Starting phenix.real_space_refine on Fri Feb 6 01:14:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mqg_48523/02_2026/9mqg_48523.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mqg_48523/02_2026/9mqg_48523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mqg_48523/02_2026/9mqg_48523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mqg_48523/02_2026/9mqg_48523.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mqg_48523/02_2026/9mqg_48523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mqg_48523/02_2026/9mqg_48523.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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 134 5.16 5 C 13363 2.51 5 N 3590 2.21 5 O 4250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21337 Number of models: 1 Model: "" Number of chains: 31 Chain: "H" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1039 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'TYS:plan-2': 3} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 869 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 9, 'TRANS': 103} Chain: "G" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "I" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "J" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "K" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "M" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "N" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "A" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3431 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 20, 'TRANS': 414} Chain breaks: 3 Chain: "B" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "C" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3431 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 20, 'TRANS': 414} Chain breaks: 3 Chain: "E" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "D" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3431 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 20, 'TRANS': 414} Chain breaks: 3 Chain: "F" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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 dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.34, per 1000 atoms: 0.25 Number of scatterers: 21337 At special positions: 0 Unit cell: (123.192, 120.06, 184.788, 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 134 16.00 O 4250 8.00 N 3590 7.00 C 13363 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.02 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.13 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN R 4 " - " MAN R 5 " ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " ALPHA1-6 " BMA P 3 " - " MAN P 5 " BETA1-4 " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " NAG-ASN " NAG A 601 " - " ASN A 392 " " NAG A 602 " - " ASN A 339 " " NAG A 603 " - " ASN A 332 " " NAG A 604 " - " ASN A 448 " " NAG A 605 " - " ASN A 301 " " NAG A 606 " - " ASN A 88 " " NAG A 607 " - " ASN A 197 " " NAG A 608 " - " ASN A 133 " " NAG A 609 " - " ASN A 234 " " NAG A 610 " - " ASN A 276 " " NAG B 701 " - " ASN B 618 " " NAG C 601 " - " ASN C 392 " " NAG C 602 " - " ASN C 448 " " NAG C 603 " - " ASN C 133 " " NAG C 604 " - " ASN C 197 " " NAG C 605 " - " ASN C 301 " " NAG C 606 " - " ASN C 332 " " NAG C 607 " - " ASN C 295 " " NAG C 608 " - " ASN C 276 " " NAG C 609 " - " ASN C 234 " " NAG C 610 " - " ASN C 88 " " NAG D 601 " - " ASN D 156 " " NAG D 602 " - " ASN D 133 " " NAG D 603 " - " ASN D 386 " " NAG D 604 " - " ASN D 392 " " NAG D 605 " - " ASN D 276 " " NAG D 606 " - " ASN D 234 " " NAG D 607 " - " ASN D 332 " " NAG D 608 " - " ASN D 301 " " NAG D 609 " - " ASN D 295 " " NAG D 610 " - " ASN D 448 " " NAG D 611 " - " ASN D 339 " " NAG D 612 " - " ASN D 355 " " NAG E 701 " - " ASN E 618 " " NAG E 702 " - " ASN E 611 " " NAG E 703 " - " ASN E 637 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 618 " " NAG O 1 " - " ASN A 386 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 156 " " NAG R 1 " - " ASN A 160 " " NAG S 1 " - " ASN C 386 " " NAG T 1 " - " ASN C 262 " " NAG U 1 " - " ASN C 156 " " NAG V 1 " - " ASN C 160 " " NAG W 1 " - " ASN D 160 " " NAG X 1 " - " ASN D 88 " " NAG Y 1 " - " ASN D 262 " Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.1 seconds 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4788 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 41 sheets defined 19.9% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.539A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.555A pdb=" N GLU G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.983A pdb=" N GLU J 83 " --> pdb=" O ALA J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.097A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 removed outlier: 4.008A pdb=" N ARG A 151 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.062A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.230A 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 390 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.798A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 596 removed outlier: 3.527A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'C' and resid 98 through 114 removed outlier: 3.935A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 334 through 354 removed outlier: 3.645A 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 390 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.834A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 425 through 429' Processing helix chain 'C' and resid 477 through 482 removed outlier: 3.844A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.394A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 542 Processing helix chain 'E' and resid 571 through 596 Processing helix chain 'E' and resid 618 through 623 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 662 Processing helix chain 'D' and resid 98 through 117 removed outlier: 4.043A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 139 through 151 removed outlier: 3.910A pdb=" N ARG D 151 " --> pdb=" O ASP D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 334 through 354 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 377 through 381 removed outlier: 3.581A pdb=" N GLY D 380 " --> pdb=" O ASN D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 390 Processing helix chain 'D' and resid 475 through 481 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.532A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 662 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100G through 100K Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.753A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AA6, first strand: chain 'G' and resid 20 through 24 Processing sheet with id=AA7, first strand: chain 'G' and resid 33 through 38 removed outlier: 6.447A pdb=" N TRP G 35 " --> pdb=" O MET G 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 45 through 48 current: chain 'G' and resid 95A through 98 Processing sheet with id=AA8, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'I' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 11 through 12 current: chain 'I' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 57 through 59 current: chain 'I' and resid 100H through 103 Processing sheet with id=AB1, first strand: chain 'J' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 9 through 13 current: chain 'J' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 45 through 48 current: chain 'J' and resid 95A through 97 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'J' and resid 19 through 24 Processing sheet with id=AB3, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'K' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 11 through 12 current: chain 'K' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 100H through 103 Processing sheet with id=AB5, first strand: chain 'M' and resid 3 through 5 Processing sheet with id=AB6, first strand: chain 'M' and resid 11 through 12 removed outlier: 6.945A pdb=" N MET M 34 " --> pdb=" O LEU M 50 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 9 through 13 current: chain 'N' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 96 through 98 No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AB9, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.385A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AC2, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.881A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AC4, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AC5, first strand: chain 'A' and resid 181 through 186 removed outlier: 4.480A pdb=" N ASN A 190 " --> pdb=" O MET A 184 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.500A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 307 removed outlier: 5.730A pdb=" N LYS A 305 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N THR A 319 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE A 307 " --> pdb=" O TYR A 317 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N TYR A 317 " --> pdb=" O ILE A 307 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 466 through 470 Processing sheet with id=AC8, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.333A pdb=" N VAL C 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR E 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AD1, first strand: chain 'C' and resid 74 through 75 removed outlier: 7.252A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AD3, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AD4, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AD5, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.604A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 311 removed outlier: 6.786A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR C 303 " --> pdb=" O GLY C 320 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLN C 314 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 314 through 323 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 466 through 470 Processing sheet with id=AD7, first strand: chain 'D' and resid 494 through 499 removed outlier: 4.931A pdb=" N VAL D 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.231A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 74 through 75 removed outlier: 7.028A pdb=" N CYS D 54 " --> pdb=" O VAL D 75 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AE2, first strand: chain 'D' and resid 130 through 133 Processing sheet with id=AE3, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AE4, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.077A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 259 through 261 current: chain 'D' and resid 284 through 308 removed outlier: 6.247A pdb=" N ASN D 301 " --> pdb=" O ILE D 322 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ILE D 322 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR D 303 " --> pdb=" O GLY D 320 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 315 through 323 current: chain 'D' and resid 382 through 385 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 382 through 385 current: chain 'D' and resid 466 through 470 608 hydrogen bonds defined for protein. 1587 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.19 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 6847 1.36 - 1.49: 6022 1.49 - 1.63: 8720 1.63 - 1.77: 5 1.77 - 1.90: 178 Bond restraints: 21772 Sorted by residual: bond pdb=" CB CYS A 218 " pdb=" SG CYS A 218 " ideal model delta sigma weight residual 1.808 1.904 -0.096 3.30e-02 9.18e+02 8.53e+00 bond pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " ideal model delta sigma weight residual 1.808 1.730 0.078 3.30e-02 9.18e+02 5.52e+00 bond pdb=" CG LEU L 33 " pdb=" CD2 LEU L 33 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.91e+00 bond pdb=" C ARG C 298 " pdb=" N PRO C 299 " ideal model delta sigma weight residual 1.339 1.404 -0.065 3.40e-02 8.65e+02 3.69e+00 bond pdb=" CB VAL H 50 " pdb=" CG2 VAL H 50 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.58e+00 ... (remaining 21767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 29036 2.98 - 5.96: 492 5.96 - 8.94: 18 8.94 - 11.91: 1 11.91 - 14.89: 2 Bond angle restraints: 29549 Sorted by residual: angle pdb=" N SER K 74 " pdb=" CA SER K 74 " pdb=" C SER K 74 " ideal model delta sigma weight residual 108.52 96.37 12.15 1.63e+00 3.76e-01 5.55e+01 angle pdb=" CA CYS A 247 " pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " ideal model delta sigma weight residual 114.40 129.29 -14.89 2.30e+00 1.89e-01 4.19e+01 angle pdb=" N LYS K 75 " pdb=" CA LYS K 75 " pdb=" C LYS K 75 " ideal model delta sigma weight residual 110.80 99.55 11.25 2.13e+00 2.20e-01 2.79e+01 angle pdb=" N GLU A 482 " pdb=" CA GLU A 482 " pdb=" C GLU A 482 " ideal model delta sigma weight residual 110.14 103.68 6.46 1.55e+00 4.16e-01 1.74e+01 angle pdb=" N LYS K 75 " pdb=" CA LYS K 75 " pdb=" CB LYS K 75 " ideal model delta sigma weight residual 110.49 117.28 -6.79 1.69e+00 3.50e-01 1.61e+01 ... (remaining 29544 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.63: 13436 21.63 - 43.26: 260 43.26 - 64.89: 74 64.89 - 86.52: 29 86.52 - 108.15: 17 Dihedral angle restraints: 13816 sinusoidal: 6336 harmonic: 7480 Sorted by residual: dihedral pdb=" CB CYS D 378 " pdb=" SG CYS D 378 " pdb=" SG CYS D 445 " pdb=" CB CYS D 445 " ideal model delta sinusoidal sigma weight residual -86.00 -133.42 47.42 1 1.00e+01 1.00e-02 3.10e+01 dihedral pdb=" CB CYS A 218 " pdb=" SG CYS A 218 " pdb=" SG CYS A 247 " pdb=" CB CYS A 247 " ideal model delta sinusoidal sigma weight residual 93.00 46.30 46.70 1 1.00e+01 1.00e-02 3.02e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -120.05 34.05 1 1.00e+01 1.00e-02 1.65e+01 ... (remaining 13813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2665 0.066 - 0.132: 681 0.132 - 0.197: 122 0.197 - 0.263: 11 0.263 - 0.329: 1 Chirality restraints: 3480 Sorted by residual: chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN A 160 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA CYS A 247 " pdb=" N CYS A 247 " pdb=" C CYS A 247 " pdb=" CB CYS A 247 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE C 181 " pdb=" N ILE C 181 " pdb=" C ILE C 181 " pdb=" CB ILE C 181 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 3477 not shown) Planarity restraints: 3734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 639 " -0.020 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C THR B 639 " 0.071 2.00e-02 2.50e+03 pdb=" O THR B 639 " -0.026 2.00e-02 2.50e+03 pdb=" N GLN B 640 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 640 " -0.019 2.00e-02 2.50e+03 3.88e-02 1.50e+01 pdb=" C GLN F 640 " 0.067 2.00e-02 2.50e+03 pdb=" O GLN F 640 " -0.025 2.00e-02 2.50e+03 pdb=" N ILE F 641 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 652 " -0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C GLN F 652 " 0.064 2.00e-02 2.50e+03 pdb=" O GLN F 652 " -0.024 2.00e-02 2.50e+03 pdb=" N GLN F 653 " -0.022 2.00e-02 2.50e+03 ... (remaining 3731 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 651 2.69 - 3.24: 19684 3.24 - 3.80: 33458 3.80 - 4.35: 45630 4.35 - 4.90: 75413 Nonbonded interactions: 174836 Sorted by model distance: nonbonded pdb=" SG CYS D 296 " pdb=" CE2 PHE D 376 " model vdw 2.139 3.700 nonbonded pdb=" OD1 ASP A 107 " pdb=" NZ LYS B 574 " model vdw 2.240 3.120 nonbonded pdb=" OE1 GLU L 50 " pdb=" ND2 ASN L 53 " model vdw 2.279 3.120 nonbonded pdb=" OH TYR G 96 " pdb=" O GLY K 96 " model vdw 2.296 3.040 nonbonded pdb=" NH1 ARG I 23 " pdb=" O LYS I 75 " model vdw 2.332 3.120 ... (remaining 174831 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = (chain 'D' and resid 32 through 610) } ncs_group { reference = chain 'B' selection = (chain 'E' and resid 519 through 701) selection = (chain 'F' and resid 519 through 701) } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' } ncs_group { reference = chain 'P' selection = chain 'R' } 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 individual isotropic 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: 4.240 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.130 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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 : 0.005 0.099 21881 Z= 0.240 Angle : 1.012 14.893 29835 Z= 0.572 Chirality : 0.059 0.329 3480 Planarity : 0.006 0.047 3684 Dihedral : 10.741 108.154 8905 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.04 % Allowed : 0.13 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.16), residues: 2558 helix: 1.18 (0.26), residues: 363 sheet: 0.88 (0.18), residues: 760 loop : 0.75 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG M 66 TYR 0.016 0.003 TYR D 217 PHE 0.023 0.003 PHE E 522 TRP 0.029 0.003 TRP H 47 HIS 0.007 0.002 HIS N 39 Details of bonding type rmsd covalent geometry : bond 0.00545 (21772) covalent geometry : angle 0.98949 (29549) SS BOND : bond 0.01637 ( 41) SS BOND : angle 2.65167 ( 82) hydrogen bonds : bond 0.13271 ( 608) hydrogen bonds : angle 6.94054 ( 1587) link_ALPHA1-2 : bond 0.00383 ( 1) link_ALPHA1-2 : angle 1.49141 ( 3) link_ALPHA1-3 : bond 0.00384 ( 2) link_ALPHA1-3 : angle 1.53872 ( 6) link_ALPHA1-6 : bond 0.00863 ( 1) link_ALPHA1-6 : angle 1.17611 ( 3) link_BETA1-4 : bond 0.00750 ( 14) link_BETA1-4 : angle 2.49143 ( 42) link_NAG-ASN : bond 0.00383 ( 50) link_NAG-ASN : angle 2.25061 ( 150) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 719 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 70 SER cc_start: 0.8854 (p) cc_final: 0.8650 (t) REVERT: H 82 MET cc_start: 0.7760 (mtt) cc_final: 0.7560 (mtt) REVERT: L 4 MET cc_start: 0.6865 (mmm) cc_final: 0.6099 (mmm) REVERT: L 27 LEU cc_start: 0.9022 (tp) cc_final: 0.8679 (tt) REVERT: L 45 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7393 (pt0) REVERT: G 24 THR cc_start: 0.9092 (m) cc_final: 0.8704 (p) REVERT: G 53 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8205 (mp10) REVERT: G 70 THR cc_start: 0.8956 (m) cc_final: 0.8753 (p) REVERT: G 95 THR cc_start: 0.8672 (m) cc_final: 0.8390 (t) REVERT: G 102 THR cc_start: 0.8405 (m) cc_final: 0.8069 (m) REVERT: I 23 ARG cc_start: 0.8169 (tpp-160) cc_final: 0.7848 (mmm160) REVERT: J 31 ASN cc_start: 0.8392 (m-40) cc_final: 0.7990 (p0) REVERT: J 74 THR cc_start: 0.8865 (m) cc_final: 0.8663 (p) REVERT: K 27 TYR cc_start: 0.8608 (p90) cc_final: 0.8242 (p90) REVERT: M 11 LEU cc_start: 0.8296 (tp) cc_final: 0.8029 (mp) REVERT: N 61 ARG cc_start: 0.8130 (mtm-85) cc_final: 0.7812 (mtm110) REVERT: A 40 TYR cc_start: 0.9103 (t80) cc_final: 0.8843 (t80) REVERT: A 100 MET cc_start: 0.9034 (mtp) cc_final: 0.8719 (mtp) REVERT: A 103 GLN cc_start: 0.7845 (mt0) cc_final: 0.7585 (tm-30) REVERT: A 107 ASP cc_start: 0.8295 (m-30) cc_final: 0.7557 (m-30) REVERT: A 114 GLN cc_start: 0.7902 (mt0) cc_final: 0.7682 (mt0) REVERT: A 205 CYS cc_start: 0.6887 (m) cc_final: 0.6541 (m) REVERT: A 305 LYS cc_start: 0.8866 (mttt) cc_final: 0.8633 (mttt) REVERT: C 97 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8512 (mtpp) REVERT: C 107 ASP cc_start: 0.8062 (m-30) cc_final: 0.7215 (m-30) REVERT: C 129 LEU cc_start: 0.8422 (mt) cc_final: 0.7988 (mp) REVERT: C 137 ASN cc_start: 0.7382 (t0) cc_final: 0.6981 (t0) REVERT: C 150 MET cc_start: 0.8152 (mmm) cc_final: 0.7897 (mmt) REVERT: C 207 LYS cc_start: 0.8155 (pttt) cc_final: 0.7571 (tptt) REVERT: C 246 GLN cc_start: 0.8054 (tp40) cc_final: 0.7779 (tp40) REVERT: C 314 GLN cc_start: 0.8320 (mm-40) cc_final: 0.7551 (mt0) REVERT: C 439 ILE cc_start: 0.8809 (mm) cc_final: 0.8560 (mm) REVERT: C 469 ARG cc_start: 0.8012 (mtt-85) cc_final: 0.7497 (mtt-85) REVERT: E 632 ASP cc_start: 0.8792 (t70) cc_final: 0.8478 (t0) REVERT: D 111 LEU cc_start: 0.8256 (tp) cc_final: 0.7942 (tt) REVERT: D 115 SER cc_start: 0.9390 (t) cc_final: 0.8995 (p) REVERT: D 123 THR cc_start: 0.8686 (m) cc_final: 0.8401 (p) REVERT: D 141 ASP cc_start: 0.8297 (m-30) cc_final: 0.8015 (m-30) REVERT: D 186 ASP cc_start: 0.7950 (t0) cc_final: 0.7709 (t0) REVERT: D 215 ILE cc_start: 0.8559 (mm) cc_final: 0.8268 (tt) REVERT: D 268 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7659 (mp0) REVERT: D 419 ARG cc_start: 0.8051 (mtt-85) cc_final: 0.7794 (mmm-85) REVERT: D 504 ARG cc_start: 0.7262 (mtt180) cc_final: 0.6783 (mtm110) REVERT: F 625 ASN cc_start: 0.8624 (t0) cc_final: 0.8302 (t0) REVERT: F 632 ASP cc_start: 0.8733 (t70) cc_final: 0.8519 (t0) outliers start: 1 outliers final: 0 residues processed: 720 average time/residue: 0.1697 time to fit residues: 183.2453 Evaluate side-chains 437 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 105 GLN ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN A 295 ASN B 570 HIS B 577 GLN B 607 ASN B 630 GLN B 637 ASN ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN C 170 GLN C 302 ASN ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 625 ASN D 33 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.126364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.098225 restraints weight = 33778.956| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.86 r_work: 0.3086 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 21881 Z= 0.215 Angle : 0.670 14.063 29835 Z= 0.344 Chirality : 0.046 0.191 3480 Planarity : 0.004 0.057 3684 Dihedral : 7.433 83.479 4231 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.61 % Allowed : 8.55 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.16), residues: 2558 helix: 2.17 (0.27), residues: 369 sheet: 0.68 (0.18), residues: 762 loop : 0.45 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 327 TYR 0.034 0.002 TYR L 49 PHE 0.021 0.002 PHE L 94 TRP 0.022 0.002 TRP D 479 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00500 (21772) covalent geometry : angle 0.64810 (29549) SS BOND : bond 0.00415 ( 41) SS BOND : angle 1.24221 ( 82) hydrogen bonds : bond 0.04931 ( 608) hydrogen bonds : angle 5.41807 ( 1587) link_ALPHA1-2 : bond 0.00426 ( 1) link_ALPHA1-2 : angle 1.69503 ( 3) link_ALPHA1-3 : bond 0.00996 ( 2) link_ALPHA1-3 : angle 2.19486 ( 6) link_ALPHA1-6 : bond 0.00654 ( 1) link_ALPHA1-6 : angle 1.57031 ( 3) link_BETA1-4 : bond 0.00356 ( 14) link_BETA1-4 : angle 1.98125 ( 42) link_NAG-ASN : bond 0.00356 ( 50) link_NAG-ASN : angle 2.05333 ( 150) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 439 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.6825 (mmm) cc_final: 0.6028 (mmm) REVERT: L 45 GLN cc_start: 0.7571 (mm-40) cc_final: 0.7130 (pt0) REVERT: L 50 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7550 (mm-30) REVERT: G 24 THR cc_start: 0.9121 (m) cc_final: 0.8745 (p) REVERT: G 70 THR cc_start: 0.9056 (m) cc_final: 0.8708 (p) REVERT: G 95 THR cc_start: 0.8837 (m) cc_final: 0.8569 (t) REVERT: I 23 ARG cc_start: 0.8113 (tpp-160) cc_final: 0.7731 (mmm160) REVERT: I 43 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8377 (mmmt) REVERT: J 74 THR cc_start: 0.8912 (m) cc_final: 0.8694 (p) REVERT: K 72 ASP cc_start: 0.8123 (t0) cc_final: 0.7726 (t0) REVERT: M 11 LEU cc_start: 0.8372 (tp) cc_final: 0.8017 (mp) REVERT: M 72 ASP cc_start: 0.8197 (t0) cc_final: 0.7952 (t0) REVERT: M 82 MET cc_start: 0.8083 (mtm) cc_final: 0.7619 (mtm) REVERT: N 61 ARG cc_start: 0.8183 (mtm-85) cc_final: 0.7982 (mtm110) REVERT: A 40 TYR cc_start: 0.9101 (t80) cc_final: 0.8841 (t80) REVERT: A 305 LYS cc_start: 0.8597 (mttt) cc_final: 0.8338 (mttp) REVERT: A 479 TRP cc_start: 0.8337 (m-10) cc_final: 0.8045 (m-10) REVERT: B 571 TRP cc_start: 0.5407 (p90) cc_final: 0.4607 (p90) REVERT: C 39 TYR cc_start: 0.9252 (m-80) cc_final: 0.9034 (m-80) REVERT: C 150 MET cc_start: 0.7995 (mmm) cc_final: 0.7767 (mmt) REVERT: C 207 LYS cc_start: 0.8129 (pttt) cc_final: 0.7758 (tttm) REVERT: C 264 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8112 (m) REVERT: C 469 ARG cc_start: 0.7935 (mtt-85) cc_final: 0.7282 (mtt-85) REVERT: C 481 SER cc_start: 0.8624 (t) cc_final: 0.8402 (p) REVERT: E 530 MET cc_start: 0.9291 (mtp) cc_final: 0.9064 (mtp) REVERT: E 632 ASP cc_start: 0.8704 (t70) cc_final: 0.8434 (t0) REVERT: D 104 MET cc_start: 0.8844 (ttt) cc_final: 0.8633 (ttt) REVERT: D 111 LEU cc_start: 0.8037 (tp) cc_final: 0.7696 (tp) REVERT: D 115 SER cc_start: 0.9379 (t) cc_final: 0.8934 (p) REVERT: D 215 ILE cc_start: 0.8526 (mm) cc_final: 0.8227 (tt) REVERT: D 419 ARG cc_start: 0.7973 (mtt-85) cc_final: 0.7670 (mmm-85) REVERT: D 504 ARG cc_start: 0.7010 (mtt180) cc_final: 0.6631 (mtm110) REVERT: F 520 LEU cc_start: 0.8765 (mp) cc_final: 0.8498 (mp) REVERT: F 625 ASN cc_start: 0.8563 (t0) cc_final: 0.8182 (t0) REVERT: F 632 ASP cc_start: 0.8672 (t70) cc_final: 0.8450 (t0) outliers start: 59 outliers final: 39 residues processed: 472 average time/residue: 0.1564 time to fit residues: 114.9149 Evaluate side-chains 422 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 382 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 89 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 432 GLN Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 612 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 118 optimal weight: 1.9990 chunk 214 optimal weight: 0.9990 chunk 163 optimal weight: 0.0770 chunk 29 optimal weight: 1.9990 chunk 184 optimal weight: 0.0030 chunk 164 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 253 optimal weight: 0.5980 chunk 206 optimal weight: 0.8980 chunk 222 optimal weight: 0.5980 overall best weight: 0.4148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 53 ASN I 105 GLN J 17 GLN J 37 GLN K 81 GLN M 39 GLN N 38 GLN A 103 GLN A 114 GLN B 577 GLN B 653 GLN C 85 HIS ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.127598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.100537 restraints weight = 33889.331| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.77 r_work: 0.3111 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21881 Z= 0.121 Angle : 0.557 10.146 29835 Z= 0.285 Chirality : 0.043 0.187 3480 Planarity : 0.004 0.045 3684 Dihedral : 6.378 75.610 4231 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.22 % Allowed : 10.94 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.16), residues: 2558 helix: 2.33 (0.28), residues: 369 sheet: 0.68 (0.19), residues: 730 loop : 0.33 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 542 TYR 0.028 0.001 TYR L 49 PHE 0.022 0.002 PHE C 391 TRP 0.022 0.001 TRP C 188 HIS 0.008 0.001 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.00269 (21772) covalent geometry : angle 0.53824 (29549) SS BOND : bond 0.00550 ( 41) SS BOND : angle 1.04746 ( 82) hydrogen bonds : bond 0.04060 ( 608) hydrogen bonds : angle 4.98702 ( 1587) link_ALPHA1-2 : bond 0.00608 ( 1) link_ALPHA1-2 : angle 1.69017 ( 3) link_ALPHA1-3 : bond 0.01000 ( 2) link_ALPHA1-3 : angle 1.93798 ( 6) link_ALPHA1-6 : bond 0.00814 ( 1) link_ALPHA1-6 : angle 1.77919 ( 3) link_BETA1-4 : bond 0.00590 ( 14) link_BETA1-4 : angle 1.81490 ( 42) link_NAG-ASN : bond 0.00208 ( 50) link_NAG-ASN : angle 1.70869 ( 150) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 412 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 32 TYR cc_start: 0.7958 (m-80) cc_final: 0.7728 (m-80) REVERT: L 45 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7039 (pt0) REVERT: L 50 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7266 (mm-30) REVERT: L 68 ASP cc_start: 0.7862 (m-30) cc_final: 0.7604 (t0) REVERT: L 89 MET cc_start: 0.7813 (ttt) cc_final: 0.7590 (ttt) REVERT: G 70 THR cc_start: 0.9081 (m) cc_final: 0.8773 (p) REVERT: G 95 THR cc_start: 0.8846 (m) cc_final: 0.8574 (t) REVERT: I 23 ARG cc_start: 0.8230 (tpp-160) cc_final: 0.7783 (mmm160) REVERT: J 74 THR cc_start: 0.8954 (m) cc_final: 0.8731 (p) REVERT: K 72 ASP cc_start: 0.8383 (t0) cc_final: 0.8110 (t0) REVERT: M 72 ASP cc_start: 0.8230 (t0) cc_final: 0.7933 (t0) REVERT: M 82 MET cc_start: 0.7980 (mtm) cc_final: 0.7574 (mtm) REVERT: A 305 LYS cc_start: 0.8603 (mttt) cc_final: 0.8367 (mttp) REVERT: B 571 TRP cc_start: 0.5306 (p90) cc_final: 0.5094 (p90) REVERT: B 621 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8071 (mt-10) REVERT: C 39 TYR cc_start: 0.9222 (m-80) cc_final: 0.8942 (m-80) REVERT: C 150 MET cc_start: 0.7982 (mmm) cc_final: 0.7755 (mmt) REVERT: C 151 ARG cc_start: 0.8245 (tpp-160) cc_final: 0.7980 (tpp-160) REVERT: C 207 LYS cc_start: 0.8176 (pttt) cc_final: 0.7753 (tttm) REVERT: C 481 SER cc_start: 0.8625 (t) cc_final: 0.8423 (p) REVERT: E 632 ASP cc_start: 0.8646 (t70) cc_final: 0.8386 (t0) REVERT: D 104 MET cc_start: 0.8843 (ttt) cc_final: 0.8562 (ttt) REVERT: D 111 LEU cc_start: 0.8172 (tp) cc_final: 0.7923 (tp) REVERT: D 115 SER cc_start: 0.9331 (t) cc_final: 0.8940 (p) REVERT: D 130 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: D 186 ASP cc_start: 0.7562 (t0) cc_final: 0.7339 (t0) REVERT: D 215 ILE cc_start: 0.8714 (mm) cc_final: 0.8299 (tt) REVERT: D 267 GLU cc_start: 0.7889 (tp30) cc_final: 0.7154 (mt-10) REVERT: D 419 ARG cc_start: 0.7928 (mtt-85) cc_final: 0.7617 (mmm-85) REVERT: D 504 ARG cc_start: 0.7047 (mtt180) cc_final: 0.6665 (mtm110) REVERT: F 520 LEU cc_start: 0.8746 (mp) cc_final: 0.8485 (mp) REVERT: F 625 ASN cc_start: 0.8464 (t0) cc_final: 0.8091 (t0) REVERT: F 632 ASP cc_start: 0.8695 (t70) cc_final: 0.8495 (t0) outliers start: 50 outliers final: 33 residues processed: 438 average time/residue: 0.1576 time to fit residues: 106.3738 Evaluate side-chains 407 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 373 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 432 GLN Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 652 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 27 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 172 optimal weight: 0.0770 chunk 230 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 250 optimal weight: 0.8980 chunk 179 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 HIS ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN N 38 GLN C 356 ASN ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.125153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.096844 restraints weight = 33962.165| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.87 r_work: 0.3052 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21881 Z= 0.167 Angle : 0.566 8.790 29835 Z= 0.287 Chirality : 0.044 0.211 3480 Planarity : 0.004 0.047 3684 Dihedral : 5.862 69.695 4231 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.92 % Allowed : 11.34 % Favored : 85.73 % 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: 0.81 (0.17), residues: 2558 helix: 1.85 (0.27), residues: 396 sheet: 0.64 (0.19), residues: 721 loop : 0.20 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 192 TYR 0.031 0.001 TYR L 49 PHE 0.020 0.002 PHE C 53 TRP 0.012 0.001 TRP C 479 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00394 (21772) covalent geometry : angle 0.54858 (29549) SS BOND : bond 0.00406 ( 41) SS BOND : angle 0.97915 ( 82) hydrogen bonds : bond 0.04086 ( 608) hydrogen bonds : angle 4.82713 ( 1587) link_ALPHA1-2 : bond 0.00603 ( 1) link_ALPHA1-2 : angle 1.42871 ( 3) link_ALPHA1-3 : bond 0.01108 ( 2) link_ALPHA1-3 : angle 1.82553 ( 6) link_ALPHA1-6 : bond 0.00964 ( 1) link_ALPHA1-6 : angle 1.77313 ( 3) link_BETA1-4 : bond 0.00466 ( 14) link_BETA1-4 : angle 1.69444 ( 42) link_NAG-ASN : bond 0.00264 ( 50) link_NAG-ASN : angle 1.69111 ( 150) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 389 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 45 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7064 (pt0) REVERT: L 50 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7595 (mm-30) REVERT: L 68 ASP cc_start: 0.7955 (m-30) cc_final: 0.7633 (t0) REVERT: L 89 MET cc_start: 0.8098 (ttt) cc_final: 0.7530 (ttt) REVERT: G 70 THR cc_start: 0.9147 (m) cc_final: 0.8771 (p) REVERT: G 95 THR cc_start: 0.8801 (m) cc_final: 0.8535 (t) REVERT: I 23 ARG cc_start: 0.8247 (tpp-160) cc_final: 0.7742 (mmm160) REVERT: J 24 THR cc_start: 0.8585 (m) cc_final: 0.8331 (p) REVERT: J 74 THR cc_start: 0.8927 (m) cc_final: 0.8692 (p) REVERT: K 72 ASP cc_start: 0.8312 (t0) cc_final: 0.7929 (t0) REVERT: K 75 LYS cc_start: 0.7866 (ptpt) cc_final: 0.7569 (pttm) REVERT: M 72 ASP cc_start: 0.8233 (t0) cc_final: 0.7913 (t0) REVERT: M 82 MET cc_start: 0.7968 (mtm) cc_final: 0.7537 (mtm) REVERT: A 121 LYS cc_start: 0.8498 (mttt) cc_final: 0.8244 (mttm) REVERT: A 305 LYS cc_start: 0.8677 (mttt) cc_final: 0.8448 (mttp) REVERT: B 621 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8076 (mt-10) REVERT: C 39 TYR cc_start: 0.9269 (m-80) cc_final: 0.8973 (m-80) REVERT: C 51 THR cc_start: 0.9331 (m) cc_final: 0.9125 (p) REVERT: C 103 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7653 (tm-30) REVERT: C 111 LEU cc_start: 0.8925 (mt) cc_final: 0.8655 (tp) REVERT: C 150 MET cc_start: 0.8008 (mmm) cc_final: 0.7782 (mmt) REVERT: C 207 LYS cc_start: 0.8191 (pttt) cc_final: 0.7787 (tttm) REVERT: C 388 SER cc_start: 0.8789 (p) cc_final: 0.8547 (m) REVERT: E 621 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7795 (mt-10) REVERT: E 632 ASP cc_start: 0.8818 (t70) cc_final: 0.8546 (t0) REVERT: D 104 MET cc_start: 0.8914 (ttt) cc_final: 0.8662 (ttt) REVERT: D 115 SER cc_start: 0.9324 (t) cc_final: 0.9057 (p) REVERT: D 137 ASN cc_start: 0.7491 (t0) cc_final: 0.6419 (p0) REVERT: D 186 ASP cc_start: 0.7472 (t0) cc_final: 0.7177 (t0) REVERT: D 419 ARG cc_start: 0.8031 (mtt-85) cc_final: 0.7599 (mmm-85) REVERT: D 502 LYS cc_start: 0.7786 (pttt) cc_final: 0.7571 (ptmt) REVERT: F 520 LEU cc_start: 0.8780 (mp) cc_final: 0.8550 (mp) REVERT: F 625 ASN cc_start: 0.8449 (t0) cc_final: 0.7981 (t0) outliers start: 66 outliers final: 48 residues processed: 425 average time/residue: 0.1535 time to fit residues: 101.5013 Evaluate side-chains 420 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 372 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 432 GLN Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 652 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 149 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 245 optimal weight: 0.8980 chunk 243 optimal weight: 0.0050 chunk 73 optimal weight: 1.9990 chunk 250 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 105 GLN C 82 GLN C 356 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.122499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.094976 restraints weight = 33918.141| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.78 r_work: 0.3040 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21881 Z= 0.183 Angle : 0.566 8.428 29835 Z= 0.288 Chirality : 0.044 0.222 3480 Planarity : 0.004 0.053 3684 Dihedral : 5.713 64.928 4231 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.15 % Allowed : 11.03 % Favored : 85.82 % 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: 0.72 (0.17), residues: 2558 helix: 1.92 (0.28), residues: 375 sheet: 0.53 (0.18), residues: 739 loop : 0.16 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 151 TYR 0.018 0.001 TYR N 49 PHE 0.020 0.002 PHE M 102 TRP 0.012 0.001 TRP C 479 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00429 (21772) covalent geometry : angle 0.54937 (29549) SS BOND : bond 0.00391 ( 41) SS BOND : angle 1.00418 ( 82) hydrogen bonds : bond 0.04033 ( 608) hydrogen bonds : angle 4.79762 ( 1587) link_ALPHA1-2 : bond 0.00659 ( 1) link_ALPHA1-2 : angle 1.34340 ( 3) link_ALPHA1-3 : bond 0.01038 ( 2) link_ALPHA1-3 : angle 1.67981 ( 6) link_ALPHA1-6 : bond 0.01042 ( 1) link_ALPHA1-6 : angle 1.83857 ( 3) link_BETA1-4 : bond 0.00458 ( 14) link_BETA1-4 : angle 1.59618 ( 42) link_NAG-ASN : bond 0.00273 ( 50) link_NAG-ASN : angle 1.68313 ( 150) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 395 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 108 LEU cc_start: 0.8864 (tp) cc_final: 0.8544 (tt) REVERT: L 45 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7098 (pt0) REVERT: L 68 ASP cc_start: 0.7985 (m-30) cc_final: 0.7672 (t0) REVERT: G 70 THR cc_start: 0.9168 (m) cc_final: 0.8801 (p) REVERT: G 95 THR cc_start: 0.8830 (m) cc_final: 0.8595 (t) REVERT: I 23 ARG cc_start: 0.8171 (tpp-160) cc_final: 0.7883 (ttm-80) REVERT: J 74 THR cc_start: 0.8921 (m) cc_final: 0.8678 (p) REVERT: J 95 THR cc_start: 0.8076 (m) cc_final: 0.7838 (p) REVERT: K 72 ASP cc_start: 0.8191 (t0) cc_final: 0.7857 (t0) REVERT: K 75 LYS cc_start: 0.7913 (ptpt) cc_final: 0.7632 (pttm) REVERT: M 72 ASP cc_start: 0.8181 (t0) cc_final: 0.7883 (t0) REVERT: M 82 MET cc_start: 0.7950 (mtm) cc_final: 0.7530 (mtm) REVERT: A 92 GLU cc_start: 0.8447 (tt0) cc_final: 0.8199 (tp30) REVERT: A 121 LYS cc_start: 0.8603 (mttt) cc_final: 0.8336 (mttm) REVERT: A 241 ASN cc_start: 0.8026 (m-40) cc_final: 0.7823 (m-40) REVERT: A 305 LYS cc_start: 0.8718 (mttt) cc_final: 0.8452 (mttp) REVERT: C 39 TYR cc_start: 0.9278 (m-80) cc_final: 0.8956 (m-80) REVERT: C 68 VAL cc_start: 0.7796 (t) cc_final: 0.7523 (m) REVERT: C 111 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8714 (tp) REVERT: C 129 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8571 (mt) REVERT: C 150 MET cc_start: 0.8034 (mmm) cc_final: 0.7827 (mmt) REVERT: C 264 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8184 (m) REVERT: C 388 SER cc_start: 0.8835 (p) cc_final: 0.8534 (m) REVERT: C 428 GLN cc_start: 0.8469 (mt0) cc_final: 0.8258 (mt0) REVERT: C 481 SER cc_start: 0.8676 (t) cc_final: 0.8447 (p) REVERT: E 632 ASP cc_start: 0.8760 (t70) cc_final: 0.8464 (t0) REVERT: D 104 MET cc_start: 0.8969 (ttt) cc_final: 0.8709 (ttt) REVERT: D 115 SER cc_start: 0.9277 (t) cc_final: 0.9005 (p) REVERT: D 137 ASN cc_start: 0.7336 (t0) cc_final: 0.6332 (p0) REVERT: D 186 ASP cc_start: 0.7419 (t0) cc_final: 0.7143 (t0) REVERT: D 419 ARG cc_start: 0.8002 (mtt-85) cc_final: 0.7647 (mtp85) REVERT: D 502 LYS cc_start: 0.7870 (pttt) cc_final: 0.7594 (ptmt) REVERT: F 520 LEU cc_start: 0.8774 (mp) cc_final: 0.8568 (mp) REVERT: F 624 ASP cc_start: 0.8136 (m-30) cc_final: 0.7879 (m-30) REVERT: F 625 ASN cc_start: 0.8385 (t0) cc_final: 0.7870 (t0) outliers start: 71 outliers final: 55 residues processed: 435 average time/residue: 0.1532 time to fit residues: 103.3819 Evaluate side-chains 420 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 362 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 97 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 432 GLN Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 652 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 0.0060 chunk 169 optimal weight: 5.9990 chunk 146 optimal weight: 0.0970 chunk 77 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 201 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN I 105 GLN C 66 HIS ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.124094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.095910 restraints weight = 33935.386| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.84 r_work: 0.3042 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21881 Z= 0.144 Angle : 0.546 8.227 29835 Z= 0.276 Chirality : 0.043 0.229 3480 Planarity : 0.004 0.053 3684 Dihedral : 5.590 61.972 4231 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.75 % Allowed : 12.10 % Favored : 85.16 % 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: 0.71 (0.17), residues: 2558 helix: 1.93 (0.28), residues: 375 sheet: 0.46 (0.18), residues: 757 loop : 0.18 (0.17), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 61 TYR 0.024 0.001 TYR L 49 PHE 0.017 0.002 PHE L 94 TRP 0.013 0.001 TRP C 479 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00334 (21772) covalent geometry : angle 0.53019 (29549) SS BOND : bond 0.00438 ( 41) SS BOND : angle 0.88696 ( 82) hydrogen bonds : bond 0.03851 ( 608) hydrogen bonds : angle 4.72623 ( 1587) link_ALPHA1-2 : bond 0.00654 ( 1) link_ALPHA1-2 : angle 1.31567 ( 3) link_ALPHA1-3 : bond 0.01113 ( 2) link_ALPHA1-3 : angle 1.64685 ( 6) link_ALPHA1-6 : bond 0.01054 ( 1) link_ALPHA1-6 : angle 1.91397 ( 3) link_BETA1-4 : bond 0.00466 ( 14) link_BETA1-4 : angle 1.54824 ( 42) link_NAG-ASN : bond 0.00232 ( 50) link_NAG-ASN : angle 1.61899 ( 150) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 379 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 108 LEU cc_start: 0.8868 (tp) cc_final: 0.8541 (tt) REVERT: L 45 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7093 (pt0) REVERT: L 49 TYR cc_start: 0.7608 (p90) cc_final: 0.7264 (p90) REVERT: L 50 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7573 (mm-30) REVERT: L 68 ASP cc_start: 0.7953 (m-30) cc_final: 0.7677 (t0) REVERT: G 70 THR cc_start: 0.9138 (m) cc_final: 0.8909 (p) REVERT: G 95 THR cc_start: 0.8835 (m) cc_final: 0.8571 (t) REVERT: I 23 ARG cc_start: 0.8216 (tpp-160) cc_final: 0.7908 (ttm-80) REVERT: J 74 THR cc_start: 0.8905 (m) cc_final: 0.8648 (p) REVERT: K 72 ASP cc_start: 0.8182 (t0) cc_final: 0.7865 (t0) REVERT: K 75 LYS cc_start: 0.7921 (ptpt) cc_final: 0.7655 (pttm) REVERT: M 72 ASP cc_start: 0.8152 (t0) cc_final: 0.7815 (t0) REVERT: M 82 MET cc_start: 0.7989 (mtm) cc_final: 0.7538 (mtm) REVERT: A 92 GLU cc_start: 0.8475 (tt0) cc_final: 0.8218 (tp30) REVERT: A 121 LYS cc_start: 0.8616 (mttt) cc_final: 0.8323 (mttm) REVERT: A 241 ASN cc_start: 0.8014 (m-40) cc_final: 0.7784 (m-40) REVERT: A 305 LYS cc_start: 0.8725 (mttt) cc_final: 0.8433 (mttp) REVERT: B 621 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8069 (mt-10) REVERT: C 39 TYR cc_start: 0.9272 (m-80) cc_final: 0.8961 (m-80) REVERT: C 68 VAL cc_start: 0.7777 (t) cc_final: 0.7504 (m) REVERT: C 103 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7893 (tm-30) REVERT: C 129 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8539 (mt) REVERT: C 150 MET cc_start: 0.8040 (mmm) cc_final: 0.7834 (mmt) REVERT: C 207 LYS cc_start: 0.8153 (ptmt) cc_final: 0.7760 (tptt) REVERT: C 264 SER cc_start: 0.8546 (OUTLIER) cc_final: 0.8189 (m) REVERT: C 388 SER cc_start: 0.8818 (p) cc_final: 0.8510 (m) REVERT: C 428 GLN cc_start: 0.8478 (mt0) cc_final: 0.8253 (mt0) REVERT: C 481 SER cc_start: 0.8696 (t) cc_final: 0.8495 (p) REVERT: E 621 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7749 (mt-10) REVERT: E 632 ASP cc_start: 0.8929 (t70) cc_final: 0.8681 (t0) REVERT: E 635 ILE cc_start: 0.8863 (mm) cc_final: 0.8464 (tt) REVERT: D 104 MET cc_start: 0.8955 (ttt) cc_final: 0.8673 (ttt) REVERT: D 115 SER cc_start: 0.9257 (t) cc_final: 0.8989 (p) REVERT: D 137 ASN cc_start: 0.7335 (t0) cc_final: 0.6268 (p0) REVERT: D 151 ARG cc_start: 0.7768 (mtp180) cc_final: 0.7330 (ttp-110) REVERT: D 186 ASP cc_start: 0.7441 (t0) cc_final: 0.7138 (t0) REVERT: D 255 VAL cc_start: 0.9276 (t) cc_final: 0.9068 (m) REVERT: D 419 ARG cc_start: 0.8039 (mtt-85) cc_final: 0.7812 (mtp85) REVERT: F 624 ASP cc_start: 0.8184 (m-30) cc_final: 0.7964 (m-30) REVERT: F 625 ASN cc_start: 0.8371 (t0) cc_final: 0.7842 (t0) outliers start: 62 outliers final: 53 residues processed: 414 average time/residue: 0.1462 time to fit residues: 93.8602 Evaluate side-chains 415 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 360 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 432 GLN Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 652 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 0 optimal weight: 10.0000 chunk 240 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 166 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 247 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.122819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.094662 restraints weight = 33820.515| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.83 r_work: 0.3036 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21881 Z= 0.173 Angle : 0.561 8.240 29835 Z= 0.284 Chirality : 0.044 0.234 3480 Planarity : 0.004 0.053 3684 Dihedral : 5.574 58.920 4231 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.01 % Allowed : 11.79 % Favored : 85.20 % 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: 0.62 (0.17), residues: 2558 helix: 1.86 (0.28), residues: 375 sheet: 0.37 (0.18), residues: 776 loop : 0.14 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 61 TYR 0.031 0.001 TYR L 49 PHE 0.019 0.002 PHE M 102 TRP 0.022 0.001 TRP L 35 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00409 (21772) covalent geometry : angle 0.54530 (29549) SS BOND : bond 0.00413 ( 41) SS BOND : angle 0.99553 ( 82) hydrogen bonds : bond 0.03895 ( 608) hydrogen bonds : angle 4.75072 ( 1587) link_ALPHA1-2 : bond 0.00630 ( 1) link_ALPHA1-2 : angle 1.29679 ( 3) link_ALPHA1-3 : bond 0.01116 ( 2) link_ALPHA1-3 : angle 1.48109 ( 6) link_ALPHA1-6 : bond 0.01084 ( 1) link_ALPHA1-6 : angle 1.91515 ( 3) link_BETA1-4 : bond 0.00445 ( 14) link_BETA1-4 : angle 1.53669 ( 42) link_NAG-ASN : bond 0.00259 ( 50) link_NAG-ASN : angle 1.63189 ( 150) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 378 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 108 LEU cc_start: 0.8846 (tp) cc_final: 0.8513 (tt) REVERT: L 33 LEU cc_start: 0.7027 (tt) cc_final: 0.6790 (tt) REVERT: L 45 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7076 (pt0) REVERT: L 46 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7732 (tp) REVERT: L 50 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7529 (mm-30) REVERT: L 68 ASP cc_start: 0.7957 (m-30) cc_final: 0.7669 (t0) REVERT: G 70 THR cc_start: 0.9142 (m) cc_final: 0.8889 (p) REVERT: G 95 THR cc_start: 0.8840 (m) cc_final: 0.8578 (t) REVERT: I 3 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8102 (tp40) REVERT: I 23 ARG cc_start: 0.8232 (tpp-160) cc_final: 0.7923 (ttm-80) REVERT: I 27 TYR cc_start: 0.8701 (p90) cc_final: 0.8483 (p90) REVERT: J 74 THR cc_start: 0.8916 (m) cc_final: 0.8636 (p) REVERT: K 3 GLN cc_start: 0.7830 (mm-40) cc_final: 0.7613 (mm110) REVERT: K 72 ASP cc_start: 0.8183 (t0) cc_final: 0.7679 (t0) REVERT: K 75 LYS cc_start: 0.7909 (ptpt) cc_final: 0.7612 (pttm) REVERT: M 72 ASP cc_start: 0.8137 (t0) cc_final: 0.7801 (t0) REVERT: M 82 MET cc_start: 0.7994 (mtm) cc_final: 0.7518 (mtm) REVERT: A 92 GLU cc_start: 0.8472 (tt0) cc_final: 0.8233 (tp30) REVERT: A 121 LYS cc_start: 0.8667 (mttt) cc_final: 0.8378 (mttm) REVERT: A 241 ASN cc_start: 0.8034 (m-40) cc_final: 0.7814 (m-40) REVERT: A 305 LYS cc_start: 0.8753 (mttt) cc_final: 0.8524 (mttp) REVERT: B 621 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8086 (mt-10) REVERT: C 39 TYR cc_start: 0.9287 (m-80) cc_final: 0.8965 (m-80) REVERT: C 103 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7886 (tm-30) REVERT: C 129 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8551 (mt) REVERT: C 150 MET cc_start: 0.8044 (mmm) cc_final: 0.7825 (mmt) REVERT: C 207 LYS cc_start: 0.8172 (ptmt) cc_final: 0.7658 (tptt) REVERT: C 264 SER cc_start: 0.8539 (OUTLIER) cc_final: 0.8175 (m) REVERT: C 428 GLN cc_start: 0.8480 (mt0) cc_final: 0.8257 (mt0) REVERT: C 475 MET cc_start: 0.7688 (tpp) cc_final: 0.7452 (tpp) REVERT: C 481 SER cc_start: 0.8738 (t) cc_final: 0.8328 (p) REVERT: E 621 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7742 (mt-10) REVERT: E 632 ASP cc_start: 0.8947 (t70) cc_final: 0.8693 (t0) REVERT: E 635 ILE cc_start: 0.8889 (mm) cc_final: 0.8511 (tt) REVERT: D 104 MET cc_start: 0.8994 (ttt) cc_final: 0.8698 (ttt) REVERT: D 137 ASN cc_start: 0.7382 (t0) cc_final: 0.6286 (p0) REVERT: D 186 ASP cc_start: 0.7532 (t0) cc_final: 0.7198 (t0) REVERT: D 419 ARG cc_start: 0.8163 (mtt-85) cc_final: 0.7915 (mtp85) REVERT: F 624 ASP cc_start: 0.8255 (m-30) cc_final: 0.8019 (m-30) REVERT: F 625 ASN cc_start: 0.8434 (t0) cc_final: 0.7868 (t0) outliers start: 68 outliers final: 55 residues processed: 419 average time/residue: 0.1456 time to fit residues: 94.6289 Evaluate side-chains 420 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 361 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 432 GLN Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 652 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 196 optimal weight: 0.5980 chunk 190 optimal weight: 2.9990 chunk 220 optimal weight: 0.6980 chunk 173 optimal weight: 3.9990 chunk 14 optimal weight: 0.2980 chunk 204 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 240 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 363 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.124072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.095986 restraints weight = 33817.547| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.83 r_work: 0.3057 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21881 Z= 0.131 Angle : 0.534 7.911 29835 Z= 0.271 Chirality : 0.043 0.249 3480 Planarity : 0.003 0.053 3684 Dihedral : 5.414 54.552 4231 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.66 % Allowed : 12.58 % Favored : 84.76 % 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 (0.17), residues: 2558 helix: 1.98 (0.28), residues: 375 sheet: 0.44 (0.18), residues: 758 loop : 0.08 (0.17), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 61 TYR 0.014 0.001 TYR N 49 PHE 0.016 0.001 PHE L 94 TRP 0.027 0.001 TRP L 35 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00306 (21772) covalent geometry : angle 0.51844 (29549) SS BOND : bond 0.00377 ( 41) SS BOND : angle 0.86592 ( 82) hydrogen bonds : bond 0.03682 ( 608) hydrogen bonds : angle 4.65079 ( 1587) link_ALPHA1-2 : bond 0.00629 ( 1) link_ALPHA1-2 : angle 1.29093 ( 3) link_ALPHA1-3 : bond 0.01108 ( 2) link_ALPHA1-3 : angle 1.45686 ( 6) link_ALPHA1-6 : bond 0.01097 ( 1) link_ALPHA1-6 : angle 1.97065 ( 3) link_BETA1-4 : bond 0.00468 ( 14) link_BETA1-4 : angle 1.50954 ( 42) link_NAG-ASN : bond 0.00202 ( 50) link_NAG-ASN : angle 1.56826 ( 150) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 379 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 108 LEU cc_start: 0.8864 (tp) cc_final: 0.8513 (tt) REVERT: L 45 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7086 (pt0) REVERT: L 46 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7718 (tp) REVERT: L 50 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7630 (mm-30) REVERT: L 68 ASP cc_start: 0.7945 (m-30) cc_final: 0.7683 (t0) REVERT: L 89 MET cc_start: 0.8292 (ttt) cc_final: 0.7922 (ttt) REVERT: G 70 THR cc_start: 0.9102 (m) cc_final: 0.8881 (p) REVERT: G 95 THR cc_start: 0.8784 (m) cc_final: 0.8536 (t) REVERT: I 3 GLN cc_start: 0.8224 (mt0) cc_final: 0.7996 (tp40) REVERT: I 23 ARG cc_start: 0.8238 (tpp-160) cc_final: 0.7937 (ttm-80) REVERT: I 27 TYR cc_start: 0.8694 (p90) cc_final: 0.8479 (p90) REVERT: I 43 LYS cc_start: 0.8352 (mmmt) cc_final: 0.8117 (mppt) REVERT: I 57 THR cc_start: 0.8995 (p) cc_final: 0.8770 (p) REVERT: I 82 MET cc_start: 0.8647 (mtm) cc_final: 0.8398 (mpp) REVERT: J 74 THR cc_start: 0.8914 (m) cc_final: 0.8635 (p) REVERT: K 3 GLN cc_start: 0.7781 (mm-40) cc_final: 0.7552 (mm110) REVERT: K 28 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8233 (p) REVERT: K 72 ASP cc_start: 0.8133 (t0) cc_final: 0.7843 (t0) REVERT: K 75 LYS cc_start: 0.7832 (ptpt) cc_final: 0.7572 (pttm) REVERT: M 72 ASP cc_start: 0.8095 (t0) cc_final: 0.7764 (t0) REVERT: M 82 MET cc_start: 0.7992 (mtm) cc_final: 0.7534 (mtm) REVERT: A 92 GLU cc_start: 0.8474 (tt0) cc_final: 0.8239 (tp30) REVERT: A 121 LYS cc_start: 0.8650 (mttt) cc_final: 0.8347 (mttm) REVERT: A 241 ASN cc_start: 0.7983 (m-40) cc_final: 0.7756 (m-40) REVERT: A 305 LYS cc_start: 0.8765 (mttt) cc_final: 0.8532 (mttp) REVERT: B 621 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8110 (mt-10) REVERT: C 39 TYR cc_start: 0.9258 (m-80) cc_final: 0.8917 (m-80) REVERT: C 103 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7890 (tm-30) REVERT: C 129 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8579 (mt) REVERT: C 207 LYS cc_start: 0.8201 (ptmt) cc_final: 0.7640 (tptt) REVERT: C 264 SER cc_start: 0.8518 (OUTLIER) cc_final: 0.8133 (m) REVERT: C 434 MET cc_start: 0.8677 (ttp) cc_final: 0.8324 (ttp) REVERT: C 475 MET cc_start: 0.7659 (tpp) cc_final: 0.7382 (tpp) REVERT: C 481 SER cc_start: 0.8689 (t) cc_final: 0.8264 (p) REVERT: E 621 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7739 (mt-10) REVERT: E 632 ASP cc_start: 0.8932 (t70) cc_final: 0.8692 (t0) REVERT: E 635 ILE cc_start: 0.8825 (mm) cc_final: 0.8493 (tt) REVERT: D 104 MET cc_start: 0.8982 (ttt) cc_final: 0.8725 (ttt) REVERT: D 137 ASN cc_start: 0.7386 (t0) cc_final: 0.6305 (p0) REVERT: D 186 ASP cc_start: 0.7510 (t0) cc_final: 0.7157 (t0) REVERT: D 419 ARG cc_start: 0.8153 (mtt-85) cc_final: 0.7755 (mtp85) REVERT: F 535 MET cc_start: 0.9321 (mtt) cc_final: 0.9084 (mtt) REVERT: F 624 ASP cc_start: 0.8229 (m-30) cc_final: 0.8000 (m-30) REVERT: F 625 ASN cc_start: 0.8489 (t0) cc_final: 0.7888 (t0) outliers start: 60 outliers final: 51 residues processed: 412 average time/residue: 0.1596 time to fit residues: 102.7744 Evaluate side-chains 415 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 360 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 432 GLN Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 652 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 44 optimal weight: 0.7980 chunk 183 optimal weight: 0.4980 chunk 146 optimal weight: 0.0870 chunk 245 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 chunk 243 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 0.0570 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN D 302 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.125712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.098366 restraints weight = 33763.571| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.77 r_work: 0.3086 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21881 Z= 0.109 Angle : 0.524 9.202 29835 Z= 0.267 Chirality : 0.042 0.223 3480 Planarity : 0.003 0.054 3684 Dihedral : 5.223 52.424 4231 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.35 % Allowed : 13.11 % Favored : 84.54 % 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: 0.69 (0.17), residues: 2558 helix: 2.07 (0.28), residues: 375 sheet: 0.52 (0.19), residues: 740 loop : 0.06 (0.17), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 61 TYR 0.015 0.001 TYR H 59 PHE 0.020 0.001 PHE M 102 TRP 0.024 0.001 TRP L 35 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00245 (21772) covalent geometry : angle 0.51000 (29549) SS BOND : bond 0.00322 ( 41) SS BOND : angle 0.82105 ( 82) hydrogen bonds : bond 0.03502 ( 608) hydrogen bonds : angle 4.56274 ( 1587) link_ALPHA1-2 : bond 0.00631 ( 1) link_ALPHA1-2 : angle 1.28710 ( 3) link_ALPHA1-3 : bond 0.01116 ( 2) link_ALPHA1-3 : angle 1.38302 ( 6) link_ALPHA1-6 : bond 0.01093 ( 1) link_ALPHA1-6 : angle 1.93425 ( 3) link_BETA1-4 : bond 0.00489 ( 14) link_BETA1-4 : angle 1.44480 ( 42) link_NAG-ASN : bond 0.00188 ( 50) link_NAG-ASN : angle 1.47206 ( 150) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 381 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 108 LEU cc_start: 0.8847 (tp) cc_final: 0.8479 (tt) REVERT: L 45 GLN cc_start: 0.7542 (mm-40) cc_final: 0.7140 (pt0) REVERT: L 46 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7767 (tp) REVERT: L 68 ASP cc_start: 0.7875 (m-30) cc_final: 0.7623 (t0) REVERT: L 89 MET cc_start: 0.8354 (ttt) cc_final: 0.8038 (ttt) REVERT: G 70 THR cc_start: 0.9105 (m) cc_final: 0.8894 (p) REVERT: G 95 THR cc_start: 0.8761 (m) cc_final: 0.8493 (t) REVERT: I 23 ARG cc_start: 0.8230 (tpp-160) cc_final: 0.7969 (ttm-80) REVERT: I 27 TYR cc_start: 0.8677 (p90) cc_final: 0.8421 (p90) REVERT: J 74 THR cc_start: 0.8915 (m) cc_final: 0.8643 (p) REVERT: K 28 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8228 (p) REVERT: K 34 MET cc_start: 0.8833 (mtt) cc_final: 0.8540 (mtp) REVERT: K 72 ASP cc_start: 0.8078 (t0) cc_final: 0.7568 (t0) REVERT: K 75 LYS cc_start: 0.7755 (ptpt) cc_final: 0.7518 (pttm) REVERT: M 72 ASP cc_start: 0.8038 (t0) cc_final: 0.7757 (t0) REVERT: M 82 MET cc_start: 0.7951 (mtm) cc_final: 0.7586 (mtm) REVERT: A 121 LYS cc_start: 0.8612 (mttt) cc_final: 0.8347 (mttm) REVERT: A 232 LYS cc_start: 0.7697 (pttt) cc_final: 0.7381 (ptpp) REVERT: A 305 LYS cc_start: 0.8757 (mttt) cc_final: 0.8530 (mttp) REVERT: C 39 TYR cc_start: 0.9230 (m-80) cc_final: 0.8899 (m-80) REVERT: C 42 VAL cc_start: 0.9060 (t) cc_final: 0.8830 (m) REVERT: C 103 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7934 (tm-30) REVERT: C 129 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8600 (mt) REVERT: C 150 MET cc_start: 0.7407 (mmt) cc_final: 0.7147 (mmt) REVERT: C 207 LYS cc_start: 0.8191 (ptmt) cc_final: 0.7635 (tptt) REVERT: C 264 SER cc_start: 0.8470 (OUTLIER) cc_final: 0.8106 (m) REVERT: C 475 MET cc_start: 0.7628 (tpp) cc_final: 0.7295 (tpp) REVERT: C 481 SER cc_start: 0.8661 (t) cc_final: 0.8249 (p) REVERT: E 574 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8541 (mmmt) REVERT: E 621 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7697 (mt-10) REVERT: E 632 ASP cc_start: 0.8901 (t70) cc_final: 0.8658 (t0) REVERT: D 104 MET cc_start: 0.8989 (ttt) cc_final: 0.8734 (ttt) REVERT: D 137 ASN cc_start: 0.7292 (t0) cc_final: 0.6209 (p0) REVERT: D 186 ASP cc_start: 0.7481 (t0) cc_final: 0.7149 (t0) REVERT: F 535 MET cc_start: 0.9270 (mtt) cc_final: 0.9047 (mtt) REVERT: F 624 ASP cc_start: 0.8171 (m-30) cc_final: 0.7935 (m-30) REVERT: F 625 ASN cc_start: 0.8380 (t0) cc_final: 0.7780 (t0) outliers start: 53 outliers final: 44 residues processed: 410 average time/residue: 0.1605 time to fit residues: 101.8129 Evaluate side-chains 410 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 362 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 432 GLN Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 652 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 27 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 62 optimal weight: 0.0870 chunk 69 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 158 optimal weight: 0.2980 chunk 0 optimal weight: 0.9980 chunk 246 optimal weight: 1.9990 chunk 239 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN K 39 GLN D 103 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.126656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.099702 restraints weight = 33827.668| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.66 r_work: 0.3099 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21881 Z= 0.117 Angle : 0.531 8.925 29835 Z= 0.270 Chirality : 0.043 0.208 3480 Planarity : 0.003 0.054 3684 Dihedral : 5.094 57.994 4231 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.26 % Allowed : 13.56 % Favored : 84.18 % 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: 0.75 (0.17), residues: 2558 helix: 2.09 (0.28), residues: 375 sheet: 0.56 (0.19), residues: 785 loop : 0.11 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG L 61 TYR 0.016 0.001 TYR H 91 PHE 0.018 0.001 PHE L 94 TRP 0.025 0.001 TRP L 35 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00270 (21772) covalent geometry : angle 0.51840 (29549) SS BOND : bond 0.00332 ( 41) SS BOND : angle 0.85008 ( 82) hydrogen bonds : bond 0.03509 ( 608) hydrogen bonds : angle 4.55793 ( 1587) link_ALPHA1-2 : bond 0.00592 ( 1) link_ALPHA1-2 : angle 1.28071 ( 3) link_ALPHA1-3 : bond 0.01070 ( 2) link_ALPHA1-3 : angle 1.31803 ( 6) link_ALPHA1-6 : bond 0.00987 ( 1) link_ALPHA1-6 : angle 1.60767 ( 3) link_BETA1-4 : bond 0.00487 ( 14) link_BETA1-4 : angle 1.43118 ( 42) link_NAG-ASN : bond 0.00184 ( 50) link_NAG-ASN : angle 1.44682 ( 150) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 373 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.8521 (tt0) cc_final: 0.8250 (tt0) REVERT: H 108 LEU cc_start: 0.8885 (tp) cc_final: 0.8495 (tt) REVERT: L 45 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7203 (pt0) REVERT: L 46 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7817 (tp) REVERT: L 61 ARG cc_start: 0.7895 (mtm110) cc_final: 0.7625 (mtm110) REVERT: L 68 ASP cc_start: 0.7935 (m-30) cc_final: 0.7675 (t0) REVERT: L 89 MET cc_start: 0.8382 (ttt) cc_final: 0.8091 (ttt) REVERT: G 70 THR cc_start: 0.9138 (m) cc_final: 0.8910 (p) REVERT: G 95 THR cc_start: 0.8807 (m) cc_final: 0.8506 (t) REVERT: I 23 ARG cc_start: 0.8342 (tpp-160) cc_final: 0.8071 (ttm-80) REVERT: I 27 TYR cc_start: 0.8737 (p90) cc_final: 0.8488 (p90) REVERT: J 74 THR cc_start: 0.8914 (m) cc_final: 0.8662 (p) REVERT: K 28 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8221 (p) REVERT: K 34 MET cc_start: 0.9028 (mtt) cc_final: 0.8777 (mtp) REVERT: K 72 ASP cc_start: 0.8270 (t0) cc_final: 0.8037 (t0) REVERT: M 72 ASP cc_start: 0.8279 (t0) cc_final: 0.7911 (t0) REVERT: M 82 MET cc_start: 0.8031 (mtm) cc_final: 0.7654 (mtm) REVERT: A 107 ASP cc_start: 0.8373 (m-30) cc_final: 0.8165 (m-30) REVERT: A 121 LYS cc_start: 0.8710 (mttt) cc_final: 0.8439 (mttm) REVERT: A 232 LYS cc_start: 0.7768 (pttt) cc_final: 0.7536 (ptpp) REVERT: A 305 LYS cc_start: 0.8886 (mttt) cc_final: 0.8600 (mttp) REVERT: C 39 TYR cc_start: 0.9335 (m-80) cc_final: 0.9023 (m-80) REVERT: C 42 VAL cc_start: 0.9105 (t) cc_final: 0.8843 (m) REVERT: C 103 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7986 (tm-30) REVERT: C 129 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8661 (mt) REVERT: C 150 MET cc_start: 0.7438 (mmt) cc_final: 0.7170 (mmt) REVERT: C 207 LYS cc_start: 0.8232 (ptmt) cc_final: 0.7568 (tptt) REVERT: C 475 MET cc_start: 0.7876 (tpp) cc_final: 0.7576 (tpp) REVERT: C 481 SER cc_start: 0.8803 (t) cc_final: 0.8464 (p) REVERT: E 574 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8567 (mmmt) REVERT: E 621 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7947 (mt-10) REVERT: E 632 ASP cc_start: 0.9060 (t70) cc_final: 0.8801 (t0) REVERT: D 104 MET cc_start: 0.9101 (ttt) cc_final: 0.8866 (ttt) REVERT: D 137 ASN cc_start: 0.7293 (t0) cc_final: 0.6078 (p0) REVERT: D 186 ASP cc_start: 0.7629 (t0) cc_final: 0.7240 (t0) REVERT: D 419 ARG cc_start: 0.8335 (mmm-85) cc_final: 0.8131 (mmm-85) REVERT: F 624 ASP cc_start: 0.8299 (m-30) cc_final: 0.8052 (m-30) REVERT: F 625 ASN cc_start: 0.8594 (t0) cc_final: 0.7948 (t0) outliers start: 51 outliers final: 45 residues processed: 403 average time/residue: 0.1525 time to fit residues: 96.2501 Evaluate side-chains 411 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 363 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 432 GLN Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 652 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 54 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 193 optimal weight: 0.9980 chunk 195 optimal weight: 0.0060 chunk 103 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 251 optimal weight: 0.9980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 3 GLN D 103 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.124906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.097058 restraints weight = 33985.517| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.81 r_work: 0.3075 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21881 Z= 0.130 Angle : 0.538 8.753 29835 Z= 0.273 Chirality : 0.043 0.207 3480 Planarity : 0.004 0.052 3684 Dihedral : 4.786 52.900 4231 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.44 % Allowed : 13.51 % Favored : 84.05 % 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: 0.73 (0.17), residues: 2558 helix: 2.06 (0.28), residues: 375 sheet: 0.55 (0.18), residues: 788 loop : 0.09 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 61 TYR 0.014 0.001 TYR H 59 PHE 0.019 0.001 PHE M 102 TRP 0.022 0.001 TRP L 35 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00303 (21772) covalent geometry : angle 0.52536 (29549) SS BOND : bond 0.00342 ( 41) SS BOND : angle 0.86007 ( 82) hydrogen bonds : bond 0.03569 ( 608) hydrogen bonds : angle 4.54641 ( 1587) link_ALPHA1-2 : bond 0.00585 ( 1) link_ALPHA1-2 : angle 1.27869 ( 3) link_ALPHA1-3 : bond 0.01002 ( 2) link_ALPHA1-3 : angle 1.30056 ( 6) link_ALPHA1-6 : bond 0.00851 ( 1) link_ALPHA1-6 : angle 1.62779 ( 3) link_BETA1-4 : bond 0.00470 ( 14) link_BETA1-4 : angle 1.43291 ( 42) link_NAG-ASN : bond 0.00196 ( 50) link_NAG-ASN : angle 1.46212 ( 150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5228.54 seconds wall clock time: 90 minutes 38.44 seconds (5438.44 seconds total)