Starting phenix.real_space_refine on Fri Jul 3 17:11:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l7u_23219/07_2026/7l7u_23219.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l7u_23219/07_2026/7l7u_23219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l7u_23219/07_2026/7l7u_23219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l7u_23219/07_2026/7l7u_23219.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7l7u_23219/07_2026/7l7u_23219.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l7u_23219/07_2026/7l7u_23219.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l7u_23219/07_2026/7l7u_23219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l7u_23219/07_2026/7l7u_23219.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 9504 2.51 5 N 2544 2.21 5 O 3105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 15258 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3491 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 20, 'TRANS': 421} Chain breaks: 3 Chain: "B" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1156 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3491 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 20, 'TRANS': 421} Chain breaks: 3 Chain: "D" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1156 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3491 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 20, 'TRANS': 421} Chain breaks: 3 Chain: "F" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1156 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "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: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "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: 3.78, per 1000 atoms: 0.25 Number of scatterers: 15258 At special positions: 0 Unit cell: (128.8, 125.35, 118.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 3105 8.00 N 2544 7.00 C 9504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.10 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=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.02 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS D 561 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.09 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.02 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS F 561 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.09 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=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA O 3 " - " MAN O 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA O 3 " - " MAN O 5 " " BMA W 3 " - " MAN W 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG 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 V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " 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-ASN " NAG A 601 " - " ASN A 160 " " NAG A 602 " - " ASN A 276 " " NAG A 603 " - " ASN A 386 " " NAG A 604 " - " ASN A 363 " " NAG A 605 " - " ASN A 234 " " NAG A 606 " - " ASN A 133 " " NAG A 607 " - " ASN A 241 " " NAG A 608 " - " ASN A 289 " " NAG A 609 " - " ASN A 339 " " NAG A 610 " - " ASN A 355 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 601 " - " ASN C 160 " " NAG C 602 " - " ASN C 276 " " NAG C 603 " - " ASN C 386 " " NAG C 604 " - " ASN C 363 " " NAG C 605 " - " ASN C 234 " " NAG C 606 " - " ASN C 133 " " NAG C 607 " - " ASN C 241 " " NAG C 608 " - " ASN C 289 " " NAG C 609 " - " ASN C 339 " " NAG C 610 " - " ASN C 355 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 611 " " NAG E 601 " - " ASN E 160 " " NAG E 602 " - " ASN E 276 " " NAG E 603 " - " ASN E 386 " " NAG E 604 " - " ASN E 363 " " NAG E 605 " - " ASN E 234 " " NAG E 606 " - " ASN E 133 " " NAG E 607 " - " ASN E 241 " " NAG E 608 " - " ASN E 289 " " NAG E 609 " - " ASN E 339 " " NAG E 610 " - " ASN E 355 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 611 " " NAG G 1 " - " ASN A 262 " " NAG H 1 " - " ASN A 448 " " NAG I 1 " - " ASN A 295 " " NAG J 1 " - " ASN A 197 " " NAG K 1 " - " ASN A 156 " " NAG L 1 " - " ASN A 301 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 332 " " NAG O 1 " - " ASN C 262 " " NAG P 1 " - " ASN C 448 " " NAG Q 1 " - " ASN C 295 " " NAG R 1 " - " ASN C 197 " " NAG S 1 " - " ASN C 156 " " NAG T 1 " - " ASN C 301 " " NAG U 1 " - " ASN C 88 " " NAG V 1 " - " ASN C 332 " " NAG W 1 " - " ASN E 262 " " NAG X 1 " - " ASN E 448 " " NAG Y 1 " - " ASN E 295 " " NAG Z 1 " - " ASN E 197 " " NAG a 1 " - " ASN E 156 " " NAG b 1 " - " ASN E 301 " " NAG c 1 " - " ASN E 88 " " NAG d 1 " - " ASN E 332 " Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 581.7 milliseconds 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 27 sheets defined 31.2% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 116 removed outlier: 3.684A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 354 removed outlier: 4.021A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.827A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.582A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 542 through 556 Processing helix chain 'B' and resid 560 through 568 Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.684A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.022A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 392 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.827A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 484 removed outlier: 4.582A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 542 through 556 Processing helix chain 'D' and resid 560 through 568 Processing helix chain 'D' and resid 568 through 596 Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 663 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 98 through 116 removed outlier: 3.684A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE E 109 " --> pdb=" O HIS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.021A 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 392 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.826A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.582A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 542 through 556 Processing helix chain 'F' and resid 560 through 568 Processing helix chain 'F' and resid 568 through 596 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 663 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.911A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.245A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.531A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.969A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.836A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 10.951A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.836A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.969A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 312 removed outlier: 6.563A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY A 321 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.911A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.245A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.531A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.969A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.836A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 274 removed outlier: 10.951A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.836A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.969A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 312 removed outlier: 6.562A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY C 321 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.910A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.245A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.531A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.969A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 274 removed outlier: 10.951A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.969A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 301 through 312 removed outlier: 6.563A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY E 321 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) 654 hydrogen bonds defined for protein. 1809 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.81 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3638 1.32 - 1.46: 4661 1.46 - 1.59: 7065 1.59 - 1.73: 50 1.73 - 1.86: 126 Bond restraints: 15540 Sorted by residual: bond pdb=" CB LEU B 520 " pdb=" CG LEU B 520 " ideal model delta sigma weight residual 1.530 1.640 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" CB LEU D 520 " pdb=" CG LEU D 520 " ideal model delta sigma weight residual 1.530 1.639 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" CB LEU F 520 " pdb=" CG LEU F 520 " ideal model delta sigma weight residual 1.530 1.639 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" CB PHE A 376 " pdb=" CG PHE A 376 " ideal model delta sigma weight residual 1.502 1.379 0.123 2.30e-02 1.89e+03 2.85e+01 bond pdb=" CB PHE E 376 " pdb=" CG PHE E 376 " ideal model delta sigma weight residual 1.502 1.380 0.122 2.30e-02 1.89e+03 2.83e+01 ... (remaining 15535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 17633 2.21 - 4.42: 2984 4.42 - 6.63: 438 6.63 - 8.85: 44 8.85 - 11.06: 3 Bond angle restraints: 21102 Sorted by residual: angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.87 128.14 -8.27 1.04e+00 9.25e-01 6.32e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.87 128.12 -8.25 1.04e+00 9.25e-01 6.30e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.87 128.11 -8.24 1.04e+00 9.25e-01 6.28e+01 angle pdb=" C GLY E 237 " pdb=" N PRO E 238 " pdb=" CA PRO E 238 " ideal model delta sigma weight residual 119.76 127.28 -7.52 1.03e+00 9.43e-01 5.33e+01 angle pdb=" C GLY A 237 " pdb=" N PRO A 238 " pdb=" CA PRO A 238 " ideal model delta sigma weight residual 119.76 127.25 -7.49 1.03e+00 9.43e-01 5.29e+01 ... (remaining 21097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 8214 17.80 - 35.60: 261 35.60 - 53.40: 66 53.40 - 71.20: 15 71.20 - 88.99: 18 Dihedral angle restraints: 8574 sinusoidal: 3483 harmonic: 5091 Sorted by residual: dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 161.68 -68.68 1 1.00e+01 1.00e-02 6.11e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 161.67 -68.67 1 1.00e+01 1.00e-02 6.11e+01 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 93.00 161.67 -68.67 1 1.00e+01 1.00e-02 6.11e+01 ... (remaining 8571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1799 0.111 - 0.221: 523 0.221 - 0.332: 210 0.332 - 0.442: 105 0.442 - 0.553: 27 Chirality restraints: 2664 Sorted by residual: chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.37e+02 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.37e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.35e+02 ... (remaining 2661 not shown) Planarity restraints: 2628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 607 " -0.349 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG A 607 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG A 607 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG A 607 " 0.531 2.00e-02 2.50e+03 pdb=" O7 NAG A 607 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 607 " 0.349 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG C 607 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG C 607 " 0.148 2.00e-02 2.50e+03 pdb=" N2 NAG C 607 " -0.531 2.00e-02 2.50e+03 pdb=" O7 NAG C 607 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 607 " -0.348 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG E 607 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG E 607 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG E 607 " 0.531 2.00e-02 2.50e+03 pdb=" O7 NAG E 607 " -0.121 2.00e-02 2.50e+03 ... (remaining 2625 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 6283 2.91 - 3.41: 13691 3.41 - 3.90: 25725 3.90 - 4.40: 28847 4.40 - 4.90: 45643 Nonbonded interactions: 120189 Sorted by model distance: nonbonded pdb=" N ILE A 213 " pdb=" O ILE A 213 " model vdw 2.411 2.496 nonbonded pdb=" N ILE C 213 " pdb=" O ILE C 213 " model vdw 2.412 2.496 nonbonded pdb=" N ILE E 213 " pdb=" O ILE E 213 " model vdw 2.412 2.496 nonbonded pdb=" O3 NAG G 1 " pdb=" O7 NAG G 1 " model vdw 2.432 3.040 nonbonded pdb=" O3 NAG W 1 " pdb=" O7 NAG W 1 " model vdw 2.432 3.040 ... (remaining 120184 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'O' selection = chain 'W' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.840 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 0.136 15660 Z= 1.217 Angle : 1.716 11.057 21438 Z= 1.096 Chirality : 0.149 0.553 2664 Planarity : 0.019 0.299 2565 Dihedral : 10.632 88.995 5202 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.19), residues: 1731 helix: -0.11 (0.21), residues: 480 sheet: 1.31 (0.22), residues: 495 loop : 0.37 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 480 TYR 0.030 0.007 TYR E 217 PHE 0.019 0.006 PHE A 93 TRP 0.068 0.013 TRP E 479 HIS 0.008 0.003 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.02266 / 1.19 (15540) covalent geometry : angle 1.68450 / 1.09 (21102) SS BOND : bond 0.02346 / 1.26 ( 24) SS BOND : angle 3.50680 / 2.30 ( 48) hydrogen bonds : bond 0.17892 / 11.62 ( 630) hydrogen bonds : angle 7.08243 / 5.01 ( 1809) link_ALPHA1-3 : bond 0.00181 / 0.09 ( 3) link_ALPHA1-3 : angle 0.79878 / 0.55 ( 9) link_ALPHA1-6 : bond 0.00015 / 0.01 ( 3) link_ALPHA1-6 : angle 0.41145 / 0.29 ( 9) link_BETA1-4 : bond 0.06374 / 3.82 ( 27) link_BETA1-4 : angle 4.13692 / 2.98 ( 81) link_NAG-ASN : bond 0.07213 / 4.52 ( 63) link_NAG-ASN : angle 2.60483 / 1.83 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 446 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8354 (mtp) cc_final: 0.8024 (mtp) REVERT: A 140 ASP cc_start: 0.7871 (t0) cc_final: 0.7420 (t0) REVERT: A 179 LEU cc_start: 0.9376 (mt) cc_final: 0.9172 (mt) REVERT: B 523 LEU cc_start: 0.9331 (mt) cc_final: 0.8967 (mt) REVERT: B 534 SER cc_start: 0.8676 (p) cc_final: 0.8343 (p) REVERT: B 543 ASN cc_start: 0.8985 (t0) cc_final: 0.8478 (t0) REVERT: B 564 HIS cc_start: 0.5295 (t70) cc_final: 0.4893 (t-90) REVERT: B 577 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8182 (tt0) REVERT: B 616 ASN cc_start: 0.8382 (p0) cc_final: 0.8160 (p0) REVERT: B 617 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7548 (ttp80) REVERT: B 647 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6714 (mt-10) REVERT: C 100 MET cc_start: 0.8542 (mtp) cc_final: 0.8030 (mtp) REVERT: C 115 SER cc_start: 0.9087 (m) cc_final: 0.8812 (t) REVERT: C 125 LEU cc_start: 0.8791 (tt) cc_final: 0.8519 (tt) REVERT: D 577 GLN cc_start: 0.8745 (tp-100) cc_final: 0.8182 (tt0) REVERT: D 627 THR cc_start: 0.8270 (p) cc_final: 0.8009 (p) REVERT: E 140 ASP cc_start: 0.7997 (t0) cc_final: 0.7782 (t0) REVERT: F 523 LEU cc_start: 0.9292 (mt) cc_final: 0.8888 (mt) REVERT: F 577 GLN cc_start: 0.8680 (tp-100) cc_final: 0.8075 (tt0) REVERT: F 617 ARG cc_start: 0.8106 (ttm-80) cc_final: 0.7777 (tpp80) REVERT: F 637 ASN cc_start: 0.7057 (m-40) cc_final: 0.6855 (m-40) outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.1319 time to fit residues: 86.2659 Evaluate side-chains 236 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 HIS A 103 GLN A 258 GLN A 302 ASN B 550 GLN B 562 GLN C 85 HIS C 103 GLN C 114 GLN C 130 GLN C 258 GLN C 302 ASN D 550 GLN D 562 GLN D 656 ASN E 85 HIS E 258 GLN E 302 ASN E 478 ASN F 562 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.136074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.111779 restraints weight = 21971.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.114659 restraints weight = 15305.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.116661 restraints weight = 12085.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.118160 restraints weight = 10310.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.119016 restraints weight = 9217.852| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15660 Z= 0.186 Angle : 0.749 10.888 21438 Z= 0.375 Chirality : 0.048 0.214 2664 Planarity : 0.004 0.056 2565 Dihedral : 5.171 20.781 1866 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.22 % Allowed : 8.51 % Favored : 89.27 % 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: 0.89 (0.19), residues: 1731 helix: 1.20 (0.24), residues: 471 sheet: 1.01 (0.23), residues: 465 loop : 0.07 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 350 TYR 0.011 0.002 TYR A 384 PHE 0.019 0.003 PHE E 468 TRP 0.024 0.002 TRP E 479 HIS 0.005 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (15540) covalent geometry : angle 0.71052 / 0.37 (21102) SS BOND : bond 0.00197 / 0.12 ( 24) SS BOND : angle 1.28175 / 0.96 ( 48) hydrogen bonds : bond 0.06261 / 4.16 ( 630) hydrogen bonds : angle 5.56624 / 3.87 ( 1809) link_ALPHA1-3 : bond 0.00876 / 0.44 ( 3) link_ALPHA1-3 : angle 1.37756 / 0.89 ( 9) link_ALPHA1-6 : bond 0.00448 / 0.22 ( 3) link_ALPHA1-6 : angle 1.33942 / 0.86 ( 9) link_BETA1-4 : bond 0.00254 / 0.13 ( 27) link_BETA1-4 : angle 1.99912 / 1.44 ( 81) link_NAG-ASN : bond 0.00466 / 0.31 ( 63) link_NAG-ASN : angle 2.23399 / 1.60 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 262 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.7911 (mtp) cc_final: 0.7701 (mtp) REVERT: B 523 LEU cc_start: 0.9267 (mt) cc_final: 0.8932 (mt) REVERT: B 535 MET cc_start: 0.7432 (mmm) cc_final: 0.7184 (mmp) REVERT: B 543 ASN cc_start: 0.8837 (t0) cc_final: 0.8445 (t0) REVERT: B 577 GLN cc_start: 0.7933 (tp-100) cc_final: 0.7517 (tt0) REVERT: B 615 SER cc_start: 0.8351 (t) cc_final: 0.8052 (m) REVERT: D 577 GLN cc_start: 0.8050 (tp-100) cc_final: 0.7485 (tt0) REVERT: D 615 SER cc_start: 0.8309 (t) cc_final: 0.8100 (m) REVERT: D 616 ASN cc_start: 0.7945 (p0) cc_final: 0.7654 (p0) REVERT: D 626 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7208 (ttm) REVERT: E 100 MET cc_start: 0.7558 (mtm) cc_final: 0.7322 (mtm) REVERT: F 577 GLN cc_start: 0.7943 (tp-100) cc_final: 0.7456 (tt0) REVERT: F 615 SER cc_start: 0.8431 (t) cc_final: 0.8071 (m) outliers start: 35 outliers final: 16 residues processed: 285 average time/residue: 0.1099 time to fit residues: 49.0899 Evaluate side-chains 211 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 626 MET Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 63 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 133 optimal weight: 0.5980 chunk 99 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN A 136 ASN A 170 GLN C 170 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.126775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.101720 restraints weight = 22699.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.104559 restraints weight = 15888.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.106519 restraints weight = 12575.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.107764 restraints weight = 10741.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108389 restraints weight = 9685.436| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15660 Z= 0.213 Angle : 0.696 10.474 21438 Z= 0.344 Chirality : 0.046 0.226 2664 Planarity : 0.004 0.071 2565 Dihedral : 4.978 17.352 1866 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.73 % Allowed : 10.60 % Favored : 86.67 % 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: 0.64 (0.19), residues: 1731 helix: 1.14 (0.24), residues: 471 sheet: 0.76 (0.22), residues: 462 loop : -0.11 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 469 TYR 0.018 0.002 TYR A 217 PHE 0.014 0.002 PHE C 376 TRP 0.013 0.002 TRP C 479 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 (15540) covalent geometry : angle 0.67307 / 0.34 (21102) SS BOND : bond 0.00308 / 0.21 ( 24) SS BOND : angle 0.92820 / 0.67 ( 48) hydrogen bonds : bond 0.05480 / 3.62 ( 630) hydrogen bonds : angle 5.28740 / 3.68 ( 1809) link_ALPHA1-3 : bond 0.00643 / 0.32 ( 3) link_ALPHA1-3 : angle 1.39305 / 0.92 ( 9) link_ALPHA1-6 : bond 0.00486 / 0.24 ( 3) link_ALPHA1-6 : angle 1.18639 / 0.84 ( 9) link_BETA1-4 : bond 0.00476 / 0.27 ( 27) link_BETA1-4 : angle 1.38422 / 0.98 ( 81) link_NAG-ASN : bond 0.00304 / 0.19 ( 63) link_NAG-ASN : angle 1.75890 / 1.24 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 208 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.6731 (ttm) REVERT: A 96 TRP cc_start: 0.8951 (m100) cc_final: 0.8663 (m100) REVERT: A 100 MET cc_start: 0.7836 (mtp) cc_final: 0.7584 (mtp) REVERT: A 161 MET cc_start: 0.8705 (tpt) cc_final: 0.8498 (tpt) REVERT: B 543 ASN cc_start: 0.8926 (t0) cc_final: 0.8370 (t0) REVERT: B 577 GLN cc_start: 0.7992 (tp-100) cc_final: 0.7657 (tt0) REVERT: B 615 SER cc_start: 0.8415 (t) cc_final: 0.8204 (m) REVERT: B 659 ASP cc_start: 0.7789 (m-30) cc_final: 0.7586 (m-30) REVERT: C 95 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.6475 (ttm) REVERT: C 342 LEU cc_start: 0.9120 (tp) cc_final: 0.8906 (mt) REVERT: C 424 ILE cc_start: 0.9227 (mp) cc_final: 0.8994 (mt) REVERT: D 615 SER cc_start: 0.8339 (t) cc_final: 0.8098 (m) REVERT: D 616 ASN cc_start: 0.7896 (p0) cc_final: 0.7545 (p0) REVERT: E 95 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.6715 (ttm) REVERT: F 577 GLN cc_start: 0.8008 (tp-100) cc_final: 0.7517 (tt0) REVERT: F 615 SER cc_start: 0.8506 (t) cc_final: 0.8201 (m) REVERT: F 616 ASN cc_start: 0.8111 (p0) cc_final: 0.7897 (p0) outliers start: 43 outliers final: 32 residues processed: 235 average time/residue: 0.1065 time to fit residues: 39.3969 Evaluate side-chains 208 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 155 optimal weight: 0.0030 chunk 1 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 124 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 162 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN A 170 GLN B 607 ASN C 82 GLN ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN E 114 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.125754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.102049 restraints weight = 22231.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.104908 restraints weight = 15084.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.106895 restraints weight = 11691.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.108110 restraints weight = 9849.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.109159 restraints weight = 8796.677| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15660 Z= 0.124 Angle : 0.614 9.373 21438 Z= 0.301 Chirality : 0.044 0.242 2664 Planarity : 0.004 0.036 2565 Dihedral : 4.686 17.305 1866 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.05 % Allowed : 10.86 % Favored : 86.10 % 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: 0.67 (0.19), residues: 1731 helix: 1.19 (0.25), residues: 486 sheet: 0.78 (0.22), residues: 480 loop : -0.17 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 419 TYR 0.010 0.001 TYR A 217 PHE 0.015 0.001 PHE C 53 TRP 0.009 0.001 TRP A 479 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (15540) covalent geometry : angle 0.59396 / 0.30 (21102) SS BOND : bond 0.00351 / 0.16 ( 24) SS BOND : angle 0.66790 / 0.45 ( 48) hydrogen bonds : bond 0.04591 / 3.03 ( 630) hydrogen bonds : angle 5.04614 / 3.51 ( 1809) link_ALPHA1-3 : bond 0.00664 / 0.33 ( 3) link_ALPHA1-3 : angle 1.41791 / 0.95 ( 9) link_ALPHA1-6 : bond 0.00430 / 0.22 ( 3) link_ALPHA1-6 : angle 1.30672 / 0.89 ( 9) link_BETA1-4 : bond 0.00455 / 0.26 ( 27) link_BETA1-4 : angle 1.22945 / 0.89 ( 81) link_NAG-ASN : bond 0.00238 / 0.15 ( 63) link_NAG-ASN : angle 1.54568 / 1.09 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 203 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.6628 (ttm) REVERT: A 100 MET cc_start: 0.7615 (mtp) cc_final: 0.7408 (mtp) REVERT: A 161 MET cc_start: 0.8584 (tpt) cc_final: 0.8313 (tpt) REVERT: B 523 LEU cc_start: 0.9297 (mt) cc_final: 0.9027 (mt) REVERT: B 543 ASN cc_start: 0.8896 (t0) cc_final: 0.8472 (t0) REVERT: B 632 ASP cc_start: 0.7694 (t0) cc_final: 0.7417 (t0) REVERT: C 95 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6537 (ttm) REVERT: C 424 ILE cc_start: 0.9174 (mp) cc_final: 0.8946 (mt) REVERT: D 523 LEU cc_start: 0.9215 (mt) cc_final: 0.8935 (mt) REVERT: D 564 HIS cc_start: 0.5087 (t-90) cc_final: 0.4604 (t-90) REVERT: D 574 LYS cc_start: 0.7846 (mmtt) cc_final: 0.7627 (mmtp) REVERT: D 615 SER cc_start: 0.8204 (t) cc_final: 0.7915 (m) REVERT: E 163 THR cc_start: 0.9297 (m) cc_final: 0.9032 (m) REVERT: F 523 LEU cc_start: 0.9304 (mt) cc_final: 0.8892 (mt) REVERT: F 577 GLN cc_start: 0.7819 (tp-100) cc_final: 0.7447 (tt0) REVERT: F 615 SER cc_start: 0.8524 (t) cc_final: 0.8229 (m) REVERT: F 616 ASN cc_start: 0.8100 (p0) cc_final: 0.7761 (p0) outliers start: 48 outliers final: 26 residues processed: 228 average time/residue: 0.0895 time to fit residues: 33.2776 Evaluate side-chains 203 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 132 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN A 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.125732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.100935 restraints weight = 22738.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.103710 restraints weight = 15863.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105635 restraints weight = 12595.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.106939 restraints weight = 10749.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.107639 restraints weight = 9684.740| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15660 Z= 0.178 Angle : 0.635 10.407 21438 Z= 0.308 Chirality : 0.045 0.251 2664 Planarity : 0.004 0.038 2565 Dihedral : 4.633 17.312 1866 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.49 % Allowed : 11.56 % Favored : 84.95 % 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: 0.45 (0.19), residues: 1731 helix: 1.14 (0.25), residues: 486 sheet: 0.63 (0.22), residues: 480 loop : -0.40 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 542 TYR 0.015 0.002 TYR A 217 PHE 0.013 0.002 PHE C 376 TRP 0.016 0.001 TRP E 96 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (15540) covalent geometry : angle 0.61672 / 0.31 (21102) SS BOND : bond 0.00323 / 0.20 ( 24) SS BOND : angle 0.72265 / 0.53 ( 48) hydrogen bonds : bond 0.04556 / 3.00 ( 630) hydrogen bonds : angle 4.99968 / 3.46 ( 1809) link_ALPHA1-3 : bond 0.00685 / 0.34 ( 3) link_ALPHA1-3 : angle 1.44935 / 0.94 ( 9) link_ALPHA1-6 : bond 0.00484 / 0.24 ( 3) link_ALPHA1-6 : angle 1.25878 / 0.87 ( 9) link_BETA1-4 : bond 0.00377 / 0.22 ( 27) link_BETA1-4 : angle 1.20877 / 0.86 ( 81) link_NAG-ASN : bond 0.00210 / 0.14 ( 63) link_NAG-ASN : angle 1.54297 / 1.08 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 199 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.7096 (ttm) REVERT: A 161 MET cc_start: 0.8606 (tpt) cc_final: 0.8280 (tpt) REVERT: B 632 ASP cc_start: 0.8059 (t0) cc_final: 0.7796 (t0) REVERT: C 95 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.6704 (ttm) REVERT: C 424 ILE cc_start: 0.9220 (mp) cc_final: 0.8976 (mt) REVERT: D 530 MET cc_start: 0.8757 (mmm) cc_final: 0.8276 (mtp) REVERT: D 564 HIS cc_start: 0.5125 (t-90) cc_final: 0.4652 (t-90) REVERT: D 574 LYS cc_start: 0.7964 (mmtt) cc_final: 0.7665 (mmtp) REVERT: D 615 SER cc_start: 0.8152 (t) cc_final: 0.7875 (m) REVERT: F 615 SER cc_start: 0.8432 (t) cc_final: 0.8195 (m) REVERT: F 616 ASN cc_start: 0.8213 (p0) cc_final: 0.7827 (p0) outliers start: 55 outliers final: 38 residues processed: 235 average time/residue: 0.0960 time to fit residues: 36.6889 Evaluate side-chains 211 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 130 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 52 optimal weight: 0.1980 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.124407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.100713 restraints weight = 22427.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.103469 restraints weight = 15363.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.105383 restraints weight = 11961.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.106655 restraints weight = 10107.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.107510 restraints weight = 9004.863| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15660 Z= 0.129 Angle : 0.595 10.087 21438 Z= 0.287 Chirality : 0.044 0.255 2664 Planarity : 0.003 0.037 2565 Dihedral : 4.478 16.969 1866 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.98 % Allowed : 12.70 % Favored : 84.32 % 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: 0.49 (0.19), residues: 1731 helix: 1.23 (0.25), residues: 486 sheet: 0.63 (0.22), residues: 480 loop : -0.40 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 542 TYR 0.007 0.001 TYR A 191 PHE 0.013 0.001 PHE C 53 TRP 0.013 0.001 TRP E 96 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (15540) covalent geometry : angle 0.57523 / 0.28 (21102) SS BOND : bond 0.00218 / 0.15 ( 24) SS BOND : angle 0.61363 / 0.43 ( 48) hydrogen bonds : bond 0.04214 / 2.79 ( 630) hydrogen bonds : angle 4.89792 / 3.39 ( 1809) link_ALPHA1-3 : bond 0.00639 / 0.32 ( 3) link_ALPHA1-3 : angle 1.41936 / 0.94 ( 9) link_ALPHA1-6 : bond 0.00459 / 0.23 ( 3) link_ALPHA1-6 : angle 1.31695 / 0.90 ( 9) link_BETA1-4 : bond 0.00404 / 0.23 ( 27) link_BETA1-4 : angle 1.19205 / 0.86 ( 81) link_NAG-ASN : bond 0.00182 / 0.12 ( 63) link_NAG-ASN : angle 1.54475 / 1.08 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6835 (ttm) REVERT: A 161 MET cc_start: 0.8621 (tpt) cc_final: 0.8372 (tpt) REVERT: B 523 LEU cc_start: 0.9369 (mt) cc_final: 0.9013 (mt) REVERT: B 574 LYS cc_start: 0.7645 (mmtt) cc_final: 0.7425 (mmtp) REVERT: B 632 ASP cc_start: 0.8051 (t0) cc_final: 0.7810 (t0) REVERT: B 653 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7403 (tm-30) REVERT: C 95 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6624 (ttm) REVERT: C 424 ILE cc_start: 0.9161 (mp) cc_final: 0.8950 (mt) REVERT: D 523 LEU cc_start: 0.9330 (mt) cc_final: 0.9034 (mt) REVERT: D 530 MET cc_start: 0.8693 (mmm) cc_final: 0.8181 (mtp) REVERT: D 564 HIS cc_start: 0.5097 (t-90) cc_final: 0.4523 (t-90) REVERT: D 574 LYS cc_start: 0.7908 (mmtt) cc_final: 0.7650 (mmtp) REVERT: D 615 SER cc_start: 0.8061 (t) cc_final: 0.7857 (m) REVERT: E 150 MET cc_start: 0.8871 (mtp) cc_final: 0.8576 (mtp) REVERT: E 195 ASN cc_start: 0.8232 (p0) cc_final: 0.7991 (p0) REVERT: F 523 LEU cc_start: 0.9354 (mt) cc_final: 0.9014 (mt) REVERT: F 530 MET cc_start: 0.8537 (mmm) cc_final: 0.8241 (mtp) REVERT: F 542 ARG cc_start: 0.7603 (ptm160) cc_final: 0.7360 (ptm160) REVERT: F 615 SER cc_start: 0.8454 (t) cc_final: 0.8190 (m) REVERT: F 616 ASN cc_start: 0.8164 (p0) cc_final: 0.7730 (p0) REVERT: F 617 ARG cc_start: 0.8101 (tpp80) cc_final: 0.7502 (ttp80) outliers start: 47 outliers final: 33 residues processed: 224 average time/residue: 0.1006 time to fit residues: 36.3310 Evaluate side-chains 214 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 161 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.128744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.104695 restraints weight = 22193.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107448 restraints weight = 15541.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.109370 restraints weight = 12368.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.110646 restraints weight = 10548.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111417 restraints weight = 9510.909| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15660 Z= 0.162 Angle : 0.627 12.206 21438 Z= 0.299 Chirality : 0.045 0.262 2664 Planarity : 0.003 0.041 2565 Dihedral : 4.503 20.055 1866 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.30 % Allowed : 13.33 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.19), residues: 1731 helix: 1.40 (0.25), residues: 468 sheet: 0.56 (0.22), residues: 474 loop : -0.29 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 542 TYR 0.012 0.001 TYR A 217 PHE 0.012 0.002 PHE C 376 TRP 0.011 0.001 TRP B 571 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (15540) covalent geometry : angle 0.60729 / 0.30 (21102) SS BOND : bond 0.00258 / 0.18 ( 24) SS BOND : angle 0.65260 / 0.48 ( 48) hydrogen bonds : bond 0.04261 / 2.81 ( 630) hydrogen bonds : angle 4.89830 / 3.38 ( 1809) link_ALPHA1-3 : bond 0.00657 / 0.33 ( 3) link_ALPHA1-3 : angle 1.44334 / 0.93 ( 9) link_ALPHA1-6 : bond 0.00520 / 0.26 ( 3) link_ALPHA1-6 : angle 1.30059 / 0.89 ( 9) link_BETA1-4 : bond 0.00381 / 0.22 ( 27) link_BETA1-4 : angle 1.16135 / 0.83 ( 81) link_NAG-ASN : bond 0.00229 / 0.16 ( 63) link_NAG-ASN : angle 1.58732 / 1.13 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 189 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.7060 (ttm) REVERT: B 523 LEU cc_start: 0.9390 (mt) cc_final: 0.9019 (mt) REVERT: B 574 LYS cc_start: 0.7739 (mmtt) cc_final: 0.7501 (mmtp) REVERT: B 653 GLN cc_start: 0.7944 (tm-30) cc_final: 0.7669 (tm-30) REVERT: C 95 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6649 (ttm) REVERT: D 530 MET cc_start: 0.8705 (mmm) cc_final: 0.8065 (mtp) REVERT: D 564 HIS cc_start: 0.5052 (t-90) cc_final: 0.4630 (t-90) REVERT: D 574 LYS cc_start: 0.7951 (mmtt) cc_final: 0.7721 (mmtp) REVERT: D 615 SER cc_start: 0.8027 (t) cc_final: 0.7778 (m) REVERT: E 150 MET cc_start: 0.8855 (mtp) cc_final: 0.8578 (mtp) REVERT: F 523 LEU cc_start: 0.9384 (mt) cc_final: 0.9106 (mt) REVERT: F 542 ARG cc_start: 0.7628 (ptm160) cc_final: 0.7391 (ptm160) REVERT: F 615 SER cc_start: 0.8415 (t) cc_final: 0.8164 (m) REVERT: F 616 ASN cc_start: 0.8072 (p0) cc_final: 0.7621 (p0) REVERT: F 617 ARG cc_start: 0.8083 (tpp80) cc_final: 0.7528 (tpp80) outliers start: 52 outliers final: 40 residues processed: 224 average time/residue: 0.0969 time to fit residues: 34.9929 Evaluate side-chains 217 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 23 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 44 optimal weight: 0.0970 chunk 46 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.124003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.100478 restraints weight = 22535.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.103244 restraints weight = 15430.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.105138 restraints weight = 11975.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.106428 restraints weight = 10127.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.107233 restraints weight = 9020.444| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15660 Z= 0.138 Angle : 0.611 16.246 21438 Z= 0.291 Chirality : 0.045 0.265 2664 Planarity : 0.003 0.036 2565 Dihedral : 4.471 19.160 1866 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.24 % Allowed : 13.71 % Favored : 83.05 % 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: 0.54 (0.20), residues: 1731 helix: 1.39 (0.25), residues: 468 sheet: 0.53 (0.22), residues: 474 loop : -0.30 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 542 TYR 0.009 0.001 TYR A 217 PHE 0.013 0.001 PHE E 53 TRP 0.010 0.001 TRP B 571 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (15540) covalent geometry : angle 0.59329 / 0.29 (21102) SS BOND : bond 0.00228 / 0.15 ( 24) SS BOND : angle 0.66849 / 0.52 ( 48) hydrogen bonds : bond 0.04077 / 2.70 ( 630) hydrogen bonds : angle 4.90226 / 3.39 ( 1809) link_ALPHA1-3 : bond 0.00633 / 0.32 ( 3) link_ALPHA1-3 : angle 1.42406 / 0.93 ( 9) link_ALPHA1-6 : bond 0.00591 / 0.30 ( 3) link_ALPHA1-6 : angle 1.37223 / 0.93 ( 9) link_BETA1-4 : bond 0.00409 / 0.23 ( 27) link_BETA1-4 : angle 1.14630 / 0.82 ( 81) link_NAG-ASN : bond 0.00211 / 0.15 ( 63) link_NAG-ASN : angle 1.50016 / 1.07 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 189 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6856 (ttm) REVERT: B 523 LEU cc_start: 0.9357 (mt) cc_final: 0.8994 (mt) REVERT: B 574 LYS cc_start: 0.7718 (mmtt) cc_final: 0.7505 (mmtp) REVERT: B 653 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7734 (tm-30) REVERT: C 95 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6606 (ttm) REVERT: D 523 LEU cc_start: 0.9341 (mt) cc_final: 0.9079 (mt) REVERT: D 530 MET cc_start: 0.8681 (mmm) cc_final: 0.7994 (mtp) REVERT: D 540 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8107 (mp10) REVERT: D 564 HIS cc_start: 0.4870 (t-90) cc_final: 0.4519 (t-90) REVERT: D 574 LYS cc_start: 0.7937 (mmtt) cc_final: 0.7723 (mmtp) REVERT: D 615 SER cc_start: 0.7894 (t) cc_final: 0.7656 (m) REVERT: E 150 MET cc_start: 0.8850 (mtp) cc_final: 0.8583 (mtp) REVERT: F 523 LEU cc_start: 0.9300 (mt) cc_final: 0.9056 (mt) REVERT: F 542 ARG cc_start: 0.7620 (ptm160) cc_final: 0.7418 (ptm160) REVERT: F 577 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7235 (tt0) REVERT: F 616 ASN cc_start: 0.8006 (p0) cc_final: 0.7540 (p0) REVERT: F 617 ARG cc_start: 0.7951 (tpp80) cc_final: 0.7693 (tpp80) outliers start: 51 outliers final: 44 residues processed: 223 average time/residue: 0.1060 time to fit residues: 38.0033 Evaluate side-chains 224 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 176 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 577 GLN Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 22 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 160 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 36 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.123296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.099794 restraints weight = 22390.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.102568 restraints weight = 15275.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.104399 restraints weight = 11841.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.105725 restraints weight = 10020.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.106659 restraints weight = 8905.623| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15660 Z= 0.146 Angle : 0.618 15.341 21438 Z= 0.296 Chirality : 0.045 0.269 2664 Planarity : 0.003 0.036 2565 Dihedral : 4.478 17.457 1866 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.17 % Allowed : 14.35 % Favored : 82.48 % 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: 0.30 (0.19), residues: 1731 helix: 1.18 (0.25), residues: 483 sheet: 0.46 (0.22), residues: 474 loop : -0.53 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 542 TYR 0.010 0.001 TYR A 217 PHE 0.010 0.001 PHE A 376 TRP 0.021 0.001 TRP E 96 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (15540) covalent geometry : angle 0.59889 / 0.29 (21102) SS BOND : bond 0.00366 / 0.29 ( 24) SS BOND : angle 0.96702 / 0.68 ( 48) hydrogen bonds : bond 0.04088 / 2.69 ( 630) hydrogen bonds : angle 4.84482 / 3.35 ( 1809) link_ALPHA1-3 : bond 0.00636 / 0.32 ( 3) link_ALPHA1-3 : angle 1.43127 / 0.92 ( 9) link_ALPHA1-6 : bond 0.00442 / 0.22 ( 3) link_ALPHA1-6 : angle 1.30847 / 0.89 ( 9) link_BETA1-4 : bond 0.00390 / 0.23 ( 27) link_BETA1-4 : angle 1.15287 / 0.83 ( 81) link_NAG-ASN : bond 0.00180 / 0.12 ( 63) link_NAG-ASN : angle 1.50782 / 1.08 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 186 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6845 (ttm) REVERT: B 523 LEU cc_start: 0.9377 (mt) cc_final: 0.9098 (mt) REVERT: B 574 LYS cc_start: 0.7680 (mmtt) cc_final: 0.7469 (mmtp) REVERT: B 653 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7752 (tm-30) REVERT: C 95 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6667 (ttm) REVERT: C 150 MET cc_start: 0.8548 (mtp) cc_final: 0.8204 (mtm) REVERT: D 523 LEU cc_start: 0.9363 (mt) cc_final: 0.9118 (mt) REVERT: D 530 MET cc_start: 0.8671 (mmm) cc_final: 0.8014 (mtp) REVERT: D 540 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8135 (mp10) REVERT: D 564 HIS cc_start: 0.4845 (t-90) cc_final: 0.4382 (t-90) REVERT: D 574 LYS cc_start: 0.7933 (mmtt) cc_final: 0.7730 (mmtp) REVERT: E 150 MET cc_start: 0.8881 (mtp) cc_final: 0.8600 (mtp) REVERT: F 523 LEU cc_start: 0.9315 (mt) cc_final: 0.9076 (mt) REVERT: F 542 ARG cc_start: 0.7631 (ptm160) cc_final: 0.7428 (ptm160) REVERT: F 616 ASN cc_start: 0.8053 (p0) cc_final: 0.7544 (p0) REVERT: F 617 ARG cc_start: 0.7927 (tpp80) cc_final: 0.7537 (tpp80) REVERT: F 626 MET cc_start: 0.7546 (ttt) cc_final: 0.6980 (ttt) outliers start: 50 outliers final: 43 residues processed: 220 average time/residue: 0.1030 time to fit residues: 36.6779 Evaluate side-chains 224 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 178 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 163 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 53 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 59 optimal weight: 0.0000 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 625 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.124457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.101164 restraints weight = 22397.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.103937 restraints weight = 15225.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.105907 restraints weight = 11768.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.107070 restraints weight = 9872.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.108135 restraints weight = 8816.842| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15660 Z= 0.126 Angle : 0.602 14.255 21438 Z= 0.293 Chirality : 0.044 0.272 2664 Planarity : 0.003 0.036 2565 Dihedral : 4.419 21.981 1866 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.86 % Allowed : 14.60 % Favored : 82.54 % 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: 0.39 (0.20), residues: 1731 helix: 1.28 (0.25), residues: 483 sheet: 0.50 (0.22), residues: 480 loop : -0.49 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 542 TYR 0.008 0.001 TYR A 217 PHE 0.010 0.001 PHE E 53 TRP 0.018 0.001 TRP E 96 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (15540) covalent geometry : angle 0.58544 / 0.29 (21102) SS BOND : bond 0.00254 / 0.18 ( 24) SS BOND : angle 0.80312 / 0.57 ( 48) hydrogen bonds : bond 0.03927 / 2.60 ( 630) hydrogen bonds : angle 4.82756 / 3.34 ( 1809) link_ALPHA1-3 : bond 0.00624 / 0.31 ( 3) link_ALPHA1-3 : angle 1.40163 / 0.91 ( 9) link_ALPHA1-6 : bond 0.00428 / 0.21 ( 3) link_ALPHA1-6 : angle 1.32784 / 0.90 ( 9) link_BETA1-4 : bond 0.00402 / 0.24 ( 27) link_BETA1-4 : angle 1.13665 / 0.82 ( 81) link_NAG-ASN : bond 0.00171 / 0.11 ( 63) link_NAG-ASN : angle 1.41156 / 1.01 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.6736 (ttm) REVERT: A 150 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8092 (ttm) REVERT: B 523 LEU cc_start: 0.9266 (mt) cc_final: 0.9021 (mt) REVERT: B 564 HIS cc_start: 0.5546 (t-90) cc_final: 0.5332 (t-90) REVERT: B 653 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7766 (tm-30) REVERT: C 95 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6636 (ttm) REVERT: D 523 LEU cc_start: 0.9342 (mt) cc_final: 0.9133 (mt) REVERT: D 530 MET cc_start: 0.8638 (mmm) cc_final: 0.7978 (mtp) REVERT: D 540 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7952 (mp10) REVERT: D 564 HIS cc_start: 0.4968 (t-90) cc_final: 0.4522 (t-90) REVERT: D 574 LYS cc_start: 0.7890 (mmtt) cc_final: 0.7659 (mmtp) REVERT: E 150 MET cc_start: 0.8899 (mtp) cc_final: 0.8592 (mtp) REVERT: F 523 LEU cc_start: 0.9288 (mt) cc_final: 0.9031 (mt) REVERT: F 542 ARG cc_start: 0.7571 (ptm160) cc_final: 0.7361 (ptm160) REVERT: F 616 ASN cc_start: 0.8057 (p0) cc_final: 0.7556 (p0) REVERT: F 617 ARG cc_start: 0.7883 (tpp80) cc_final: 0.7541 (tpp80) outliers start: 45 outliers final: 37 residues processed: 226 average time/residue: 0.1068 time to fit residues: 38.6978 Evaluate side-chains 223 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 625 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 78 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 53 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 625 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.124971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.101498 restraints weight = 22264.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.104216 restraints weight = 15347.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.106066 restraints weight = 11968.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.107442 restraints weight = 10117.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108236 restraints weight = 9014.811| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.320 15660 Z= 0.246 Angle : 0.807 59.198 21438 Z= 0.446 Chirality : 0.049 0.890 2664 Planarity : 0.004 0.072 2565 Dihedral : 4.515 38.015 1866 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.67 % Allowed : 15.05 % Favored : 82.29 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.19), residues: 1731 helix: 1.26 (0.25), residues: 483 sheet: 0.50 (0.22), residues: 480 loop : -0.49 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.000 ARG D 617 TYR 0.019 0.002 TYR E 191 PHE 0.013 0.002 PHE A 468 TRP 0.019 0.001 TRP A 96 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.25 (15540) covalent geometry : angle 0.79733 / 0.45 (21102) SS BOND : bond 0.00261 / 0.18 ( 24) SS BOND : angle 0.77375 / 0.55 ( 48) hydrogen bonds : bond 0.03963 / 2.62 ( 630) hydrogen bonds : angle 4.83363 / 3.35 ( 1809) link_ALPHA1-3 : bond 0.00607 / 0.30 ( 3) link_ALPHA1-3 : angle 1.38701 / 0.89 ( 9) link_ALPHA1-6 : bond 0.00428 / 0.21 ( 3) link_ALPHA1-6 : angle 1.30994 / 0.89 ( 9) link_BETA1-4 : bond 0.00403 / 0.24 ( 27) link_BETA1-4 : angle 1.13300 / 0.82 ( 81) link_NAG-ASN : bond 0.00173 / 0.11 ( 63) link_NAG-ASN : angle 1.40994 / 1.00 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2173.93 seconds wall clock time: 38 minutes 45.07 seconds (2325.07 seconds total)