Starting phenix.real_space_refine on Fri Jul 3 19:08:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l8b_23228/07_2026/7l8b_23228.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8b_23228/07_2026/7l8b_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7l8b_23228/07_2026/7l8b_23228.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l8b_23228/07_2026/7l8b_23228.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l8b_23228/07_2026/7l8b_23228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8b_23228/07_2026/7l8b_23228.map" model { file = "/net/cci-nas-00/data/ceres_data/7l8b_23228/07_2026/7l8b_23228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8b_23228/07_2026/7l8b_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-dev-6108/lib/python3.11/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 chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 3.73, per 1000 atoms: 0.24 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: 1.73 Conformation dependent library (CDL) restraints added in 538.4 milliseconds 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: 1.99 Time building geometry restraints manager: 2.16 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 - 15.93: 8488 15.93 - 31.87: 256 31.87 - 47.80: 81 47.80 - 63.74: 38 63.74 - 79.67: 12 Dihedral angle restraints: 8875 sinusoidal: 3340 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 8872 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: 3.530 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.420 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 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 : 10.148 79.673 5172 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 are 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/Z covalent geometry : bond 0.02245 / 1.20 (15973) covalent geometry : angle 1.71861 / 1.10 (21732) SS BOND : bond 0.01014 / 0.62 ( 33) SS BOND : angle 2.69630 / 1.89 ( 66) hydrogen bonds : bond 0.19092 / 12.43 ( 301) hydrogen bonds : angle 5.98695 / 4.32 ( 819) link_ALPHA1-3 : bond 0.08908 / 4.47 ( 3) link_ALPHA1-3 : angle 4.46583 / 3.08 ( 9) link_ALPHA1-6 : bond 0.05623 / 2.81 ( 3) link_ALPHA1-6 : angle 3.46481 / 2.37 ( 9) link_BETA1-4 : bond 0.06944 / 4.21 ( 31) link_BETA1-4 : angle 4.56221 / 3.19 ( 93) link_NAG-ASN : bond 0.07659 / 5.02 ( 57) link_NAG-ASN : angle 3.89556 / 2.35 ( 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 : 0.566 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: 0.1318 time to fit residues: 81.3664 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 : 0.694 ------------------------------------------------------------------------------- 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... 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 130 GLN E 302 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.119806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103458 restraints weight = 29183.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.106296 restraints weight = 16326.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.108213 restraints weight = 11025.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.109518 restraints weight = 8358.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.110391 restraints weight = 6840.283| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 16100 Z= 0.164 Angle : 0.752 14.163 22080 Z= 0.357 Chirality : 0.048 0.432 2781 Planarity : 0.004 0.029 2662 Dihedral : 4.761 22.247 2000 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.27 % Allowed : 8.28 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.20), residues: 1642 helix: 2.01 (0.26), residues: 402 sheet: 0.79 (0.23), residues: 424 loop : 0.34 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 444 TYR 0.024 0.002 TYR A 217 PHE 0.016 0.002 PHE E 361 TRP 0.013 0.002 TRP A 112 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (15973) covalent geometry : angle 0.69615 / 0.35 (21732) SS BOND : bond 0.00475 / 0.26 ( 33) SS BOND : angle 1.30813 / 1.05 ( 66) hydrogen bonds : bond 0.06620 / 4.25 ( 301) hydrogen bonds : angle 4.21963 / 2.96 ( 819) link_ALPHA1-3 : bond 0.00977 / 0.49 ( 3) link_ALPHA1-3 : angle 1.83286 / 1.05 ( 9) link_ALPHA1-6 : bond 0.00751 / 0.38 ( 3) link_ALPHA1-6 : angle 1.33327 / 0.85 ( 9) link_BETA1-4 : bond 0.00548 / 0.29 ( 31) link_BETA1-4 : angle 2.29031 / 1.58 ( 93) link_NAG-ASN : bond 0.00516 / 0.37 ( 57) link_NAG-ASN : angle 2.77227 / 1.95 ( 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 296 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 262 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8962 (m-80) cc_final: 0.8671 (m-10) REVERT: C 202 THR cc_start: 0.9247 (m) cc_final: 0.8945 (p) REVERT: A 75 VAL cc_start: 0.8584 (t) cc_final: 0.8352 (m) REVERT: B 625 ASN cc_start: 0.8348 (m110) cc_final: 0.8113 (m110) REVERT: F 536 THR cc_start: 0.9554 (p) cc_final: 0.9341 (p) REVERT: F 543 ASN cc_start: 0.8297 (m-40) cc_final: 0.7769 (m110) outliers start: 34 outliers final: 17 residues processed: 289 average time/residue: 0.1037 time to fit residues: 46.6313 Evaluate side-chains 216 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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: 0.9980 chunk 145 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 33 ASN C 302 ASN A 203 GLN A 289 ASN B 543 ASN B 577 GLN E 411 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.113666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.097248 restraints weight = 29803.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.099968 restraints weight = 16974.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101758 restraints weight = 11600.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.103019 restraints weight = 8931.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103844 restraints weight = 7373.112| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 16100 Z= 0.239 Angle : 0.734 14.325 22080 Z= 0.351 Chirality : 0.047 0.227 2781 Planarity : 0.004 0.035 2662 Dihedral : 4.644 22.240 2000 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.07 % Allowed : 11.02 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.20), residues: 1642 helix: 1.97 (0.26), residues: 402 sheet: 0.81 (0.24), residues: 413 loop : 0.04 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 298 TYR 0.017 0.002 TYR A 173 PHE 0.018 0.002 PHE A 176 TRP 0.017 0.002 TRP C 112 HIS 0.007 0.002 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.24 (15973) covalent geometry : angle 0.69233 / 0.34 (21732) SS BOND : bond 0.00669 / 0.39 ( 33) SS BOND : angle 1.30742 / 1.05 ( 66) hydrogen bonds : bond 0.06202 / 3.94 ( 301) hydrogen bonds : angle 4.00163 / 2.80 ( 819) link_ALPHA1-3 : bond 0.00923 / 0.46 ( 3) link_ALPHA1-3 : angle 1.53826 / 0.99 ( 9) link_ALPHA1-6 : bond 0.00642 / 0.32 ( 3) link_ALPHA1-6 : angle 1.38734 / 0.93 ( 9) link_BETA1-4 : bond 0.00676 / 0.40 ( 31) link_BETA1-4 : angle 1.78398 / 1.25 ( 93) link_NAG-ASN : bond 0.00476 / 0.28 ( 57) link_NAG-ASN : angle 2.46343 / 1.72 ( 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 251 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.9094 (m-80) cc_final: 0.8729 (m-10) REVERT: C 202 THR cc_start: 0.9359 (m) cc_final: 0.8847 (p) REVERT: A 75 VAL cc_start: 0.8671 (t) cc_final: 0.8415 (m) REVERT: A 161 MET cc_start: 0.8357 (tpt) cc_final: 0.7988 (tpt) REVERT: B 625 ASN cc_start: 0.8352 (m110) cc_final: 0.8036 (m110) REVERT: F 543 ASN cc_start: 0.8265 (m-40) cc_final: 0.7722 (m110) outliers start: 46 outliers final: 34 residues processed: 236 average time/residue: 0.1114 time to fit residues: 40.0325 Evaluate side-chains 212 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 201 ILE 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 545 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 633 LYS 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 265 LEU Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 430 ILE 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 655 LYS Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 613 SER 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: 2.9990 chunk 25 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 167 optimal weight: 20.0000 chunk 81 optimal weight: 0.7980 chunk 5 optimal weight: 0.0030 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN D 640 GLN A 289 ASN B 543 ASN B 577 GLN E 72 HIS E 377 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098772 restraints weight = 29538.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.101504 restraints weight = 16692.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.103351 restraints weight = 11374.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104613 restraints weight = 8698.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.105411 restraints weight = 7166.790| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16100 Z= 0.145 Angle : 0.610 13.702 22080 Z= 0.290 Chirality : 0.043 0.248 2781 Planarity : 0.003 0.030 2662 Dihedral : 4.376 23.391 2000 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.54 % Allowed : 11.89 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.20), residues: 1642 helix: 2.22 (0.26), residues: 402 sheet: 0.97 (0.25), residues: 393 loop : -0.12 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 542 TYR 0.015 0.001 TYR C 484 PHE 0.012 0.002 PHE A 176 TRP 0.012 0.001 TRP A 96 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (15973) covalent geometry : angle 0.56895 / 0.28 (21732) SS BOND : bond 0.00444 / 0.24 ( 33) SS BOND : angle 1.03953 / 0.79 ( 66) hydrogen bonds : bond 0.05215 / 3.33 ( 301) hydrogen bonds : angle 3.70644 / 2.59 ( 819) link_ALPHA1-3 : bond 0.00798 / 0.40 ( 3) link_ALPHA1-3 : angle 1.36139 / 0.87 ( 9) link_ALPHA1-6 : bond 0.00612 / 0.31 ( 3) link_ALPHA1-6 : angle 1.41971 / 0.99 ( 9) link_BETA1-4 : bond 0.00482 / 0.29 ( 31) link_BETA1-4 : angle 1.51336 / 1.08 ( 93) link_NAG-ASN : bond 0.00271 / 0.17 ( 57) link_NAG-ASN : angle 2.23740 / 1.57 ( 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 242 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.9102 (m-80) cc_final: 0.8768 (m-10) REVERT: C 202 THR cc_start: 0.9262 (m) cc_final: 0.8792 (p) REVERT: D 657 GLU cc_start: 0.8192 (tt0) cc_final: 0.7937 (tt0) REVERT: A 75 VAL cc_start: 0.8681 (t) cc_final: 0.8418 (m) REVERT: A 161 MET cc_start: 0.8339 (tpt) cc_final: 0.7930 (tpt) REVERT: E 46 LYS cc_start: 0.8271 (mtmt) cc_final: 0.7606 (mtmt) REVERT: E 194 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8940 (tp) REVERT: E 217 TYR cc_start: 0.8060 (m-80) cc_final: 0.7612 (t80) REVERT: E 492 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7350 (mt-10) REVERT: F 543 ASN cc_start: 0.8198 (m-40) cc_final: 0.7897 (m110) outliers start: 38 outliers final: 25 residues processed: 231 average time/residue: 0.1153 time to fit residues: 40.5766 Evaluate side-chains 213 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 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 89 VAL Chi-restraints excluded: chain A residue 100 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 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 95 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 8 optimal weight: 0.0270 chunk 149 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 48 optimal weight: 0.0670 chunk 73 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN B 543 ASN E 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.098647 restraints weight = 29616.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.101183 restraints weight = 17490.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.102884 restraints weight = 12178.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.104036 restraints weight = 9469.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104773 restraints weight = 7889.126| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16100 Z= 0.144 Angle : 0.592 12.931 22080 Z= 0.280 Chirality : 0.043 0.242 2781 Planarity : 0.003 0.030 2662 Dihedral : 4.199 27.508 2000 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.81 % Allowed : 12.02 % Favored : 85.17 % 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 are not related in a simple way. whole: 1.03 (0.20), residues: 1642 helix: 2.26 (0.26), residues: 402 sheet: 0.97 (0.25), residues: 386 loop : -0.20 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 617 TYR 0.019 0.001 TYR C 484 PHE 0.011 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/Z covalent geometry : bond 0.00336 / 0.14 (15973) covalent geometry : angle 0.55457 / 0.27 (21732) SS BOND : bond 0.00433 / 0.24 ( 33) SS BOND : angle 0.91027 / 0.70 ( 66) hydrogen bonds : bond 0.04954 / 3.17 ( 301) hydrogen bonds : angle 3.60745 / 2.53 ( 819) link_ALPHA1-3 : bond 0.00788 / 0.39 ( 3) link_ALPHA1-3 : angle 1.33351 / 0.86 ( 9) link_ALPHA1-6 : bond 0.00568 / 0.28 ( 3) link_ALPHA1-6 : angle 1.42377 / 0.99 ( 9) link_BETA1-4 : bond 0.00475 / 0.29 ( 31) link_BETA1-4 : angle 1.42872 / 1.03 ( 93) link_NAG-ASN : bond 0.00245 / 0.16 ( 57) link_NAG-ASN : angle 2.13113 / 1.49 ( 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: 42 poor density : 202 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.9110 (m-80) cc_final: 0.8790 (m-10) REVERT: D 657 GLU cc_start: 0.8084 (tt0) cc_final: 0.7861 (tt0) REVERT: A 75 VAL cc_start: 0.8715 (t) cc_final: 0.8451 (m) REVERT: A 161 MET cc_start: 0.8359 (tpt) cc_final: 0.8012 (tpt) REVERT: E 46 LYS cc_start: 0.8157 (mtmt) cc_final: 0.7282 (mtmt) REVERT: E 194 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8963 (tp) REVERT: E 217 TYR cc_start: 0.8041 (m-80) cc_final: 0.7699 (t80) REVERT: F 543 ASN cc_start: 0.8137 (m-40) cc_final: 0.7821 (m110) outliers start: 42 outliers final: 38 residues processed: 229 average time/residue: 0.1186 time to fit residues: 41.1874 Evaluate side-chains 226 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 187 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 50 THR 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 440 GLN 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 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 289 ASN Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 371 VAL 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 655 LYS Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 95 MET 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 E residue 455 THR 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 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: 2.9990 chunk 140 optimal weight: 1.9990 chunk 175 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 98 optimal weight: 0.2980 chunk 74 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN A 246 GLN B 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.113092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.097606 restraints weight = 29683.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.100021 restraints weight = 17705.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.101648 restraints weight = 12469.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.102773 restraints weight = 9760.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103534 restraints weight = 8149.056| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3937 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= 0.199 Angle : 0.641 11.038 22080 Z= 0.302 Chirality : 0.044 0.232 2781 Planarity : 0.003 0.031 2662 Dihedral : 4.268 28.023 2000 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.67 % Allowed : 12.63 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.20), residues: 1642 helix: 2.11 (0.26), residues: 402 sheet: 0.81 (0.25), residues: 386 loop : -0.32 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 166 TYR 0.018 0.002 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 E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (15973) covalent geometry : angle 0.60512 / 0.29 (21732) SS BOND : bond 0.00458 / 0.27 ( 33) SS BOND : angle 0.93640 / 0.72 ( 66) hydrogen bonds : bond 0.05178 / 3.33 ( 301) hydrogen bonds : angle 3.72048 / 2.62 ( 819) link_ALPHA1-3 : bond 0.00770 / 0.38 ( 3) link_ALPHA1-3 : angle 1.31806 / 0.84 ( 9) link_ALPHA1-6 : bond 0.00503 / 0.25 ( 3) link_ALPHA1-6 : angle 1.44594 / 0.99 ( 9) link_BETA1-4 : bond 0.00481 / 0.30 ( 31) link_BETA1-4 : angle 1.46011 / 1.06 ( 93) link_NAG-ASN : bond 0.00274 / 0.18 ( 57) link_NAG-ASN : angle 2.17805 / 1.53 ( 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 243 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 188 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.9170 (m-80) cc_final: 0.8861 (m-10) REVERT: D 650 GLN cc_start: 0.8818 (tp40) cc_final: 0.8453 (tp40) REVERT: D 657 GLU cc_start: 0.8142 (tt0) cc_final: 0.7933 (tt0) REVERT: A 75 VAL cc_start: 0.8707 (t) cc_final: 0.8448 (m) REVERT: A 161 MET cc_start: 0.8446 (tpt) cc_final: 0.7914 (tpt) REVERT: E 46 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7611 (pttt) REVERT: E 194 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.9008 (tp) REVERT: E 217 TYR cc_start: 0.8132 (m-80) cc_final: 0.7785 (t80) REVERT: E 492 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7431 (mt-10) outliers start: 55 outliers final: 40 residues processed: 226 average time/residue: 0.1113 time to fit residues: 38.4414 Evaluate side-chains 220 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 50 THR 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 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 371 VAL 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 655 LYS 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 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: 3.9990 chunk 163 optimal weight: 2.9990 chunk 162 optimal weight: 0.2980 chunk 122 optimal weight: 2.9990 chunk 184 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS B 543 ASN B 577 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.098035 restraints weight = 29395.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.100739 restraints weight = 16544.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.102576 restraints weight = 11253.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.103812 restraints weight = 8582.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.104653 restraints weight = 7063.490| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16100 Z= 0.139 Angle : 0.585 10.360 22080 Z= 0.277 Chirality : 0.043 0.247 2781 Planarity : 0.003 0.029 2662 Dihedral : 4.107 27.332 2000 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.07 % Allowed : 13.23 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.20), residues: 1642 helix: 2.25 (0.26), residues: 402 sheet: 0.71 (0.26), residues: 367 loop : -0.29 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 166 TYR 0.018 0.001 TYR C 484 PHE 0.011 0.001 PHE A 176 TRP 0.013 0.001 TRP A 35 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (15973) covalent geometry : angle 0.54921 / 0.27 (21732) SS BOND : bond 0.00412 / 0.23 ( 33) SS BOND : angle 0.86092 / 0.67 ( 66) hydrogen bonds : bond 0.04758 / 3.05 ( 301) hydrogen bonds : angle 3.60150 / 2.53 ( 819) link_ALPHA1-3 : bond 0.00775 / 0.38 ( 3) link_ALPHA1-3 : angle 1.31925 / 0.85 ( 9) link_ALPHA1-6 : bond 0.00507 / 0.25 ( 3) link_ALPHA1-6 : angle 1.42265 / 0.98 ( 9) link_BETA1-4 : bond 0.00457 / 0.28 ( 31) link_BETA1-4 : angle 1.37603 / 1.00 ( 93) link_NAG-ASN : bond 0.00240 / 0.15 ( 57) link_NAG-ASN : angle 2.07711 / 1.46 ( 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 239 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.9140 (m-80) cc_final: 0.8845 (m-10) REVERT: D 650 GLN cc_start: 0.8801 (tp40) cc_final: 0.8333 (tp40) REVERT: D 657 GLU cc_start: 0.8207 (tt0) cc_final: 0.7991 (tt0) REVERT: A 75 VAL cc_start: 0.8714 (t) cc_final: 0.8430 (m) REVERT: A 161 MET cc_start: 0.8479 (tpt) cc_final: 0.7892 (tpt) REVERT: B 633 LYS cc_start: 0.8911 (mttp) cc_final: 0.8602 (mptt) REVERT: E 46 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7641 (pttt) REVERT: E 110 SER cc_start: 0.9118 (t) cc_final: 0.8908 (t) REVERT: E 194 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8980 (tp) REVERT: E 217 TYR cc_start: 0.8090 (m-80) cc_final: 0.7854 (t80) REVERT: E 492 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7525 (mt-10) outliers start: 46 outliers final: 36 residues processed: 223 average time/residue: 0.1182 time to fit residues: 40.3078 Evaluate side-chains 222 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 184 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 138 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 440 GLN Chi-restraints excluded: chain C residue 494 LEU 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 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 595 ILE Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 620 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 128 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 185 optimal weight: 20.0000 chunk 152 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN B 543 ASN B 577 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.098401 restraints weight = 29680.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.100847 restraints weight = 17541.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.102501 restraints weight = 12281.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.103564 restraints weight = 9562.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104387 restraints weight = 8025.375| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16100 Z= 0.140 Angle : 0.576 9.273 22080 Z= 0.273 Chirality : 0.043 0.240 2781 Planarity : 0.003 0.029 2662 Dihedral : 4.004 26.449 2000 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.81 % Allowed : 13.49 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.21), residues: 1642 helix: 2.21 (0.27), residues: 408 sheet: 0.87 (0.26), residues: 366 loop : -0.34 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 617 TYR 0.019 0.001 TYR C 484 PHE 0.011 0.001 PHE A 176 TRP 0.015 0.001 TRP A 35 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (15973) covalent geometry : angle 0.54402 / 0.27 (21732) SS BOND : bond 0.00390 / 0.22 ( 33) SS BOND : angle 0.83400 / 0.64 ( 66) hydrogen bonds : bond 0.04691 / 3.01 ( 301) hydrogen bonds : angle 3.62200 / 2.55 ( 819) link_ALPHA1-3 : bond 0.00751 / 0.37 ( 3) link_ALPHA1-3 : angle 1.31434 / 0.85 ( 9) link_ALPHA1-6 : bond 0.00466 / 0.23 ( 3) link_ALPHA1-6 : angle 1.41295 / 0.97 ( 9) link_BETA1-4 : bond 0.00453 / 0.28 ( 31) link_BETA1-4 : angle 1.35157 / 0.99 ( 93) link_NAG-ASN : bond 0.00247 / 0.16 ( 57) link_NAG-ASN : angle 1.95382 / 1.38 ( 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 235 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: C 39 TYR cc_start: 0.9147 (m-80) cc_final: 0.8862 (m-10) REVERT: C 247 CYS cc_start: 0.6061 (m) cc_final: 0.5786 (m) REVERT: D 624 ASP cc_start: 0.7943 (m-30) cc_final: 0.7687 (m-30) REVERT: D 650 GLN cc_start: 0.8748 (tp40) cc_final: 0.8352 (tp40) REVERT: D 657 GLU cc_start: 0.8132 (tt0) cc_final: 0.7928 (tt0) REVERT: A 75 VAL cc_start: 0.8740 (t) cc_final: 0.8468 (m) REVERT: A 161 MET cc_start: 0.8450 (tpt) cc_final: 0.7893 (tpt) REVERT: B 633 LYS cc_start: 0.8868 (mttp) cc_final: 0.8592 (mptt) REVERT: E 46 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7692 (pttt) REVERT: E 110 SER cc_start: 0.9114 (t) cc_final: 0.8909 (t) REVERT: E 194 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8968 (tp) REVERT: E 492 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7477 (mt-10) outliers start: 42 outliers final: 34 residues processed: 224 average time/residue: 0.1124 time to fit residues: 38.2408 Evaluate side-chains 221 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 54 CYS 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 C residue 494 LEU 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 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 289 ASN 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 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 595 ILE Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 620 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 151 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 153 optimal weight: 0.3980 chunk 184 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 177 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN B 543 ASN B 577 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.096967 restraints weight = 29958.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.099633 restraints weight = 16905.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.101439 restraints weight = 11523.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.102675 restraints weight = 8808.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103504 restraints weight = 7245.704| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16100 Z= 0.169 Angle : 0.605 8.272 22080 Z= 0.286 Chirality : 0.044 0.235 2781 Planarity : 0.003 0.036 2662 Dihedral : 4.072 26.618 2000 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.67 % Allowed : 13.83 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.21), residues: 1642 helix: 2.16 (0.27), residues: 408 sheet: 0.75 (0.26), residues: 378 loop : -0.39 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 166 TYR 0.020 0.001 TYR C 484 PHE 0.013 0.002 PHE A 176 TRP 0.016 0.001 TRP A 35 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (15973) covalent geometry : angle 0.57305 / 0.28 (21732) SS BOND : bond 0.00410 / 0.24 ( 33) SS BOND : angle 0.83566 / 0.64 ( 66) hydrogen bonds : bond 0.04819 / 3.11 ( 301) hydrogen bonds : angle 3.66840 / 2.59 ( 819) link_ALPHA1-3 : bond 0.00775 / 0.38 ( 3) link_ALPHA1-3 : angle 1.31430 / 0.84 ( 9) link_ALPHA1-6 : bond 0.00443 / 0.22 ( 3) link_ALPHA1-6 : angle 1.43667 / 0.98 ( 9) link_BETA1-4 : bond 0.00443 / 0.27 ( 31) link_BETA1-4 : angle 1.37810 / 1.01 ( 93) link_NAG-ASN : bond 0.00248 / 0.16 ( 57) link_NAG-ASN : angle 2.02474 / 1.42 ( 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 229 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.9158 (m-80) cc_final: 0.8884 (m-10) REVERT: C 247 CYS cc_start: 0.6112 (m) cc_final: 0.5832 (m) REVERT: D 650 GLN cc_start: 0.8784 (tp40) cc_final: 0.8489 (tp40) REVERT: D 657 GLU cc_start: 0.8231 (tt0) cc_final: 0.8025 (tt0) REVERT: A 75 VAL cc_start: 0.8708 (t) cc_final: 0.8428 (m) REVERT: A 161 MET cc_start: 0.8483 (tpt) cc_final: 0.7901 (tpt) REVERT: B 590 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8776 (mm-40) REVERT: B 633 LYS cc_start: 0.8905 (mttp) cc_final: 0.8594 (mptt) REVERT: E 46 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7724 (pttt) REVERT: E 110 SER cc_start: 0.9127 (t) cc_final: 0.8923 (t) REVERT: E 194 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8974 (tp) REVERT: E 492 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7556 (mt-10) outliers start: 40 outliers final: 35 residues processed: 217 average time/residue: 0.1097 time to fit residues: 36.4176 Evaluate side-chains 221 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 THR 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 C residue 494 LEU 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 66 HIS 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 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 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 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 620 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 100 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 144 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN B 543 ASN B 577 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.114589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.098539 restraints weight = 29528.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101232 restraints weight = 16685.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103047 restraints weight = 11353.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104175 restraints weight = 8665.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.105042 restraints weight = 7194.236| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16100 Z= 0.120 Angle : 0.559 8.114 22080 Z= 0.265 Chirality : 0.042 0.247 2781 Planarity : 0.003 0.035 2662 Dihedral : 3.929 25.612 2000 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.54 % Allowed : 13.69 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.21), residues: 1642 helix: 2.20 (0.27), residues: 414 sheet: 0.86 (0.27), residues: 366 loop : -0.37 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 617 TYR 0.018 0.001 TYR C 484 PHE 0.009 0.001 PHE A 176 TRP 0.018 0.001 TRP A 35 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (15973) covalent geometry : angle 0.52795 / 0.26 (21732) SS BOND : bond 0.00366 / 0.20 ( 33) SS BOND : angle 0.77270 / 0.59 ( 66) hydrogen bonds : bond 0.04435 / 2.86 ( 301) hydrogen bonds : angle 3.57844 / 2.52 ( 819) link_ALPHA1-3 : bond 0.00748 / 0.37 ( 3) link_ALPHA1-3 : angle 1.32133 / 0.85 ( 9) link_ALPHA1-6 : bond 0.00470 / 0.24 ( 3) link_ALPHA1-6 : angle 1.41256 / 0.97 ( 9) link_BETA1-4 : bond 0.00439 / 0.27 ( 31) link_BETA1-4 : angle 1.31484 / 0.96 ( 93) link_NAG-ASN : bond 0.00234 / 0.16 ( 57) link_NAG-ASN : angle 1.89400 / 1.33 ( 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 237 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.9136 (m-80) cc_final: 0.8863 (m-10) REVERT: C 42 VAL cc_start: 0.9052 (OUTLIER) cc_final: 0.8691 (m) REVERT: C 90 THR cc_start: 0.8849 (m) cc_final: 0.8399 (p) REVERT: C 247 CYS cc_start: 0.6071 (m) cc_final: 0.5778 (m) REVERT: D 650 GLN cc_start: 0.8744 (tp40) cc_final: 0.8372 (tp40) REVERT: D 657 GLU cc_start: 0.8211 (tt0) cc_final: 0.7929 (tt0) REVERT: A 75 VAL cc_start: 0.8717 (t) cc_final: 0.8425 (m) REVERT: A 99 ASN cc_start: 0.8209 (t0) cc_final: 0.7719 (t0) REVERT: A 161 MET cc_start: 0.8453 (tpt) cc_final: 0.7859 (tpt) REVERT: B 590 GLN cc_start: 0.9096 (mm-40) cc_final: 0.8780 (mm-40) REVERT: B 633 LYS cc_start: 0.8888 (mttp) cc_final: 0.8570 (mptt) REVERT: E 46 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7609 (pttt) REVERT: E 110 SER cc_start: 0.9082 (t) cc_final: 0.8875 (t) REVERT: E 194 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8940 (tp) REVERT: E 492 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7421 (mt-10) REVERT: F 543 ASN cc_start: 0.8260 (m-40) cc_final: 0.7943 (m-40) outliers start: 38 outliers final: 29 residues processed: 226 average time/residue: 0.1095 time to fit residues: 38.1011 Evaluate side-chains 224 residues out of total 1497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 54 CYS 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 C residue 494 LEU 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 66 HIS 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 450 THR Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 620 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 620 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 149 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 170 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 172 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 30 optimal weight: 0.0060 chunk 159 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 overall best weight: 2.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN B 543 ASN B 577 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.096416 restraints weight = 29416.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.099084 restraints weight = 16680.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.100874 restraints weight = 11342.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.102069 restraints weight = 8670.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.102845 restraints weight = 7166.385| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16100 Z= 0.190 Angle : 0.623 7.306 22080 Z= 0.294 Chirality : 0.044 0.232 2781 Planarity : 0.003 0.040 2662 Dihedral : 4.142 28.376 2000 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.47 % Allowed : 14.09 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.21), residues: 1642 helix: 2.11 (0.27), residues: 408 sheet: 0.70 (0.26), residues: 380 loop : -0.45 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 617 TYR 0.020 0.002 TYR C 484 PHE 0.014 0.002 PHE A 176 TRP 0.019 0.001 TRP A 35 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (15973) covalent geometry : angle 0.59178 / 0.29 (21732) SS BOND : bond 0.00439 / 0.26 ( 33) SS BOND : angle 0.83387 / 0.63 ( 66) hydrogen bonds : bond 0.04957 / 3.22 ( 301) hydrogen bonds : angle 3.70369 / 2.62 ( 819) link_ALPHA1-3 : bond 0.00760 / 0.37 ( 3) link_ALPHA1-3 : angle 1.31176 / 0.83 ( 9) link_ALPHA1-6 : bond 0.00416 / 0.21 ( 3) link_ALPHA1-6 : angle 1.43586 / 0.97 ( 9) link_BETA1-4 : bond 0.00453 / 0.28 ( 31) link_BETA1-4 : angle 1.39964 / 1.03 ( 93) link_NAG-ASN : bond 0.00271 / 0.18 ( 57) link_NAG-ASN : angle 2.03483 / 1.43 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2277.84 seconds wall clock time: 40 minutes 18.63 seconds (2418.63 seconds total)