Starting phenix.real_space_refine on Fri Sep 19 01:16:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mqg_48523/09_2025/9mqg_48523.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mqg_48523/09_2025/9mqg_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mqg_48523/09_2025/9mqg_48523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mqg_48523/09_2025/9mqg_48523.map" model { file = "/net/cci-nas-00/data/ceres_data/9mqg_48523/09_2025/9mqg_48523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mqg_48523/09_2025/9mqg_48523.cif" } 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-2.0-5805/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: 5.24, 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: 2.16 Conformation dependent library (CDL) restraints added in 983.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.85 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: 4.60 Time building geometry restraints manager: 2.84 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: 5.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.420 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.620 ------------------------------------------------------------------------------- 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 aren 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 : 0.608 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: L 4 MET cc_start: 0.6865 (mmm) cc_final: 0.6099 (mmm) REVERT: L 27 LEU cc_start: 0.9023 (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: 0.8153 (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: 0.8994 (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: 0.1575 time to fit residues: 170.3233 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 : 0.835 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.126279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.098122 restraints weight = 33723.145| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.85 r_work: 0.3072 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 21881 Z= 0.215 Angle : 0.671 14.498 29835 Z= 0.345 Chirality : 0.046 0.192 3480 Planarity : 0.004 0.058 3684 Dihedral : 7.408 83.243 4231 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.66 % Allowed : 8.42 % Favored : 88.92 % 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 aren not related in a simple way. whole: 1.07 (0.16), residues: 2558 helix: 2.16 (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 0.033 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 0.00498 (21772) covalent geometry : angle 0.65013 (29549) SS BOND : bond 0.00472 ( 41) SS BOND : angle 1.22909 ( 82) hydrogen bonds : bond 0.04924 ( 608) hydrogen bonds : angle 5.41414 ( 1587) link_ALPHA1-2 : bond 0.00418 ( 1) link_ALPHA1-2 : angle 1.69599 ( 3) link_ALPHA1-3 : bond 0.00910 ( 2) link_ALPHA1-3 : angle 2.10130 ( 6) link_ALPHA1-6 : bond 0.00661 ( 1) link_ALPHA1-6 : angle 1.61184 ( 3) link_BETA1-4 : bond 0.00347 ( 14) link_BETA1-4 : angle 1.96338 ( 42) link_NAG-ASN : bond 0.00357 ( 50) link_NAG-ASN : angle 2.05339 ( 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 499 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 439 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 49 SER cc_start: 0.8919 (p) cc_final: 0.8716 (m) REVERT: L 4 MET cc_start: 0.6821 (mmm) cc_final: 0.6016 (mmm) REVERT: L 45 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7116 (pt0) REVERT: G 24 THR cc_start: 0.9124 (m) cc_final: 0.8745 (p) REVERT: G 70 THR cc_start: 0.9055 (m) cc_final: 0.8710 (p) REVERT: G 95 THR cc_start: 0.8840 (m) cc_final: 0.8569 (t) REVERT: I 23 ARG cc_start: 0.8194 (tpp-160) cc_final: 0.7744 (mmm160) REVERT: I 43 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8369 (mmmt) REVERT: J 74 THR cc_start: 0.8907 (m) cc_final: 0.8685 (p) REVERT: K 72 ASP cc_start: 0.8109 (t0) cc_final: 0.7683 (t0) REVERT: M 11 LEU cc_start: 0.8384 (tp) cc_final: 0.8019 (mp) REVERT: M 72 ASP cc_start: 0.8216 (t0) cc_final: 0.7943 (t0) REVERT: M 82 MET cc_start: 0.8061 (mtm) cc_final: 0.7587 (mtm) REVERT: N 61 ARG cc_start: 0.8185 (mtm-85) cc_final: 0.7975 (mtm110) REVERT: A 40 TYR cc_start: 0.9101 (t80) cc_final: 0.8838 (t80) REVERT: A 305 LYS cc_start: 0.8592 (mttt) cc_final: 0.8321 (mttp) REVERT: A 479 TRP cc_start: 0.8339 (m-10) cc_final: 0.8023 (m-10) REVERT: B 571 TRP cc_start: 0.5395 (p90) cc_final: 0.4622 (p90) REVERT: C 39 TYR cc_start: 0.9251 (m-80) cc_final: 0.9036 (m-80) REVERT: C 150 MET cc_start: 0.7999 (mmm) cc_final: 0.7781 (mmt) REVERT: C 207 LYS cc_start: 0.8147 (pttt) cc_final: 0.7748 (tttm) REVERT: C 264 SER cc_start: 0.8536 (OUTLIER) cc_final: 0.8118 (m) REVERT: C 469 ARG cc_start: 0.7932 (mtt-85) cc_final: 0.7306 (mtt-85) REVERT: C 481 SER cc_start: 0.8642 (t) cc_final: 0.8421 (p) REVERT: E 530 MET cc_start: 0.9277 (mtp) cc_final: 0.9053 (mtp) REVERT: E 632 ASP cc_start: 0.8701 (t70) cc_final: 0.8433 (t0) REVERT: D 104 MET cc_start: 0.8839 (ttt) cc_final: 0.8629 (ttt) REVERT: D 111 LEU cc_start: 0.8026 (tp) cc_final: 0.7679 (tp) REVERT: D 115 SER cc_start: 0.9380 (t) cc_final: 0.8933 (p) REVERT: D 215 ILE cc_start: 0.8522 (mm) cc_final: 0.8233 (tt) REVERT: D 419 ARG cc_start: 0.7978 (mtt-85) cc_final: 0.7672 (mmm-85) REVERT: D 504 ARG cc_start: 0.7028 (mtt180) cc_final: 0.6626 (mtm110) REVERT: F 520 LEU cc_start: 0.8771 (mp) cc_final: 0.8505 (mp) REVERT: F 625 ASN cc_start: 0.8572 (t0) cc_final: 0.8185 (t0) REVERT: F 632 ASP cc_start: 0.8691 (t70) cc_final: 0.8467 (t0) outliers start: 60 outliers final: 41 residues processed: 474 average time/residue: 0.1465 time to fit residues: 107.5152 Evaluate side-chains 427 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 385 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 38 ARG 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 595 ILE 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: 0.7980 chunk 214 optimal weight: 0.4980 chunk 163 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 164 optimal weight: 0.6980 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: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.127019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.099041 restraints weight = 34039.405| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.87 r_work: 0.3083 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21881 Z= 0.134 Angle : 0.563 10.727 29835 Z= 0.289 Chirality : 0.044 0.197 3480 Planarity : 0.004 0.045 3684 Dihedral : 6.355 75.208 4231 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.17 % Allowed : 11.03 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.16), residues: 2558 helix: 2.08 (0.28), residues: 378 sheet: 0.73 (0.19), residues: 715 loop : 0.29 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 542 TYR 0.029 0.001 TYR L 49 PHE 0.022 0.002 PHE C 391 TRP 0.013 0.001 TRP D 479 HIS 0.008 0.001 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.00306 (21772) covalent geometry : angle 0.54551 (29549) SS BOND : bond 0.00335 ( 41) SS BOND : angle 0.92610 ( 82) hydrogen bonds : bond 0.04106 ( 608) hydrogen bonds : angle 4.97998 ( 1587) link_ALPHA1-2 : bond 0.00602 ( 1) link_ALPHA1-2 : angle 1.67081 ( 3) link_ALPHA1-3 : bond 0.01022 ( 2) link_ALPHA1-3 : angle 1.86577 ( 6) link_ALPHA1-6 : bond 0.00843 ( 1) link_ALPHA1-6 : angle 1.75476 ( 3) link_BETA1-4 : bond 0.00468 ( 14) link_BETA1-4 : angle 1.68391 ( 42) link_NAG-ASN : bond 0.00219 ( 50) link_NAG-ASN : angle 1.70893 ( 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 457 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 408 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 45 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7059 (pt0) REVERT: L 50 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7611 (mm-30) REVERT: L 68 ASP cc_start: 0.7947 (m-30) cc_final: 0.7620 (t0) REVERT: L 89 MET cc_start: 0.7811 (ttt) cc_final: 0.7583 (ttt) REVERT: G 24 THR cc_start: 0.9046 (m) cc_final: 0.8834 (p) REVERT: G 70 THR cc_start: 0.9086 (m) cc_final: 0.8774 (p) REVERT: G 95 THR cc_start: 0.8869 (m) cc_final: 0.8589 (t) REVERT: I 23 ARG cc_start: 0.8238 (tpp-160) cc_final: 0.7736 (mmm160) REVERT: J 74 THR cc_start: 0.8947 (m) cc_final: 0.8702 (p) REVERT: K 72 ASP cc_start: 0.8407 (t0) cc_final: 0.8135 (t0) REVERT: M 72 ASP cc_start: 0.8241 (t0) cc_final: 0.7960 (t0) REVERT: M 82 MET cc_start: 0.7974 (mtm) cc_final: 0.7565 (mtm) REVERT: A 305 LYS cc_start: 0.8642 (mttt) cc_final: 0.8391 (mttp) REVERT: A 479 TRP cc_start: 0.8199 (m-10) cc_final: 0.7976 (m-10) REVERT: B 571 TRP cc_start: 0.5342 (p90) cc_final: 0.5124 (p90) REVERT: B 621 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8089 (mt-10) REVERT: C 39 TYR cc_start: 0.9255 (m-80) cc_final: 0.8966 (m-80) REVERT: C 150 MET cc_start: 0.7988 (mmm) cc_final: 0.7770 (mmt) REVERT: C 151 ARG cc_start: 0.8190 (tpp-160) cc_final: 0.7969 (tpp-160) REVERT: C 207 LYS cc_start: 0.8158 (pttt) cc_final: 0.7800 (tttm) REVERT: C 481 SER cc_start: 0.8652 (t) cc_final: 0.8439 (p) REVERT: E 632 ASP cc_start: 0.8675 (t70) cc_final: 0.8397 (t0) REVERT: D 104 MET cc_start: 0.8872 (ttt) cc_final: 0.8591 (ttt) REVERT: D 111 LEU cc_start: 0.8224 (tp) cc_final: 0.7953 (tp) REVERT: D 115 SER cc_start: 0.9326 (t) cc_final: 0.8925 (p) REVERT: D 186 ASP cc_start: 0.7520 (t0) cc_final: 0.7275 (t0) REVERT: D 215 ILE cc_start: 0.8728 (mm) cc_final: 0.8295 (tt) REVERT: D 419 ARG cc_start: 0.7998 (mtt-85) cc_final: 0.7638 (mmm-85) REVERT: D 504 ARG cc_start: 0.7084 (mtt180) cc_final: 0.6663 (mtm110) REVERT: F 520 LEU cc_start: 0.8763 (mp) cc_final: 0.8511 (mp) REVERT: F 625 ASN cc_start: 0.8477 (t0) cc_final: 0.8084 (t0) REVERT: F 632 ASP cc_start: 0.8713 (t70) cc_final: 0.8500 (t0) outliers start: 49 outliers final: 36 residues processed: 437 average time/residue: 0.1505 time to fit residues: 102.0286 Evaluate side-chains 407 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 371 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 52 THR 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 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 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 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 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 652 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 27 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 250 optimal weight: 0.7980 chunk 179 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 HIS I 105 GLN ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 356 ASN ** 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 = 0.3578 r_free = 0.3578 target = 0.123134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.094958 restraints weight = 34049.608| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.84 r_work: 0.3027 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21881 Z= 0.209 Angle : 0.603 9.543 29835 Z= 0.304 Chirality : 0.045 0.210 3480 Planarity : 0.004 0.046 3684 Dihedral : 5.992 69.846 4231 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.23 % Allowed : 11.17 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.16), residues: 2558 helix: 1.71 (0.27), residues: 396 sheet: 0.67 (0.19), residues: 694 loop : 0.13 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 151 TYR 0.034 0.002 TYR L 49 PHE 0.019 0.002 PHE C 53 TRP 0.029 0.002 TRP C 188 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00490 (21772) covalent geometry : angle 0.58455 (29549) SS BOND : bond 0.00478 ( 41) SS BOND : angle 1.00608 ( 82) hydrogen bonds : bond 0.04270 ( 608) hydrogen bonds : angle 4.91747 ( 1587) link_ALPHA1-2 : bond 0.00590 ( 1) link_ALPHA1-2 : angle 1.39420 ( 3) link_ALPHA1-3 : bond 0.01132 ( 2) link_ALPHA1-3 : angle 1.81023 ( 6) link_ALPHA1-6 : bond 0.00965 ( 1) link_ALPHA1-6 : angle 1.73949 ( 3) link_BETA1-4 : bond 0.00569 ( 14) link_BETA1-4 : angle 1.88190 ( 42) link_NAG-ASN : bond 0.00325 ( 50) link_NAG-ASN : angle 1.79913 ( 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 462 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 389 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 11 LEU cc_start: 0.6562 (OUTLIER) cc_final: 0.6318 (tt) REVERT: L 45 GLN cc_start: 0.7613 (mm-40) cc_final: 0.7083 (pt0) REVERT: L 68 ASP cc_start: 0.7960 (m-30) cc_final: 0.7638 (t0) REVERT: L 89 MET cc_start: 0.8207 (ttt) cc_final: 0.7562 (ttt) REVERT: G 24 THR cc_start: 0.9070 (m) cc_final: 0.8848 (p) REVERT: G 70 THR cc_start: 0.9145 (m) cc_final: 0.8792 (p) REVERT: G 95 THR cc_start: 0.8884 (m) cc_final: 0.8614 (t) REVERT: I 23 ARG cc_start: 0.8238 (tpp-160) cc_final: 0.7715 (mmm160) REVERT: J 24 THR cc_start: 0.8638 (m) cc_final: 0.8391 (p) REVERT: J 74 THR cc_start: 0.8911 (m) cc_final: 0.8672 (p) REVERT: J 95 THR cc_start: 0.8081 (m) cc_final: 0.7790 (p) REVERT: K 72 ASP cc_start: 0.8298 (t0) cc_final: 0.7996 (t0) REVERT: K 75 LYS cc_start: 0.7929 (ptpt) cc_final: 0.7633 (pttm) REVERT: M 72 ASP cc_start: 0.8187 (t0) cc_final: 0.7877 (t0) REVERT: M 82 MET cc_start: 0.8002 (mtm) cc_final: 0.7561 (mtm) REVERT: A 121 LYS cc_start: 0.8614 (mttt) cc_final: 0.8317 (mttm) REVERT: A 305 LYS cc_start: 0.8690 (mttt) cc_final: 0.8456 (mttp) REVERT: B 621 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8123 (mt-10) REVERT: C 39 TYR cc_start: 0.9292 (m-80) cc_final: 0.8991 (m-80) REVERT: C 68 VAL cc_start: 0.7652 (t) cc_final: 0.7312 (m) REVERT: C 103 GLN cc_start: 0.7990 (tm-30) cc_final: 0.7737 (tm-30) REVERT: C 111 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8618 (tp) REVERT: C 129 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8487 (mt) REVERT: C 207 LYS cc_start: 0.8285 (pttt) cc_final: 0.7970 (tttm) REVERT: C 388 SER cc_start: 0.8823 (p) cc_final: 0.8511 (m) REVERT: E 621 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7830 (mt-10) REVERT: E 632 ASP cc_start: 0.8795 (t70) cc_final: 0.8504 (t0) REVERT: D 102 GLU cc_start: 0.7755 (tp30) cc_final: 0.7527 (mt-10) REVERT: D 104 MET cc_start: 0.8961 (ttt) cc_final: 0.8707 (ttt) REVERT: D 111 LEU cc_start: 0.8395 (tp) cc_final: 0.8189 (tp) REVERT: D 115 SER cc_start: 0.9331 (t) cc_final: 0.9052 (p) REVERT: D 137 ASN cc_start: 0.7331 (t0) cc_final: 0.6340 (p0) REVERT: D 186 ASP cc_start: 0.7375 (t0) cc_final: 0.7110 (t0) REVERT: D 419 ARG cc_start: 0.8058 (mtt-85) cc_final: 0.7778 (mmm-85) REVERT: D 502 LYS cc_start: 0.7901 (pttt) cc_final: 0.7612 (ptmt) REVERT: F 520 LEU cc_start: 0.8810 (mp) cc_final: 0.8593 (mp) REVERT: F 624 ASP cc_start: 0.8116 (m-30) cc_final: 0.7830 (m-30) REVERT: F 625 ASN cc_start: 0.8460 (t0) cc_final: 0.7983 (t0) outliers start: 73 outliers final: 54 residues processed: 430 average time/residue: 0.1481 time to fit residues: 98.7222 Evaluate side-chains 427 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 370 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 11 LEU 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 3 GLN 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 J residue 97 ILE 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 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 539 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 198 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 346 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 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 612 SER 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: 3.9990 chunk 195 optimal weight: 0.1980 chunk 129 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 245 optimal weight: 0.8980 chunk 243 optimal weight: 0.0030 chunk 73 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 105 GLN C 356 ASN ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 GLN ** 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 = 0.3593 r_free = 0.3593 target = 0.124236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.096121 restraints weight = 33843.299| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.84 r_work: 0.3046 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21881 Z= 0.143 Angle : 0.541 8.092 29835 Z= 0.275 Chirality : 0.043 0.221 3480 Planarity : 0.004 0.051 3684 Dihedral : 5.673 65.030 4231 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.84 % Allowed : 11.96 % 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 aren not related in a simple way. whole: 0.68 (0.17), residues: 2558 helix: 1.80 (0.27), residues: 393 sheet: 0.51 (0.18), residues: 739 loop : 0.12 (0.17), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 588 TYR 0.016 0.001 TYR N 49 PHE 0.017 0.002 PHE L 94 TRP 0.013 0.001 TRP C 479 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00333 (21772) covalent geometry : angle 0.52421 (29549) SS BOND : bond 0.00373 ( 41) SS BOND : angle 0.90021 ( 82) hydrogen bonds : bond 0.03833 ( 608) hydrogen bonds : angle 4.77434 ( 1587) link_ALPHA1-2 : bond 0.00675 ( 1) link_ALPHA1-2 : angle 1.33473 ( 3) link_ALPHA1-3 : bond 0.01117 ( 2) link_ALPHA1-3 : angle 1.76200 ( 6) link_ALPHA1-6 : bond 0.01026 ( 1) link_ALPHA1-6 : angle 1.87725 ( 3) link_BETA1-4 : bond 0.00517 ( 14) link_BETA1-4 : angle 1.60721 ( 42) link_NAG-ASN : bond 0.00209 ( 50) link_NAG-ASN : angle 1.63958 ( 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 460 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 396 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 108 LEU cc_start: 0.8859 (tp) cc_final: 0.8530 (tt) REVERT: L 45 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7068 (pt0) REVERT: L 50 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7748 (mm-30) REVERT: L 68 ASP cc_start: 0.7953 (m-30) cc_final: 0.7665 (t0) REVERT: L 89 MET cc_start: 0.8454 (ttt) cc_final: 0.8052 (ttt) REVERT: G 70 THR cc_start: 0.9114 (m) cc_final: 0.8790 (p) REVERT: G 95 THR cc_start: 0.8910 (m) cc_final: 0.8639 (t) REVERT: I 23 ARG cc_start: 0.8218 (tpp-160) cc_final: 0.7898 (ttm-80) REVERT: J 74 THR cc_start: 0.8898 (m) cc_final: 0.8654 (p) REVERT: K 72 ASP cc_start: 0.8196 (t0) cc_final: 0.7927 (t0) REVERT: K 75 LYS cc_start: 0.7861 (ptpt) cc_final: 0.7583 (pttm) REVERT: M 72 ASP cc_start: 0.8215 (t0) cc_final: 0.7905 (t0) REVERT: M 82 MET cc_start: 0.7976 (mtm) cc_final: 0.7535 (mtm) REVERT: N 61 ARG cc_start: 0.8132 (mtm110) cc_final: 0.7884 (mtm110) REVERT: A 92 GLU cc_start: 0.8515 (tt0) cc_final: 0.8251 (tp30) REVERT: A 121 LYS cc_start: 0.8626 (mttt) cc_final: 0.8327 (mttm) REVERT: A 241 ASN cc_start: 0.8050 (m-40) cc_final: 0.7836 (m-40) REVERT: A 305 LYS cc_start: 0.8700 (mttt) cc_final: 0.8459 (mttp) REVERT: C 39 TYR cc_start: 0.9269 (m-80) cc_final: 0.8925 (m-80) REVERT: C 68 VAL cc_start: 0.7787 (t) cc_final: 0.7506 (m) REVERT: C 111 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8702 (tp) REVERT: C 129 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8471 (mt) REVERT: C 150 MET cc_start: 0.7401 (mmt) cc_final: 0.7143 (mmt) REVERT: C 207 LYS cc_start: 0.8286 (pttt) cc_final: 0.7952 (tttm) REVERT: C 264 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8164 (m) REVERT: C 388 SER cc_start: 0.8772 (p) cc_final: 0.8470 (m) REVERT: C 481 SER cc_start: 0.8701 (t) cc_final: 0.8487 (p) REVERT: E 621 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7894 (mt-10) REVERT: E 632 ASP cc_start: 0.8798 (t70) cc_final: 0.8518 (t0) REVERT: D 102 GLU cc_start: 0.7700 (tp30) cc_final: 0.7485 (mt-10) REVERT: D 104 MET cc_start: 0.8939 (ttt) cc_final: 0.8675 (ttt) REVERT: D 111 LEU cc_start: 0.8371 (tp) cc_final: 0.8168 (tp) REVERT: D 115 SER cc_start: 0.9273 (t) cc_final: 0.9013 (p) REVERT: D 137 ASN cc_start: 0.7332 (t0) cc_final: 0.6300 (p0) REVERT: D 151 ARG cc_start: 0.7715 (mtp180) cc_final: 0.7264 (ttp-110) REVERT: D 186 ASP cc_start: 0.7509 (t0) cc_final: 0.7190 (t0) REVERT: D 255 VAL cc_start: 0.9278 (t) cc_final: 0.9062 (m) REVERT: D 419 ARG cc_start: 0.8027 (mtt-85) cc_final: 0.7720 (mmm-85) REVERT: F 520 LEU cc_start: 0.8784 (mp) cc_final: 0.8583 (mp) REVERT: F 624 ASP cc_start: 0.8121 (m-30) cc_final: 0.7852 (m-30) REVERT: F 625 ASN cc_start: 0.8385 (t0) cc_final: 0.7884 (t0) outliers start: 64 outliers final: 50 residues processed: 432 average time/residue: 0.1585 time to fit residues: 106.2299 Evaluate side-chains 420 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 367 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 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 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 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 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 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 612 SER 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: 0.0010 chunk 169 optimal weight: 5.9990 chunk 146 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 201 optimal weight: 0.6980 chunk 223 optimal weight: 4.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- 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** C 355 ASN C 356 ASN ** 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 = 0.3585 r_free = 0.3585 target = 0.123723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.095505 restraints weight = 33961.128| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.84 r_work: 0.3037 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21881 Z= 0.160 Angle : 0.550 8.538 29835 Z= 0.279 Chirality : 0.043 0.228 3480 Planarity : 0.004 0.051 3684 Dihedral : 5.608 62.533 4231 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.06 % Allowed : 11.65 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.17), residues: 2558 helix: 1.75 (0.27), residues: 393 sheet: 0.45 (0.19), residues: 740 loop : 0.09 (0.17), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 61 TYR 0.024 0.001 TYR L 49 PHE 0.017 0.002 PHE M 102 TRP 0.021 0.001 TRP N 35 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00375 (21772) covalent geometry : angle 0.53318 (29549) SS BOND : bond 0.00380 ( 41) SS BOND : angle 1.04986 ( 82) hydrogen bonds : bond 0.03866 ( 608) hydrogen bonds : angle 4.74394 ( 1587) link_ALPHA1-2 : bond 0.00646 ( 1) link_ALPHA1-2 : angle 1.32022 ( 3) link_ALPHA1-3 : bond 0.01133 ( 2) link_ALPHA1-3 : angle 1.64403 ( 6) link_ALPHA1-6 : bond 0.01051 ( 1) link_ALPHA1-6 : angle 1.89534 ( 3) link_BETA1-4 : bond 0.00470 ( 14) link_BETA1-4 : angle 1.59649 ( 42) link_NAG-ASN : bond 0.00239 ( 50) link_NAG-ASN : angle 1.63884 ( 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 449 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 380 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 108 LEU cc_start: 0.8843 (tp) cc_final: 0.8513 (tt) REVERT: L 45 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7026 (pt0) REVERT: L 46 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7785 (tp) REVERT: L 49 TYR cc_start: 0.7613 (p90) cc_final: 0.7297 (p90) REVERT: L 50 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7829 (mm-30) REVERT: L 68 ASP cc_start: 0.7961 (m-30) cc_final: 0.7699 (t0) REVERT: L 89 MET cc_start: 0.8397 (ttt) cc_final: 0.7867 (ttt) REVERT: G 70 THR cc_start: 0.9123 (m) cc_final: 0.8765 (p) REVERT: G 95 THR cc_start: 0.8901 (m) cc_final: 0.8669 (t) REVERT: I 23 ARG cc_start: 0.8209 (tpp-160) cc_final: 0.7905 (ttm-80) REVERT: I 27 TYR cc_start: 0.8674 (p90) cc_final: 0.8374 (p90) REVERT: J 74 THR cc_start: 0.8904 (m) cc_final: 0.8653 (p) REVERT: K 72 ASP cc_start: 0.8178 (t0) cc_final: 0.7871 (t0) REVERT: K 75 LYS cc_start: 0.7928 (ptpt) cc_final: 0.7664 (pttm) REVERT: M 72 ASP cc_start: 0.8222 (t0) cc_final: 0.7906 (t0) REVERT: M 82 MET cc_start: 0.8020 (mtm) cc_final: 0.7556 (mtm) REVERT: N 35 TRP cc_start: 0.8443 (m100) cc_final: 0.8200 (m100) REVERT: N 61 ARG cc_start: 0.8219 (mtm110) cc_final: 0.7961 (mtm110) REVERT: A 92 GLU cc_start: 0.8489 (tt0) cc_final: 0.8237 (tp30) REVERT: A 121 LYS cc_start: 0.8622 (mttt) cc_final: 0.8328 (mttm) REVERT: A 241 ASN cc_start: 0.8031 (m-40) cc_final: 0.7799 (m-40) REVERT: A 305 LYS cc_start: 0.8723 (mttt) cc_final: 0.8490 (mttp) REVERT: B 621 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8079 (mt-10) REVERT: C 39 TYR cc_start: 0.9273 (m-80) cc_final: 0.8921 (m-80) REVERT: C 68 VAL cc_start: 0.7962 (t) cc_final: 0.7629 (m) REVERT: C 103 GLN cc_start: 0.8242 (tm-30) cc_final: 0.7921 (tm-30) REVERT: C 129 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8540 (mt) REVERT: C 264 SER cc_start: 0.8537 (OUTLIER) cc_final: 0.8173 (m) REVERT: C 388 SER cc_start: 0.8817 (p) cc_final: 0.8507 (m) REVERT: E 632 ASP cc_start: 0.8930 (t70) cc_final: 0.8686 (t0) REVERT: E 635 ILE cc_start: 0.8879 (mm) cc_final: 0.8477 (tt) REVERT: D 104 MET cc_start: 0.8940 (ttt) cc_final: 0.8669 (ttt) REVERT: D 115 SER cc_start: 0.9275 (t) cc_final: 0.9017 (p) REVERT: D 137 ASN cc_start: 0.7367 (t0) cc_final: 0.6285 (p0) REVERT: D 151 ARG cc_start: 0.7717 (mtp180) cc_final: 0.7261 (ttp-110) REVERT: D 186 ASP cc_start: 0.7461 (t0) cc_final: 0.7147 (t0) REVERT: D 255 VAL cc_start: 0.9280 (t) cc_final: 0.9078 (m) REVERT: D 419 ARG cc_start: 0.8049 (mtt-85) cc_final: 0.7828 (mtp85) REVERT: F 520 LEU cc_start: 0.8763 (mp) cc_final: 0.8561 (mp) REVERT: F 535 MET cc_start: 0.9325 (mtt) cc_final: 0.9087 (mtt) REVERT: F 624 ASP cc_start: 0.8172 (m-30) cc_final: 0.7936 (m-30) REVERT: F 625 ASN cc_start: 0.8403 (t0) cc_final: 0.7847 (t0) outliers start: 69 outliers final: 57 residues processed: 420 average time/residue: 0.1482 time to fit residues: 96.5245 Evaluate side-chains 429 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 369 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 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 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 J residue 105 THR 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 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 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 E residue 636 SER Chi-restraints excluded: chain D residue 42 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 198 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 244 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: 7.9990 chunk 166 optimal weight: 0.4980 chunk 183 optimal weight: 0.0870 chunk 86 optimal weight: 8.9990 chunk 247 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.8160 ------------------------------------------------------------------------------- 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** C 66 HIS C 356 ASN ** 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 = 0.3587 r_free = 0.3587 target = 0.123752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.095675 restraints weight = 33752.830| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.82 r_work: 0.3047 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21881 Z= 0.144 Angle : 0.541 9.407 29835 Z= 0.274 Chirality : 0.043 0.234 3480 Planarity : 0.004 0.053 3684 Dihedral : 5.500 58.970 4231 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.06 % Allowed : 12.01 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.17), residues: 2558 helix: 1.77 (0.27), residues: 393 sheet: 0.39 (0.18), residues: 758 loop : 0.10 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 61 TYR 0.028 0.001 TYR L 49 PHE 0.016 0.001 PHE L 94 TRP 0.021 0.001 TRP L 35 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00335 (21772) covalent geometry : angle 0.52525 (29549) SS BOND : bond 0.00370 ( 41) SS BOND : angle 0.89786 ( 82) hydrogen bonds : bond 0.03735 ( 608) hydrogen bonds : angle 4.73554 ( 1587) link_ALPHA1-2 : bond 0.00644 ( 1) link_ALPHA1-2 : angle 1.29683 ( 3) link_ALPHA1-3 : bond 0.01114 ( 2) link_ALPHA1-3 : angle 1.52016 ( 6) link_ALPHA1-6 : bond 0.01086 ( 1) link_ALPHA1-6 : angle 1.93921 ( 3) link_BETA1-4 : bond 0.00477 ( 14) link_BETA1-4 : angle 1.54904 ( 42) link_NAG-ASN : bond 0.00216 ( 50) link_NAG-ASN : angle 1.58819 ( 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 455 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 386 time to evaluate : 0.688 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: 0.8860 (tp) cc_final: 0.8521 (tt) REVERT: L 45 GLN cc_start: 0.7526 (mm-40) cc_final: 0.7041 (pt0) REVERT: L 46 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7704 (tp) REVERT: L 50 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7767 (mm-30) REVERT: L 68 ASP cc_start: 0.7914 (m-30) cc_final: 0.7646 (t0) REVERT: L 89 MET cc_start: 0.8351 (ttt) cc_final: 0.7866 (ttt) REVERT: G 70 THR cc_start: 0.9140 (m) cc_final: 0.8918 (p) REVERT: G 95 THR cc_start: 0.8872 (m) cc_final: 0.8658 (t) REVERT: I 3 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8085 (tp40) REVERT: I 23 ARG cc_start: 0.8225 (tpp-160) cc_final: 0.7922 (ttm-80) REVERT: I 27 TYR cc_start: 0.8667 (p90) cc_final: 0.8343 (p90) REVERT: J 74 THR cc_start: 0.8903 (m) cc_final: 0.8631 (p) REVERT: K 3 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7574 (mm110) REVERT: K 28 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8255 (p) REVERT: K 72 ASP cc_start: 0.8154 (t0) cc_final: 0.7778 (t0) REVERT: K 75 LYS cc_start: 0.7834 (ptpt) cc_final: 0.7544 (pttm) REVERT: M 32 PHE cc_start: 0.8941 (m-80) cc_final: 0.8739 (m-80) REVERT: M 72 ASP cc_start: 0.8216 (t0) cc_final: 0.7894 (t0) REVERT: M 82 MET cc_start: 0.8020 (mtm) cc_final: 0.7575 (mtm) REVERT: A 92 GLU cc_start: 0.8476 (tt0) cc_final: 0.8238 (tp30) REVERT: A 121 LYS cc_start: 0.8644 (mttt) cc_final: 0.8370 (mttm) REVERT: A 241 ASN cc_start: 0.8015 (m-40) cc_final: 0.7781 (m-40) REVERT: A 305 LYS cc_start: 0.8740 (mttt) cc_final: 0.8523 (mttp) REVERT: B 621 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8093 (mt-10) REVERT: C 39 TYR cc_start: 0.9261 (m-80) cc_final: 0.8923 (m-80) REVERT: C 100 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8660 (mtm) REVERT: C 103 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7840 (tm-30) REVERT: C 129 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8495 (mt) REVERT: C 207 LYS cc_start: 0.8137 (ptmt) cc_final: 0.7609 (tptt) REVERT: C 264 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8154 (m) REVERT: E 621 GLU cc_start: 0.8175 (tp30) cc_final: 0.7847 (tt0) REVERT: E 632 ASP cc_start: 0.8903 (t70) cc_final: 0.8656 (t0) REVERT: D 104 MET cc_start: 0.8947 (ttt) cc_final: 0.8678 (ttt) REVERT: D 137 ASN cc_start: 0.7375 (t0) cc_final: 0.6286 (p0) REVERT: D 151 ARG cc_start: 0.7706 (mtp180) cc_final: 0.7248 (ttp-110) REVERT: D 186 ASP cc_start: 0.7521 (t0) cc_final: 0.7187 (t0) REVERT: D 419 ARG cc_start: 0.8054 (mtt-85) cc_final: 0.7818 (mtp85) REVERT: F 535 MET cc_start: 0.9334 (mtt) cc_final: 0.9105 (mtt) REVERT: F 624 ASP cc_start: 0.8222 (m-30) cc_final: 0.7995 (m-30) REVERT: F 625 ASN cc_start: 0.8487 (t0) cc_final: 0.7872 (t0) outliers start: 69 outliers final: 55 residues processed: 429 average time/residue: 0.1490 time to fit residues: 99.9491 Evaluate side-chains 425 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 364 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 89 VAL 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 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 J residue 105 THR 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 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 42 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 185 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 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: 1.9990 chunk 190 optimal weight: 2.9990 chunk 220 optimal weight: 0.6980 chunk 173 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 240 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3539 r_free = 0.3539 target = 0.119979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.092642 restraints weight = 33858.178| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.74 r_work: 0.3004 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21881 Z= 0.220 Angle : 0.602 8.448 29835 Z= 0.304 Chirality : 0.045 0.316 3480 Planarity : 0.004 0.052 3684 Dihedral : 5.716 56.777 4231 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.01 % Allowed : 12.27 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.17), residues: 2558 helix: 1.57 (0.27), residues: 393 sheet: 0.22 (0.18), residues: 776 loop : 0.02 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 61 TYR 0.018 0.002 TYR N 49 PHE 0.020 0.002 PHE M 102 TRP 0.024 0.002 TRP L 35 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00522 (21772) covalent geometry : angle 0.58492 (29549) SS BOND : bond 0.00456 ( 41) SS BOND : angle 1.09052 ( 82) hydrogen bonds : bond 0.04124 ( 608) hydrogen bonds : angle 4.84763 ( 1587) link_ALPHA1-2 : bond 0.00576 ( 1) link_ALPHA1-2 : angle 1.29892 ( 3) link_ALPHA1-3 : bond 0.01103 ( 2) link_ALPHA1-3 : angle 1.32027 ( 6) link_ALPHA1-6 : bond 0.01102 ( 1) link_ALPHA1-6 : angle 1.90359 ( 3) link_BETA1-4 : bond 0.00452 ( 14) link_BETA1-4 : angle 1.60988 ( 42) link_NAG-ASN : bond 0.00367 ( 50) link_NAG-ASN : angle 1.74913 ( 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 431 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 363 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 45 GLN cc_start: 0.7613 (mm-40) cc_final: 0.7066 (pt0) REVERT: L 46 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7740 (tp) REVERT: L 68 ASP cc_start: 0.7985 (m-30) cc_final: 0.7719 (t0) REVERT: L 89 MET cc_start: 0.8375 (ttt) cc_final: 0.7879 (ttt) REVERT: G 70 THR cc_start: 0.9152 (m) cc_final: 0.8915 (p) REVERT: G 95 THR cc_start: 0.8868 (m) cc_final: 0.8644 (t) REVERT: I 3 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8107 (tp40) REVERT: I 23 ARG cc_start: 0.8213 (tpp-160) cc_final: 0.7921 (ttm-80) REVERT: I 27 TYR cc_start: 0.8698 (p90) cc_final: 0.8358 (p90) REVERT: J 74 THR cc_start: 0.8950 (m) cc_final: 0.8658 (p) REVERT: K 3 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7636 (mm110) REVERT: K 72 ASP cc_start: 0.8130 (t0) cc_final: 0.7830 (t0) REVERT: K 75 LYS cc_start: 0.7883 (ptpt) cc_final: 0.7602 (pttm) REVERT: M 32 PHE cc_start: 0.8996 (m-80) cc_final: 0.8777 (m-80) REVERT: M 72 ASP cc_start: 0.8225 (t0) cc_final: 0.7913 (t0) REVERT: M 82 MET cc_start: 0.8036 (mtm) cc_final: 0.7560 (mtm) REVERT: A 92 GLU cc_start: 0.8473 (tt0) cc_final: 0.8238 (tp30) REVERT: A 121 LYS cc_start: 0.8697 (mttt) cc_final: 0.8437 (mttm) REVERT: A 232 LYS cc_start: 0.7918 (pttt) cc_final: 0.7651 (ptpp) REVERT: A 305 LYS cc_start: 0.8738 (mttt) cc_final: 0.8508 (mttp) REVERT: B 621 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8110 (mt-10) REVERT: C 39 TYR cc_start: 0.9273 (m-80) cc_final: 0.8945 (m-80) REVERT: C 103 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7931 (tm-30) REVERT: C 129 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8633 (mt) REVERT: C 207 LYS cc_start: 0.8287 (ptmt) cc_final: 0.7719 (tptt) REVERT: E 621 GLU cc_start: 0.8219 (tp30) cc_final: 0.7936 (tp30) REVERT: E 632 ASP cc_start: 0.8964 (t70) cc_final: 0.8685 (t0) REVERT: E 635 ILE cc_start: 0.8902 (mm) cc_final: 0.8565 (tt) REVERT: D 104 MET cc_start: 0.8967 (ttt) cc_final: 0.8700 (ttt) REVERT: D 137 ASN cc_start: 0.7469 (t0) cc_final: 0.6330 (p0) REVERT: D 186 ASP cc_start: 0.7602 (t0) cc_final: 0.7223 (t0) REVERT: D 419 ARG cc_start: 0.8259 (mtt-85) cc_final: 0.7992 (mtp85) REVERT: F 535 MET cc_start: 0.9326 (mtt) cc_final: 0.9091 (mtt) REVERT: F 624 ASP cc_start: 0.8244 (m-30) cc_final: 0.7998 (m-30) REVERT: F 625 ASN cc_start: 0.8514 (t0) cc_final: 0.7884 (t0) outliers start: 68 outliers final: 57 residues processed: 406 average time/residue: 0.1583 time to fit residues: 99.7098 Evaluate side-chains 413 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 353 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 46 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 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 J residue 97 ILE Chi-restraints excluded: chain J residue 105 THR 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 67 ASN 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 182 VAL 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 42 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 185 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 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: 0.9990 chunk 183 optimal weight: 0.9980 chunk 146 optimal weight: 0.0970 chunk 245 optimal weight: 0.9980 chunk 240 optimal weight: 0.6980 chunk 243 optimal weight: 0.3980 chunk 128 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 108 optimal weight: 0.0370 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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** C 356 ASN C 363 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 = 0.3595 r_free = 0.3595 target = 0.124421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.096526 restraints weight = 33779.894| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.82 r_work: 0.3063 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21881 Z= 0.113 Angle : 0.534 8.671 29835 Z= 0.271 Chirality : 0.043 0.233 3480 Planarity : 0.003 0.055 3684 Dihedral : 5.425 56.160 4231 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.35 % Allowed : 13.20 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.17), residues: 2558 helix: 2.00 (0.28), residues: 375 sheet: 0.30 (0.18), residues: 776 loop : 0.08 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 61 TYR 0.014 0.001 TYR I 27 PHE 0.014 0.001 PHE L 94 TRP 0.020 0.001 TRP L 35 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00256 (21772) covalent geometry : angle 0.51948 (29549) SS BOND : bond 0.00339 ( 41) SS BOND : angle 0.87047 ( 82) hydrogen bonds : bond 0.03545 ( 608) hydrogen bonds : angle 4.65026 ( 1587) link_ALPHA1-2 : bond 0.00703 ( 1) link_ALPHA1-2 : angle 1.29176 ( 3) link_ALPHA1-3 : bond 0.01000 ( 2) link_ALPHA1-3 : angle 1.38106 ( 6) link_ALPHA1-6 : bond 0.01148 ( 1) link_ALPHA1-6 : angle 2.04082 ( 3) link_BETA1-4 : bond 0.00528 ( 14) link_BETA1-4 : angle 1.47462 ( 42) link_NAG-ASN : bond 0.00193 ( 50) link_NAG-ASN : angle 1.52247 ( 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 441 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 388 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 58 TYR cc_start: 0.8443 (t80) cc_final: 0.8164 (t80) REVERT: H 105 GLN cc_start: 0.7628 (mm-40) cc_final: 0.7376 (mm-40) REVERT: L 45 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7317 (pt0) REVERT: L 68 ASP cc_start: 0.7930 (m-30) cc_final: 0.7677 (t0) REVERT: L 89 MET cc_start: 0.8282 (ttt) cc_final: 0.8019 (ttt) REVERT: G 95 THR cc_start: 0.8855 (m) cc_final: 0.8632 (t) REVERT: I 3 GLN cc_start: 0.8272 (mt0) cc_final: 0.8051 (tp40) REVERT: I 23 ARG cc_start: 0.8248 (tpp-160) cc_final: 0.7952 (ttm-80) REVERT: I 27 TYR cc_start: 0.8719 (p90) cc_final: 0.8442 (p90) REVERT: I 43 LYS cc_start: 0.8259 (mmmt) cc_final: 0.8024 (mppt) REVERT: J 74 THR cc_start: 0.8915 (m) cc_final: 0.8650 (p) REVERT: K 3 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7496 (mm110) REVERT: K 28 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8202 (p) REVERT: K 72 ASP cc_start: 0.8094 (t0) cc_final: 0.7602 (t0) REVERT: K 75 LYS cc_start: 0.7755 (ptpt) cc_final: 0.7500 (pttm) REVERT: M 72 ASP cc_start: 0.8180 (t0) cc_final: 0.7872 (t0) REVERT: M 82 MET cc_start: 0.7997 (mtm) cc_final: 0.7593 (mtm) REVERT: A 92 GLU cc_start: 0.8487 (tt0) cc_final: 0.8255 (tp30) REVERT: A 121 LYS cc_start: 0.8658 (mttt) cc_final: 0.8350 (mttm) REVERT: A 232 LYS cc_start: 0.7687 (pttt) cc_final: 0.7381 (ptpp) REVERT: A 305 LYS cc_start: 0.8744 (mttt) cc_final: 0.8512 (mttp) REVERT: B 621 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8135 (mt-10) REVERT: C 39 TYR cc_start: 0.9230 (m-80) cc_final: 0.8909 (m-80) REVERT: C 103 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7875 (tm-30) REVERT: C 129 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8491 (mt) REVERT: C 207 LYS cc_start: 0.8224 (ptmt) cc_final: 0.7646 (tptt) REVERT: C 484 TYR cc_start: 0.8496 (p90) cc_final: 0.8242 (p90) REVERT: E 621 GLU cc_start: 0.8186 (tp30) cc_final: 0.7762 (tt0) REVERT: E 632 ASP cc_start: 0.8886 (t70) cc_final: 0.8640 (t0) REVERT: D 104 MET cc_start: 0.8953 (ttt) cc_final: 0.8682 (ttt) REVERT: D 137 ASN cc_start: 0.7366 (t0) cc_final: 0.6214 (p0) REVERT: D 186 ASP cc_start: 0.7553 (t0) cc_final: 0.7241 (t0) REVERT: D 419 ARG cc_start: 0.8131 (mtt-85) cc_final: 0.7723 (mtp85) REVERT: F 535 MET cc_start: 0.9282 (mtt) cc_final: 0.9050 (mtt) REVERT: F 624 ASP cc_start: 0.8197 (m-30) cc_final: 0.7962 (m-30) REVERT: F 625 ASN cc_start: 0.8486 (t0) cc_final: 0.7836 (t0) REVERT: F 636 SER cc_start: 0.9216 (t) cc_final: 0.8706 (p) outliers start: 53 outliers final: 47 residues processed: 421 average time/residue: 0.1454 time to fit residues: 94.9725 Evaluate side-chains 413 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 364 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 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 28 THR Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 28 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 52 THR 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 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 303 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 42 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 185 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 278 THR 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 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: 1.9990 chunk 9 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 126 optimal weight: 0.3980 chunk 62 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 246 optimal weight: 4.9990 chunk 239 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 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 = 0.3563 r_free = 0.3563 target = 0.121979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.093897 restraints weight = 34042.195| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.81 r_work: 0.3020 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21881 Z= 0.187 Angle : 0.585 8.313 29835 Z= 0.295 Chirality : 0.044 0.220 3480 Planarity : 0.004 0.054 3684 Dihedral : 5.509 56.331 4231 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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 aren not related in a simple way. whole: 0.43 (0.17), residues: 2558 helix: 1.75 (0.28), residues: 393 sheet: 0.21 (0.18), residues: 776 loop : -0.01 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG L 61 TYR 0.017 0.001 TYR N 49 PHE 0.019 0.002 PHE M 102 TRP 0.020 0.001 TRP L 35 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00445 (21772) covalent geometry : angle 0.57018 (29549) SS BOND : bond 0.00415 ( 41) SS BOND : angle 1.00554 ( 82) hydrogen bonds : bond 0.03917 ( 608) hydrogen bonds : angle 4.72270 ( 1587) link_ALPHA1-2 : bond 0.00555 ( 1) link_ALPHA1-2 : angle 1.29820 ( 3) link_ALPHA1-3 : bond 0.01117 ( 2) link_ALPHA1-3 : angle 1.23046 ( 6) link_ALPHA1-6 : bond 0.01065 ( 1) link_ALPHA1-6 : angle 1.86817 ( 3) link_BETA1-4 : bond 0.00479 ( 14) link_BETA1-4 : angle 1.52602 ( 42) link_NAG-ASN : bond 0.00288 ( 50) link_NAG-ASN : angle 1.64017 ( 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 412 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 357 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 58 TYR cc_start: 0.8514 (t80) cc_final: 0.8242 (t80) REVERT: L 45 GLN cc_start: 0.7575 (mm-40) cc_final: 0.7189 (pt0) REVERT: L 61 ARG cc_start: 0.7861 (mtm110) cc_final: 0.7558 (mtm110) REVERT: L 68 ASP cc_start: 0.7920 (m-30) cc_final: 0.7657 (t0) REVERT: L 89 MET cc_start: 0.8334 (ttt) cc_final: 0.7879 (ttt) REVERT: G 95 THR cc_start: 0.8854 (m) cc_final: 0.8614 (t) REVERT: I 23 ARG cc_start: 0.8239 (tpp-160) cc_final: 0.7923 (ttm-80) REVERT: I 27 TYR cc_start: 0.8711 (p90) cc_final: 0.8407 (p90) REVERT: I 43 LYS cc_start: 0.8362 (mmmt) cc_final: 0.8059 (mppt) REVERT: I 57 THR cc_start: 0.9020 (p) cc_final: 0.8799 (p) REVERT: J 74 THR cc_start: 0.8929 (m) cc_final: 0.8641 (p) REVERT: K 28 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8245 (p) REVERT: K 72 ASP cc_start: 0.8122 (t0) cc_final: 0.7749 (t0) REVERT: K 75 LYS cc_start: 0.7755 (ptpt) cc_final: 0.7483 (pttm) REVERT: M 72 ASP cc_start: 0.8201 (t0) cc_final: 0.7873 (t0) REVERT: M 82 MET cc_start: 0.8035 (mtm) cc_final: 0.7599 (mtm) REVERT: A 92 GLU cc_start: 0.8505 (tt0) cc_final: 0.8289 (tp30) REVERT: A 107 ASP cc_start: 0.8175 (m-30) cc_final: 0.7939 (m-30) REVERT: A 121 LYS cc_start: 0.8698 (mttt) cc_final: 0.8425 (mttm) REVERT: A 232 LYS cc_start: 0.7828 (pttt) cc_final: 0.7614 (ptpp) REVERT: A 305 LYS cc_start: 0.8737 (mttt) cc_final: 0.8498 (mttp) REVERT: C 39 TYR cc_start: 0.9272 (m-80) cc_final: 0.8932 (m-80) REVERT: C 103 GLN cc_start: 0.8077 (tm-30) cc_final: 0.7858 (tm-30) REVERT: C 129 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8592 (mt) REVERT: C 207 LYS cc_start: 0.8337 (ptmt) cc_final: 0.7702 (tptt) REVERT: C 475 MET cc_start: 0.7593 (tpp) cc_final: 0.7304 (tpp) REVERT: E 621 GLU cc_start: 0.8256 (tp30) cc_final: 0.7919 (tt0) REVERT: E 632 ASP cc_start: 0.8957 (t70) cc_final: 0.8682 (t0) REVERT: E 635 ILE cc_start: 0.8866 (mm) cc_final: 0.8531 (tt) REVERT: D 104 MET cc_start: 0.8958 (ttt) cc_final: 0.8687 (ttt) REVERT: D 137 ASN cc_start: 0.7424 (t0) cc_final: 0.6284 (p0) REVERT: D 186 ASP cc_start: 0.7628 (t0) cc_final: 0.7268 (t0) REVERT: D 419 ARG cc_start: 0.8210 (mtt-85) cc_final: 0.8005 (mmm-85) REVERT: F 535 MET cc_start: 0.9310 (mtt) cc_final: 0.9064 (mtt) REVERT: F 624 ASP cc_start: 0.8262 (m-30) cc_final: 0.8027 (m-30) REVERT: F 625 ASN cc_start: 0.8518 (t0) cc_final: 0.7839 (t0) REVERT: F 636 SER cc_start: 0.9237 (t) cc_final: 0.8764 (p) outliers start: 55 outliers final: 51 residues processed: 393 average time/residue: 0.1508 time to fit residues: 92.4594 Evaluate side-chains 408 residues out of total 2257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 355 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 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 28 THR Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 28 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 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 E residue 595 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 185 VAL 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 373 THR Chi-restraints excluded: chain D residue 432 GLN Chi-restraints excluded: chain D residue 443 ILE 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: 3.9990 chunk 57 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 193 optimal weight: 0.5980 chunk 195 optimal weight: 0.4980 chunk 103 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 251 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.123395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.095360 restraints weight = 33998.438| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.82 r_work: 0.3039 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21881 Z= 0.138 Angle : 0.558 8.311 29835 Z= 0.283 Chirality : 0.043 0.218 3480 Planarity : 0.004 0.054 3684 Dihedral : 5.355 57.843 4231 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.48 % Allowed : 13.65 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.17), residues: 2558 helix: 1.94 (0.28), residues: 375 sheet: 0.22 (0.18), residues: 779 loop : 0.01 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 61 TYR 0.015 0.001 TYR N 49 PHE 0.018 0.001 PHE L 94 TRP 0.016 0.001 TRP L 35 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00320 (21772) covalent geometry : angle 0.54389 (29549) SS BOND : bond 0.00375 ( 41) SS BOND : angle 0.92608 ( 82) hydrogen bonds : bond 0.03698 ( 608) hydrogen bonds : angle 4.65898 ( 1587) link_ALPHA1-2 : bond 0.00595 ( 1) link_ALPHA1-2 : angle 1.27424 ( 3) link_ALPHA1-3 : bond 0.00981 ( 2) link_ALPHA1-3 : angle 1.25311 ( 6) link_ALPHA1-6 : bond 0.01029 ( 1) link_ALPHA1-6 : angle 1.72182 ( 3) link_BETA1-4 : bond 0.00527 ( 14) link_BETA1-4 : angle 1.48801 ( 42) link_NAG-ASN : bond 0.00209 ( 50) link_NAG-ASN : angle 1.56225 ( 150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4746.19 seconds wall clock time: 82 minutes 22.58 seconds (4942.58 seconds total)