pdb=" O GLY C 471 " model vdw 2.301 3.040 ... (remaining 120858 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 57 or resid 66 through 458 or resid 463 through \ 605)) selection = (chain 'C' and (resid 33 through 397 or resid 411 through 605)) selection = (chain 'E' and resid 33 through 605) } ncs_group { reference = (chain 'B' and resid 519 through 703) selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' 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' } ncs_group { reference = (chain 'H' and resid 12 through 119) selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'U' selection = chain 'e' } 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: 2.930 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 11.250 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 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 0.155 16100 Z= 1.225 Angle : 1.774 26.462 22080 Z= 1.104 Chirality : 0.149 1.087 2781 Planarity : 0.015 0.306 2662 Dihedral : 11.185 106.162 7128 Min Nonbonded Distance : 1.218 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.19), residues: 1642 helix: 0.71 (0.24), residues: 396 sheet: 1.35 (0.24), residues: 384 loop : 0.61 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 542 TYR 0.047 0.007 TYR B 638 PHE 0.029 0.006 PHE A 383 TRP 0.049 0.008 TRP A 96 HIS 0.008 0.002 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.02245 (15973) covalent geometry : angle 1.71861 (21732) SS BOND : bond 0.01014 ( 33) SS BOND : angle 2.69630 ( 66) hydrogen bonds : bond 0.19092 ( 301) hydrogen bonds : angle 5.98695 ( 819) link_ALPHA1-3 : bond 0.08908 ( 3) link_ALPHA1-3 : angle 4.46583 ( 9) link_ALPHA1-6 : bond 0.05623 ( 3) link_ALPHA1-6 : angle 3.46481 ( 9) link_BETA1-4 : bond 0.06944 ( 31) link_BETA1-4 : angle 4.56221 ( 93) link_NAG-ASN : bond 0.07659 ( 57) link_NAG-ASN : angle 3.89556 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 202 THR cc_start: 0.9412 (m) cc_final: 0.9132 (p) REVERT: D 602 LEU cc_start: 0.9090 (mt) cc_final: 0.8804 (mt) REVERT: D 603 ILE cc_start: 0.9380 (mt) cc_final: 0.9174 (mp) REVERT: D 616 ASN cc_start: 0.8682 (p0) cc_final: 0.8446 (p0) REVERT: D 653 GLN cc_start: 0.8226 (tt0) cc_final: 0.7977 (tm-30) REVERT: A 75 VAL cc_start: 0.8617 (t) cc_final: 0.8139 (m) REVERT: B 590 GLN cc_start: 0.9301 (mm-40) cc_final: 0.8939 (mm-40) REVERT: E 248 THR cc_start: 0.9502 (p) cc_final: 0.9255 (p) REVERT: F 536 THR cc_start: 0.9582 (p) cc_final: 0.9368 (p) REVERT: F 543 ASN cc_start: 0.8439 (m-40) cc_final: 0.8094 (m110) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.1082 time to fit residues: 66.8307 Evaluate side-chains 197 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 ASN A 114 GLN A 185 ASN A 203 GLN B 577 GLN E 33 ASN E 302 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.119760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.103345 restraints weight = 29194.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.106193 restraints weight = 16378.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.108103 restraints weight = 11066.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.109342 restraints weight = 8411.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.110258 restraints weight = 6944.216| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16100 Z= 0.165 Angle : 0.757 14.851 22080 Z= 0.360 Chirality : 0.048 0.366 2781 Planarity : 0.004 0.030 2662 Dihedral : 8.495 84.546 3956 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.27 % Allowed : 8.22 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.20), residues: 1642 helix: 2.03 (0.26), residues: 402 sheet: 0.80 (0.23), residues: 424 loop : 0.36 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 444 TYR 0.023 0.002 TYR A 217 PHE 0.017 0.002 PHE E 210 TRP 0.013 0.002 TRP D 571 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00365 (15973) covalent geometry : angle 0.69381 (21732) SS BOND : bond 0.00418 ( 33) SS BOND : angle 1.35815 ( 66) hydrogen bonds : bond 0.06851 ( 301) hydrogen bonds : angle 4.21558 ( 819) link_ALPHA1-3 : bond 0.01177 ( 3) link_ALPHA1-3 : angle 2.32579 ( 9) link_ALPHA1-6 : bond 0.00663 ( 3) link_ALPHA1-6 : angle 1.78596 ( 9) link_BETA1-4 : bond 0.00598 ( 31) link_BETA1-4 : angle 2.49338 ( 93) link_NAG-ASN : bond 0.00407 ( 57) link_NAG-ASN : angle 2.88265 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 259 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8956 (m-80) cc_final: 0.8676 (m-10) REVERT: C 202 THR cc_start: 0.9258 (m) cc_final: 0.8968 (p) REVERT: A 75 VAL cc_start: 0.8586 (t) cc_final: 0.8345 (m) REVERT: A 95 MET cc_start: 0.9038 (ptm) cc_final: 0.8831 (ptm) REVERT: B 625 ASN cc_start: 0.8350 (m110) cc_final: 0.8118 (m110) REVERT: F 536 THR cc_start: 0.9554 (p) cc_final: 0.9339 (p) REVERT: F 543 ASN cc_start: 0.8313 (m-40) cc_final: 0.7778 (m110) outliers start: 34 outliers final: 17 residues processed: 286 average time/residue: 0.1018 time to fit residues: 45.0491 Evaluate side-chains 213 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 450 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 108 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 145 optimal weight: 0.3980 chunk 131 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 156 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN D 652 GLN A 203 GLN A 289 ASN B 543 ASN E 411 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.118160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.101876 restraints weight = 29490.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.104663 restraints weight = 16588.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106549 restraints weight = 11260.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107834 restraints weight = 8570.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.108718 restraints weight = 7024.596| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16100 Z= 0.144 Angle : 0.649 13.932 22080 Z= 0.309 Chirality : 0.045 0.270 2781 Planarity : 0.003 0.040 2662 Dihedral : 7.683 78.707 3956 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.20 % Allowed : 11.16 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.20), residues: 1642 helix: 2.17 (0.26), residues: 402 sheet: 0.84 (0.23), residues: 442 loop : 0.28 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 617 TYR 0.015 0.001 TYR A 173 PHE 0.012 0.002 PHE C 353 TRP 0.018 0.001 TRP C 112 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00329 (15973) covalent geometry : angle 0.59813 (21732) SS BOND : bond 0.00516 ( 33) SS BOND : angle 1.24075 ( 66) hydrogen bonds : bond 0.05761 ( 301) hydrogen bonds : angle 3.91336 ( 819) link_ALPHA1-3 : bond 0.01227 ( 3) link_ALPHA1-3 : angle 1.33462 ( 9) link_ALPHA1-6 : bond 0.00902 ( 3) link_ALPHA1-6 : angle 1.85576 ( 9) link_BETA1-4 : bond 0.00627 ( 31) link_BETA1-4 : angle 1.95868 ( 93) link_NAG-ASN : bond 0.00398 ( 57) link_NAG-ASN : angle 2.45135 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 209 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.9016 (m-80) cc_final: 0.8673 (m-10) REVERT: C 202 THR cc_start: 0.9261 (m) cc_final: 0.8818 (p) REVERT: D 621 GLU cc_start: 0.8618 (tp30) cc_final: 0.8415 (tp30) REVERT: A 75 VAL cc_start: 0.8632 (t) cc_final: 0.8413 (m) REVERT: A 95 MET cc_start: 0.9014 (ptm) cc_final: 0.8738 (ptm) REVERT: A 161 MET cc_start: 0.8262 (tpt) cc_final: 0.7666 (tpt) REVERT: B 625 ASN cc_start: 0.8341 (m110) cc_final: 0.8112 (m110) REVERT: F 543 ASN cc_start: 0.8247 (m-40) cc_final: 0.7767 (m110) outliers start: 33 outliers final: 22 residues processed: 230 average time/residue: 0.1080 time to fit residues: 37.9654 Evaluate side-chains 212 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 620 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 167 optimal weight: 20.0000 chunk 81 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN D 591 GLN D 652 GLN A 289 ASN A 377 ASN B 543 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.117220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.100856 restraints weight = 29429.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103648 restraints weight = 16649.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105504 restraints weight = 11306.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106771 restraints weight = 8660.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.107651 restraints weight = 7139.027| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16100 Z= 0.132 Angle : 0.587 12.847 22080 Z= 0.278 Chirality : 0.044 0.260 2781 Planarity : 0.003 0.027 2662 Dihedral : 6.775 69.304 3956 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.40 % Allowed : 11.16 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.20), residues: 1642 helix: 2.30 (0.26), residues: 402 sheet: 0.89 (0.24), residues: 430 loop : 0.08 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 298 TYR 0.010 0.001 TYR A 173 PHE 0.012 0.002 PHE A 176 TRP 0.010 0.001 TRP A 96 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00303 (15973) covalent geometry : angle 0.54344 (21732) SS BOND : bond 0.00495 ( 33) SS BOND : angle 0.95796 ( 66) hydrogen bonds : bond 0.04868 ( 301) hydrogen bonds : angle 3.66711 ( 819) link_ALPHA1-3 : bond 0.01262 ( 3) link_ALPHA1-3 : angle 1.68371 ( 9) link_ALPHA1-6 : bond 0.00964 ( 3) link_ALPHA1-6 : angle 1.96846 ( 9) link_BETA1-4 : bond 0.00525 ( 31) link_BETA1-4 : angle 1.62878 ( 93) link_NAG-ASN : bond 0.00299 ( 57) link_NAG-ASN : angle 2.19425 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.9036 (m-80) cc_final: 0.8683 (m-10) REVERT: C 202 THR cc_start: 0.9246 (m) cc_final: 0.8782 (p) REVERT: D 650 GLN cc_start: 0.8850 (tp40) cc_final: 0.8440 (tp40) REVERT: D 657 GLU cc_start: 0.8190 (tt0) cc_final: 0.7971 (tt0) REVERT: A 75 VAL cc_start: 0.8711 (t) cc_final: 0.8483 (m) REVERT: A 95 MET cc_start: 0.9030 (ptm) cc_final: 0.8756 (ptm) REVERT: A 112 TRP cc_start: 0.8982 (t-100) cc_final: 0.8645 (t-100) REVERT: A 161 MET cc_start: 0.8311 (tpt) cc_final: 0.7894 (tpt) REVERT: B 625 ASN cc_start: 0.8315 (m110) cc_final: 0.8059 (m110) REVERT: E 46 LYS cc_start: 0.8254 (mtmt) cc_final: 0.7598 (pttt) REVERT: E 111 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8931 (mp) REVERT: E 492 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7328 (mt-10) REVERT: F 543 ASN cc_start: 0.8190 (m-40) cc_final: 0.7681 (m110) outliers start: 36 outliers final: 24 residues processed: 236 average time/residue: 0.1016 time to fit residues: 36.7534 Evaluate side-chains 211 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 620 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 8 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 GLN A 289 ASN A 377 ASN B 543 ASN B 577 GLN E 72 HIS E 302 ASN E 377 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.099006 restraints weight = 29530.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101729 restraints weight = 16777.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103594 restraints weight = 11493.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104841 restraints weight = 8793.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.105698 restraints weight = 7278.065| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16100 Z= 0.165 Angle : 0.606 12.170 22080 Z= 0.285 Chirality : 0.044 0.279 2781 Planarity : 0.003 0.030 2662 Dihedral : 6.523 64.211 3956 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.01 % Allowed : 11.69 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.20), residues: 1642 helix: 2.37 (0.26), residues: 402 sheet: 0.99 (0.25), residues: 392 loop : -0.15 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 360 TYR 0.020 0.001 TYR C 484 PHE 0.014 0.002 PHE A 176 TRP 0.013 0.001 TRP A 35 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00390 (15973) covalent geometry : angle 0.56530 (21732) SS BOND : bond 0.00442 ( 33) SS BOND : angle 0.95165 ( 66) hydrogen bonds : bond 0.04918 ( 301) hydrogen bonds : angle 3.59940 ( 819) link_ALPHA1-3 : bond 0.01263 ( 3) link_ALPHA1-3 : angle 1.58319 ( 9) link_ALPHA1-6 : bond 0.00916 ( 3) link_ALPHA1-6 : angle 1.93401 ( 9) link_BETA1-4 : bond 0.00505 ( 31) link_BETA1-4 : angle 1.56875 ( 93) link_NAG-ASN : bond 0.00259 ( 57) link_NAG-ASN : angle 2.19424 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.9081 (m-80) cc_final: 0.8741 (m-10) REVERT: C 202 THR cc_start: 0.9294 (m) cc_final: 0.8836 (p) REVERT: D 657 GLU cc_start: 0.8197 (tt0) cc_final: 0.7960 (tt0) REVERT: A 75 VAL cc_start: 0.8717 (t) cc_final: 0.8462 (m) REVERT: A 95 MET cc_start: 0.9026 (ptm) cc_final: 0.8822 (ptm) REVERT: A 112 TRP cc_start: 0.8977 (t-100) cc_final: 0.8664 (t-100) REVERT: A 161 MET cc_start: 0.8331 (tpt) cc_final: 0.7954 (tpt) REVERT: B 625 ASN cc_start: 0.8332 (m110) cc_final: 0.8044 (m110) REVERT: E 46 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7430 (mtmt) REVERT: E 302 ASN cc_start: 0.9028 (OUTLIER) cc_final: 0.8634 (p0) REVERT: E 368 ASP cc_start: 0.6877 (p0) cc_final: 0.6528 (p0) REVERT: E 492 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7461 (mt-10) REVERT: F 543 ASN cc_start: 0.8107 (m-40) cc_final: 0.7786 (m110) outliers start: 45 outliers final: 34 residues processed: 226 average time/residue: 0.1045 time to fit residues: 35.8486 Evaluate side-chains 222 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 641 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 56 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 175 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN A 377 ASN B 543 ASN B 577 GLN E 302 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.113400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.097651 restraints weight = 29573.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.100108 restraints weight = 17603.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.101775 restraints weight = 12379.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.102900 restraints weight = 9663.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.103665 restraints weight = 8115.724| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16100 Z= 0.191 Angle : 0.623 10.354 22080 Z= 0.293 Chirality : 0.045 0.286 2781 Planarity : 0.003 0.031 2662 Dihedral : 6.537 60.865 3956 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.27 % Allowed : 11.82 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.20), residues: 1642 helix: 2.27 (0.26), residues: 402 sheet: 0.86 (0.26), residues: 372 loop : -0.26 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 298 TYR 0.018 0.001 TYR C 484 PHE 0.014 0.002 PHE A 176 TRP 0.012 0.001 TRP A 35 HIS 0.005 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00453 (15973) covalent geometry : angle 0.58095 (21732) SS BOND : bond 0.00459 ( 33) SS BOND : angle 0.92022 ( 66) hydrogen bonds : bond 0.05032 ( 301) hydrogen bonds : angle 3.63189 ( 819) link_ALPHA1-3 : bond 0.01261 ( 3) link_ALPHA1-3 : angle 1.60823 ( 9) link_ALPHA1-6 : bond 0.00854 ( 3) link_ALPHA1-6 : angle 1.90963 ( 9) link_BETA1-4 : bond 0.00504 ( 31) link_BETA1-4 : angle 1.57474 ( 93) link_NAG-ASN : bond 0.00274 ( 57) link_NAG-ASN : angle 2.27415 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.9119 (m-80) cc_final: 0.8781 (m-10) REVERT: D 657 GLU cc_start: 0.8251 (tt0) cc_final: 0.8033 (tt0) REVERT: A 75 VAL cc_start: 0.8721 (t) cc_final: 0.8453 (m) REVERT: A 95 MET cc_start: 0.9058 (ptm) cc_final: 0.8838 (ptm) REVERT: A 161 MET cc_start: 0.8371 (tpt) cc_final: 0.7996 (tpt) REVERT: B 625 ASN cc_start: 0.8263 (m110) cc_final: 0.8017 (m-40) REVERT: E 46 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7429 (mtmt) REVERT: E 443 ILE cc_start: 0.9675 (mm) cc_final: 0.9414 (mp) REVERT: E 492 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7410 (mt-10) outliers start: 49 outliers final: 39 residues processed: 224 average time/residue: 0.1016 time to fit residues: 34.5260 Evaluate side-chains 221 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 641 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 43 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 184 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 652 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN B 543 ASN B 577 GLN E 302 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.111973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.095627 restraints weight = 29710.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098275 restraints weight = 16951.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.100053 restraints weight = 11640.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.101234 restraints weight = 8970.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.102064 restraints weight = 7459.871| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16100 Z= 0.238 Angle : 0.679 9.170 22080 Z= 0.320 Chirality : 0.047 0.275 2781 Planarity : 0.003 0.033 2662 Dihedral : 6.758 58.572 3956 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.27 % Allowed : 12.36 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.20), residues: 1642 helix: 2.13 (0.26), residues: 402 sheet: 0.72 (0.27), residues: 360 loop : -0.43 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 350 TYR 0.018 0.002 TYR C 484 PHE 0.017 0.002 PHE A 176 TRP 0.014 0.001 TRP A 112 HIS 0.006 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00564 (15973) covalent geometry : angle 0.63852 (21732) SS BOND : bond 0.00525 ( 33) SS BOND : angle 0.96942 ( 66) hydrogen bonds : bond 0.05365 ( 301) hydrogen bonds : angle 3.74811 ( 819) link_ALPHA1-3 : bond 0.01259 ( 3) link_ALPHA1-3 : angle 1.51696 ( 9) link_ALPHA1-6 : bond 0.00870 ( 3) link_ALPHA1-6 : angle 1.90848 ( 9) link_BETA1-4 : bond 0.00500 ( 31) link_BETA1-4 : angle 1.62578 ( 93) link_NAG-ASN : bond 0.00303 ( 57) link_NAG-ASN : angle 2.36236 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 189 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.9167 (m-80) cc_final: 0.8875 (m-10) REVERT: C 247 CYS cc_start: 0.6036 (m) cc_final: 0.5747 (m) REVERT: D 657 GLU cc_start: 0.8230 (tt0) cc_final: 0.8014 (tt0) REVERT: A 75 VAL cc_start: 0.8698 (t) cc_final: 0.8428 (m) REVERT: A 95 MET cc_start: 0.9056 (ptm) cc_final: 0.8831 (ptm) REVERT: A 161 MET cc_start: 0.8478 (tpt) cc_final: 0.8097 (tpt) REVERT: E 46 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7344 (mtmt) REVERT: E 443 ILE cc_start: 0.9643 (mm) cc_final: 0.9400 (mp) REVERT: E 492 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7491 (mt-10) outliers start: 49 outliers final: 38 residues processed: 224 average time/residue: 0.1066 time to fit residues: 36.2650 Evaluate side-chains 219 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 641 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 128 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 185 optimal weight: 20.0000 chunk 152 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN A 66 HIS A 289 ASN B 543 ASN B 577 GLN E 302 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.115182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.099137 restraints weight = 29431.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.101845 restraints weight = 16484.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103671 restraints weight = 11160.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.104912 restraints weight = 8484.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.105769 restraints weight = 6965.866| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16100 Z= 0.110 Angle : 0.566 9.282 22080 Z= 0.268 Chirality : 0.043 0.273 2781 Planarity : 0.003 0.028 2662 Dihedral : 6.123 56.070 3956 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.94 % Allowed : 13.76 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.21), residues: 1642 helix: 2.33 (0.27), residues: 408 sheet: 0.68 (0.26), residues: 368 loop : -0.35 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 617 TYR 0.015 0.001 TYR C 484 PHE 0.009 0.001 PHE C 53 TRP 0.015 0.001 TRP A 35 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00247 (15973) covalent geometry : angle 0.52681 (21732) SS BOND : bond 0.00449 ( 33) SS BOND : angle 0.81425 ( 66) hydrogen bonds : bond 0.04589 ( 301) hydrogen bonds : angle 3.51086 ( 819) link_ALPHA1-3 : bond 0.01202 ( 3) link_ALPHA1-3 : angle 1.68167 ( 9) link_ALPHA1-6 : bond 0.00885 ( 3) link_ALPHA1-6 : angle 1.50808 ( 9) link_BETA1-4 : bond 0.00510 ( 31) link_BETA1-4 : angle 1.49616 ( 93) link_NAG-ASN : bond 0.00277 ( 57) link_NAG-ASN : angle 2.08156 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.9121 (m-80) cc_final: 0.8829 (m-10) REVERT: C 269 GLU cc_start: 0.7506 (tp30) cc_final: 0.6917 (tp30) REVERT: D 650 GLN cc_start: 0.8756 (tp40) cc_final: 0.8290 (tp40) REVERT: A 75 VAL cc_start: 0.8707 (t) cc_final: 0.8430 (m) REVERT: A 95 MET cc_start: 0.9035 (ptm) cc_final: 0.8804 (ptm) REVERT: A 161 MET cc_start: 0.8476 (tpt) cc_final: 0.8094 (tpt) REVERT: B 633 LYS cc_start: 0.8918 (mttp) cc_final: 0.8609 (mptt) REVERT: E 46 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7376 (mtmt) REVERT: E 492 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7431 (mt-10) outliers start: 29 outliers final: 21 residues processed: 229 average time/residue: 0.1064 time to fit residues: 37.4031 Evaluate side-chains 216 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 613 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 151 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 184 optimal weight: 20.0000 chunk 30 optimal weight: 0.7980 chunk 177 optimal weight: 20.0000 chunk 99 optimal weight: 0.0970 chunk 12 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN A 289 ASN B 543 ASN B 577 GLN E 302 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.098435 restraints weight = 29730.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.101148 restraints weight = 16747.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.102931 restraints weight = 11349.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104176 restraints weight = 8677.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105022 restraints weight = 7140.367| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16100 Z= 0.140 Angle : 0.584 8.266 22080 Z= 0.276 Chirality : 0.044 0.255 2781 Planarity : 0.003 0.029 2662 Dihedral : 6.029 59.250 3956 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.94 % Allowed : 13.89 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.21), residues: 1642 helix: 2.31 (0.26), residues: 408 sheet: 0.80 (0.27), residues: 357 loop : -0.37 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 617 TYR 0.016 0.001 TYR C 484 PHE 0.011 0.001 PHE A 176 TRP 0.016 0.001 TRP A 35 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00329 (15973) covalent geometry : angle 0.54564 (21732) SS BOND : bond 0.00393 ( 33) SS BOND : angle 0.86658 ( 66) hydrogen bonds : bond 0.04640 ( 301) hydrogen bonds : angle 3.60460 ( 819) link_ALPHA1-3 : bond 0.01134 ( 3) link_ALPHA1-3 : angle 1.55859 ( 9) link_ALPHA1-6 : bond 0.00754 ( 3) link_ALPHA1-6 : angle 1.37184 ( 9) link_BETA1-4 : bond 0.00516 ( 31) link_BETA1-4 : angle 1.51241 ( 93) link_NAG-ASN : bond 0.00271 ( 57) link_NAG-ASN : angle 2.10780 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.9136 (m-80) cc_final: 0.8828 (m-10) REVERT: A 75 VAL cc_start: 0.8696 (t) cc_final: 0.8426 (m) REVERT: A 95 MET cc_start: 0.9041 (ptm) cc_final: 0.8802 (ptm) REVERT: A 161 MET cc_start: 0.8463 (tpt) cc_final: 0.8026 (tpt) REVERT: B 590 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8766 (mm-40) REVERT: B 633 LYS cc_start: 0.8904 (mttp) cc_final: 0.8604 (mptt) REVERT: E 46 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7309 (mtmt) REVERT: E 492 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7419 (mt-10) REVERT: F 543 ASN cc_start: 0.8282 (m-40) cc_final: 0.7999 (m-40) outliers start: 29 outliers final: 26 residues processed: 210 average time/residue: 0.0996 time to fit residues: 31.8425 Evaluate side-chains 213 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 100 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 16 optimal weight: 0.0670 chunk 90 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.0370 chunk 24 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 577 GLN E 302 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.116795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.100713 restraints weight = 29229.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103442 restraints weight = 16384.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105248 restraints weight = 11113.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.106512 restraints weight = 8490.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.107371 restraints weight = 6975.378| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16100 Z= 0.101 Angle : 0.547 8.027 22080 Z= 0.261 Chirality : 0.042 0.261 2781 Planarity : 0.003 0.027 2662 Dihedral : 5.340 55.407 3956 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.34 % Allowed : 14.63 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.21), residues: 1642 helix: 2.33 (0.27), residues: 412 sheet: 0.96 (0.27), residues: 356 loop : -0.32 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 617 TYR 0.015 0.001 TYR C 484 PHE 0.009 0.001 PHE C 53 TRP 0.019 0.001 TRP A 35 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00224 (15973) covalent geometry : angle 0.51080 (21732) SS BOND : bond 0.00346 ( 33) SS BOND : angle 0.78610 ( 66) hydrogen bonds : bond 0.04196 ( 301) hydrogen bonds : angle 3.51717 ( 819) link_ALPHA1-3 : bond 0.01110 ( 3) link_ALPHA1-3 : angle 1.51706 ( 9) link_ALPHA1-6 : bond 0.00871 ( 3) link_ALPHA1-6 : angle 1.50818 ( 9) link_BETA1-4 : bond 0.00522 ( 31) link_BETA1-4 : angle 1.44927 ( 93) link_NAG-ASN : bond 0.00289 ( 57) link_NAG-ASN : angle 1.95126 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.9111 (m-80) cc_final: 0.8816 (m-10) REVERT: D 650 GLN cc_start: 0.8685 (tp40) cc_final: 0.8265 (tp40) REVERT: A 75 VAL cc_start: 0.8733 (t) cc_final: 0.8464 (m) REVERT: A 95 MET cc_start: 0.9034 (ptm) cc_final: 0.8808 (ptm) REVERT: A 99 ASN cc_start: 0.8092 (t0) cc_final: 0.7700 (t0) REVERT: B 590 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8777 (mm-40) REVERT: B 633 LYS cc_start: 0.8878 (mttp) cc_final: 0.8568 (mptt) REVERT: E 46 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7640 (pttt) REVERT: F 543 ASN cc_start: 0.8210 (m-40) cc_final: 0.7913 (m-40) outliers start: 20 outliers final: 15 residues processed: 217 average time/residue: 0.1107 time to fit residues: 36.4991 Evaluate side-chains 205 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 613 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 149 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 170 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 30 optimal weight: 0.0000 chunk 159 optimal weight: 0.0980 chunk 88 optimal weight: 4.9990 overall best weight: 2.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN E 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.113718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.097593 restraints weight = 29392.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.100257 restraints weight = 16759.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.102026 restraints weight = 11450.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.103231 restraints weight = 8809.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.104045 restraints weight = 7283.940| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16100 Z= 0.179 Angle : 0.611 7.845 22080 Z= 0.289 Chirality : 0.044 0.236 2781 Planarity : 0.004 0.072 2662 Dihedral : 5.589 56.754 3956 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.67 % Allowed : 14.76 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.21), residues: 1642 helix: 2.27 (0.27), residues: 408 sheet: 0.90 (0.27), residues: 354 loop : -0.47 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 617 TYR 0.022 0.002 TYR A 486 PHE 0.013 0.002 PHE A 176 TRP 0.019 0.001 TRP A 35 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00425 (15973) covalent geometry : angle 0.57501 (21732) SS BOND : bond 0.00418 ( 33) SS BOND : angle 0.85055 ( 66) hydrogen bonds : bond 0.04797 ( 301) hydrogen bonds : angle 3.67252 ( 819) link_ALPHA1-3 : bond 0.01011 ( 3) link_ALPHA1-3 : angle 1.32473 ( 9) link_ALPHA1-6 : bond 0.00736 ( 3) link_ALPHA1-6 : angle 1.46917 ( 9) link_BETA1-4 : bond 0.00514 ( 31) link_BETA1-4 : angle 1.52202 ( 93) link_NAG-ASN : bond 0.00268 ( 57) link_NAG-ASN : angle 2.09370 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2029.98 seconds wall clock time: 36 minutes 3.72 seconds (2163.72 seconds total)