Starting phenix.real_space_refine on Fri Jul 3 20:07:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l8f_23232/07_2026/7l8f_23232.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8f_23232/07_2026/7l8f_23232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7l8f_23232/07_2026/7l8f_23232.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l8f_23232/07_2026/7l8f_23232.cif" model { file = "/net/cci-nas-00/data/ceres_data/7l8f_23232/07_2026/7l8f_23232.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8f_23232/07_2026/7l8f_23232.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l8f_23232/07_2026/7l8f_23232.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8f_23232/07_2026/7l8f_23232.map" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 9855 2.51 5 N 2684 2.21 5 O 3199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15840 Number of models: 1 Model: "" Number of chains: 28 Chain: "C" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3523 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Chain: "D" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "E" Number of atoms: 3508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3508 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 20, 'TRANS': 423} Chain breaks: 3 Chain: "F" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 980 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "A" Number of atoms: 3515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3515 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 3 Chain: "B" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "H" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 635 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'TRANS': 126} Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 127 Planarities with less than four sites: {'UNK:plan-1': 127} Unresolved non-hydrogen planarities: 127 Chain: "L" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 535 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'TRANS': 106} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 107 Planarities with less than four sites: {'UNK:plan-1': 107} Unresolved non-hydrogen planarities: 107 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.71, per 1000 atoms: 0.23 Number of scatterers: 15840 At special positions: 0 Unit cell: (143.17, 126.69, 134.93, 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 102 16.00 O 3199 8.00 N 2684 7.00 C 9855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.12 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.10 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA K 3 " - " MAN K 4 " " BMA Q 3 " - " MAN Q 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA K 3 " - " MAN K 5 " " BMA Q 3 " - " MAN Q 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A 701 " - " ASN A 160 " " NAG A 702 " - " ASN A 276 " " NAG A 703 " - " ASN A 386 " " NAG A 704 " - " ASN A 363 " " NAG A 705 " - " ASN A 234 " " NAG A 706 " - " ASN A 197 " " NAG A 707 " - " ASN A 133 " " NAG A 708 " - " ASN A 88 " " NAG A 709 " - " ASN A 241 " " NAG A 710 " - " ASN A 289 " " NAG A 711 " - " ASN A 339 " " NAG A 712 " - " ASN A 355 " " NAG A 713 " - " ASN A 392 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 701 " - " ASN C 448 " " NAG C 702 " - " ASN C 160 " " NAG C 703 " - " ASN C 276 " " NAG C 704 " - " ASN C 295 " " NAG C 705 " - " ASN C 386 " " NAG C 706 " - " ASN C 363 " " NAG C 707 " - " ASN C 234 " " NAG C 708 " - " ASN C 197 " " NAG C 709 " - " ASN C 133 " " NAG C 710 " - " ASN C 301 " " NAG C 711 " - " ASN C 88 " " NAG C 712 " - " ASN C 241 " " NAG C 713 " - " ASN C 289 " " NAG C 714 " - " ASN C 339 " " NAG C 715 " - " ASN C 392 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 611 " " NAG E 701 " - " ASN E 448 " " NAG E 702 " - " ASN E 160 " " NAG E 703 " - " ASN E 276 " " NAG E 704 " - " ASN E 386 " " NAG E 705 " - " ASN E 363 " " NAG E 706 " - " ASN E 234 " " NAG E 707 " - " ASN E 133 " " NAG E 708 " - " ASN E 301 " " NAG E 709 " - " ASN E 88 " " NAG E 710 " - " ASN E 241 " " NAG E 711 " - " ASN E 289 " " NAG E 712 " - " ASN E 355 " " NAG E 713 " - " ASN E 392 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 611 " " NAG G 1 " - " ASN C 262 " " NAG I 1 " - " ASN C 156 " " NAG J 1 " - " ASN C 332 " " NAG K 1 " - " ASN E 262 " " NAG M 1 " - " ASN E 295 " " NAG N 1 " - " ASN E 197 " " NAG O 1 " - " ASN E 156 " " NAG P 1 " - " ASN E 332 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 448 " " NAG S 1 " - " ASN A 295 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN A 301 " " NAG V 1 " - " ASN A 332 " Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 661.7 milliseconds 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 28 sheets defined 29.3% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.572A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASP C 113 " --> pdb=" O ILE C 109 " (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 335 through 351 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 475 through 484 removed outlier: 4.190A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 536 through 549 removed outlier: 3.505A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 544 " --> pdb=" O GLN D 540 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 596 Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.982A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 392 removed outlier: 3.620A pdb=" N ASN E 392 " --> pdb=" O SER E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 4.089A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU E 483 " --> pdb=" O TRP E 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 removed outlier: 3.519A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 547 removed outlier: 3.871A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 633 Processing helix chain 'F' and resid 634 through 636 No H-bonds generated for 'chain 'F' and resid 634 through 636' Processing helix chain 'F' and resid 638 through 654 Processing helix chain 'F' and resid 654 through 661 removed outlier: 4.280A pdb=" N GLN F 658 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP F 659 " --> pdb=" O LYS F 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.113A 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 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.996A pdb=" N VAL A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.811A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.500A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 537 No H-bonds generated for 'chain 'B' and resid 535 through 537' Processing helix chain 'B' and resid 538 through 543 removed outlier: 3.912A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 550 Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 660 Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 61 through 65 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 90 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.426A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'C' and resid 75 through 76 removed outlier: 4.197A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.316A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 271 through 273 Processing sheet with id=AA8, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.829A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 301 through 312 removed outlier: 7.180A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.414A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.452A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 6.673A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY E 321 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323A current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AB8, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.371A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'A' and resid 75 through 76 removed outlier: 5.610A pdb=" N VAL A 75 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AC4, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.514A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AC5, 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 283 through 312 removed outlier: 6.609A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A 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 465 through 470 Processing sheet with id=AC6, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AC7, first strand: chain 'H' and resid 9 through 11 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 9 through 11 current: chain 'H' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 45 through 52 current: chain 'H' and resid 116 through 117 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'H' and resid 102 through 104 Processing sheet with id=AC9, first strand: chain 'L' and resid 5 through 7 removed outlier: 4.077A pdb=" N UNK L 22 " --> pdb=" O UNK L 7 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.210A pdb=" N UNK L 33 " --> pdb=" O UNK L 49 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N UNK L 49 " --> pdb=" O UNK L 33 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) 541 hydrogen bonds defined for protein. 1452 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.95 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3704 1.32 - 1.46: 5025 1.46 - 1.60: 7219 1.60 - 1.74: 35 1.74 - 1.88: 128 Bond restraints: 16111 Sorted by residual: bond pdb=" CB LEU B 661 " pdb=" CG LEU B 661 " ideal model delta sigma weight residual 1.530 1.668 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.18e+01 bond pdb=" CG GLN E 348 " pdb=" CD GLN E 348 " ideal model delta sigma weight residual 1.516 1.385 0.131 2.50e-02 1.60e+03 2.76e+01 bond pdb=" CB LEU F 520 " pdb=" CG LEU F 520 " ideal model delta sigma weight residual 1.530 1.629 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" CB LEU D 661 " pdb=" CG LEU D 661 " ideal model delta sigma weight residual 1.530 1.626 -0.096 2.00e-02 2.50e+03 2.32e+01 ... (remaining 16106 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 18217 2.16 - 4.32: 3122 4.32 - 6.48: 502 6.48 - 8.63: 68 8.63 - 10.79: 5 Bond angle restraints: 21914 Sorted by residual: angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 128.15 -8.59 1.02e+00 9.61e-01 7.09e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 127.85 -8.29 1.01e+00 9.80e-01 6.74e+01 angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.56 127.71 -8.15 1.02e+00 9.61e-01 6.38e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.48 -7.92 1.01e+00 9.80e-01 6.15e+01 angle pdb=" N PRO C 437 " pdb=" CA PRO C 437 " pdb=" C PRO C 437 " ideal model delta sigma weight residual 110.47 103.13 7.34 9.60e-01 1.09e+00 5.84e+01 ... (remaining 21909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 8690 17.35 - 34.70: 212 34.70 - 52.05: 75 52.05 - 69.40: 23 69.40 - 86.75: 11 Dihedral angle restraints: 9011 sinusoidal: 3391 harmonic: 5620 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 159.96 -66.96 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 157.43 -64.43 1 1.00e+01 1.00e-02 5.46e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 146.06 -53.06 1 1.00e+01 1.00e-02 3.83e+01 ... (remaining 9008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 2031 0.127 - 0.255: 463 0.255 - 0.382: 197 0.382 - 0.509: 78 0.509 - 0.636: 6 Chirality restraints: 2775 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.48e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.40e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.09e+02 ... (remaining 2772 not shown) Planarity restraints: 2759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 706 " 0.339 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG E 706 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG E 706 " 0.073 2.00e-02 2.50e+03 pdb=" N2 NAG E 706 " -0.519 2.00e-02 2.50e+03 pdb=" O7 NAG E 706 " 0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 701 " 0.343 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG D 701 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG D 701 " 0.159 2.00e-02 2.50e+03 pdb=" N2 NAG D 701 " -0.520 2.00e-02 2.50e+03 pdb=" O7 NAG D 701 " 0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 710 " 0.340 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG E 710 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG E 710 " 0.158 2.00e-02 2.50e+03 pdb=" N2 NAG E 710 " -0.516 2.00e-02 2.50e+03 pdb=" O7 NAG E 710 " 0.103 2.00e-02 2.50e+03 ... (remaining 2756 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 500 2.67 - 3.23: 14641 3.23 - 3.79: 23344 3.79 - 4.34: 31977 4.34 - 4.90: 50384 Nonbonded interactions: 120846 Sorted by model distance: nonbonded pdb=" O ASP F 624 " pdb=" OD1 ASP F 624 " model vdw 2.118 3.040 nonbonded pdb=" O3 NAG B 703 " pdb=" O7 NAG B 703 " model vdw 2.244 3.040 nonbonded pdb=" OD2 ASP A 167 " pdb=" NZ LYS A 168 " model vdw 2.413 3.120 nonbonded pdb=" NZ LYS E 232 " pdb=" OE2 GLU E 269 " model vdw 2.418 3.120 nonbonded pdb=" CG2 ILE C 294 " pdb=" OG SER C 447 " model vdw 2.428 3.460 ... (remaining 120841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 505 or resid 701 through 713)) selection = (chain 'C' and (resid 33 through 64 or resid 66 through 397 or resid 411 through \ 505 or resid 702 through 714)) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 521 through 548 or resid 568 through 702)) selection = (chain 'D' and (resid 521 through 548 or resid 568 through 702)) selection = (chain 'F' and resid 521 through 702) } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'Q' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.810 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.138 16230 Z= 1.186 Angle : 1.725 10.793 22238 Z= 1.095 Chirality : 0.144 0.636 2775 Planarity : 0.017 0.294 2696 Dihedral : 9.916 86.754 5256 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.19), residues: 1669 helix: 0.21 (0.23), residues: 440 sheet: 0.91 (0.23), residues: 415 loop : 0.88 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 419 TYR 0.042 0.007 TYR F 638 PHE 0.026 0.006 PHE A 383 TRP 0.055 0.009 TRP A 479 HIS 0.014 0.002 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.02211 / 1.16 (16111) covalent geometry : angle 1.69172 / 1.09 (21914) SS BOND : bond 0.02167 / 1.28 ( 33) SS BOND : angle 3.11929 / 2.15 ( 66) hydrogen bonds : bond 0.17625 / 11.53 ( 541) hydrogen bonds : angle 7.30043 / 5.08 ( 1452) link_ALPHA1-3 : bond 0.09449 / 4.73 ( 3) link_ALPHA1-3 : angle 4.77589 / 3.18 ( 9) link_ALPHA1-6 : bond 0.05804 / 2.92 ( 3) link_ALPHA1-6 : angle 2.96085 / 2.16 ( 9) link_BETA1-4 : bond 0.07002 / 4.42 ( 17) link_BETA1-4 : angle 4.49834 / 3.20 ( 51) link_NAG-ASN : bond 0.07406 / 4.77 ( 63) link_NAG-ASN : angle 2.82680 / 1.99 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 377 ASN cc_start: 0.8016 (t0) cc_final: 0.7579 (t0) REVERT: D 588 ARG cc_start: 0.8599 (ttp80) cc_final: 0.8209 (mtm-85) REVERT: D 591 GLN cc_start: 0.8907 (tt0) cc_final: 0.8542 (tp-100) REVERT: D 639 THR cc_start: 0.8233 (m) cc_final: 0.7517 (p) REVERT: A 125 LEU cc_start: 0.8607 (mt) cc_final: 0.8253 (mt) REVERT: A 153 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7224 (tp30) REVERT: A 207 LYS cc_start: 0.8654 (mmtt) cc_final: 0.8402 (mmtm) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.1274 time to fit residues: 85.2613 Evaluate side-chains 226 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 130 GLN C 137 ASN C 352 HIS D 630 GLN E 114 GLN E 302 ASN F 540 GLN F 607 ASN A 188 ASN A 425 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.140224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.114418 restraints weight = 26723.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.117519 restraints weight = 16353.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.118070 restraints weight = 11642.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.118670 restraints weight = 10282.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118767 restraints weight = 9397.812| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16230 Z= 0.177 Angle : 0.820 11.195 22238 Z= 0.393 Chirality : 0.051 0.726 2775 Planarity : 0.005 0.051 2696 Dihedral : 4.964 23.559 2036 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.35 % Allowed : 9.53 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.20), residues: 1669 helix: 1.46 (0.25), residues: 414 sheet: 0.64 (0.21), residues: 486 loop : 0.28 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 617 TYR 0.020 0.002 TYR A 435 PHE 0.025 0.002 PHE E 391 TRP 0.024 0.002 TRP A 479 HIS 0.011 0.001 HIS D 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (16111) covalent geometry : angle 0.75586 / 0.38 (21914) SS BOND : bond 0.00280 / 0.16 ( 33) SS BOND : angle 1.71577 / 1.27 ( 66) hydrogen bonds : bond 0.06316 / 4.10 ( 541) hydrogen bonds : angle 5.42693 / 3.77 ( 1452) link_ALPHA1-3 : bond 0.01394 / 0.69 ( 3) link_ALPHA1-3 : angle 1.52047 / 0.95 ( 9) link_ALPHA1-6 : bond 0.00615 / 0.31 ( 3) link_ALPHA1-6 : angle 1.55190 / 1.01 ( 9) link_BETA1-4 : bond 0.00772 / 0.45 ( 17) link_BETA1-4 : angle 2.47944 / 1.66 ( 51) link_NAG-ASN : bond 0.00498 / 0.33 ( 63) link_NAG-ASN : angle 3.14282 / 2.27 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 308 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7657 (mm110) REVERT: C 161 MET cc_start: 0.8519 (tpt) cc_final: 0.8005 (tpt) REVERT: C 349 LEU cc_start: 0.8173 (mp) cc_final: 0.7933 (mp) REVERT: C 377 ASN cc_start: 0.8058 (t0) cc_final: 0.7696 (t0) REVERT: C 450 THR cc_start: 0.8984 (m) cc_final: 0.8784 (t) REVERT: D 588 ARG cc_start: 0.8440 (ttp80) cc_final: 0.7846 (ttm-80) REVERT: D 617 ARG cc_start: 0.5352 (OUTLIER) cc_final: 0.5041 (tpt170) REVERT: D 632 ASP cc_start: 0.8533 (t0) cc_final: 0.8256 (t0) REVERT: E 233 PHE cc_start: 0.7828 (t80) cc_final: 0.6899 (t80) REVERT: F 591 GLN cc_start: 0.8391 (tt0) cc_final: 0.8118 (tt0) REVERT: F 647 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7390 (tm-30) REVERT: B 634 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7117 (mt-10) outliers start: 51 outliers final: 31 residues processed: 347 average time/residue: 0.1157 time to fit residues: 60.6133 Evaluate side-chains 241 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 617 ARG Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 614 TRP Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 595 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 101 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 186 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 300 ASN C 432 GLN D 630 GLN D 658 GLN E 114 GLN E 302 ASN E 352 HIS F 653 GLN A 188 ASN B 625 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.134159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.107784 restraints weight = 27362.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.109966 restraints weight = 16887.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.111029 restraints weight = 13450.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.111651 restraints weight = 11172.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.112174 restraints weight = 10503.438| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16230 Z= 0.199 Angle : 0.768 15.573 22238 Z= 0.371 Chirality : 0.048 0.406 2775 Planarity : 0.004 0.066 2696 Dihedral : 5.060 30.179 2036 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.61 % Allowed : 11.37 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.20), residues: 1669 helix: 1.25 (0.26), residues: 424 sheet: 0.67 (0.23), residues: 455 loop : -0.08 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 480 TYR 0.022 0.002 TYR E 217 PHE 0.022 0.002 PHE A 53 TRP 0.024 0.002 TRP F 610 HIS 0.006 0.001 HIS D 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (16111) covalent geometry : angle 0.70760 / 0.36 (21914) SS BOND : bond 0.00591 / 0.38 ( 33) SS BOND : angle 2.40834 / 1.81 ( 66) hydrogen bonds : bond 0.05571 / 3.60 ( 541) hydrogen bonds : angle 5.20734 / 3.65 ( 1452) link_ALPHA1-3 : bond 0.01012 / 0.51 ( 3) link_ALPHA1-3 : angle 1.39085 / 0.83 ( 9) link_ALPHA1-6 : bond 0.00628 / 0.32 ( 3) link_ALPHA1-6 : angle 1.40507 / 0.94 ( 9) link_BETA1-4 : bond 0.00722 / 0.43 ( 17) link_BETA1-4 : angle 2.03210 / 1.39 ( 51) link_NAG-ASN : bond 0.00586 / 0.35 ( 63) link_NAG-ASN : angle 2.82485 / 2.01 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 219 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 LEU cc_start: 0.8245 (mp) cc_final: 0.7872 (mp) REVERT: D 530 MET cc_start: 0.7695 (mtp) cc_final: 0.7318 (mtt) REVERT: D 588 ARG cc_start: 0.8407 (ttp80) cc_final: 0.7842 (ttm-80) REVERT: E 233 PHE cc_start: 0.8183 (t80) cc_final: 0.7217 (t80) REVERT: B 530 MET cc_start: 0.7163 (mtt) cc_final: 0.5940 (mtt) REVERT: B 615 SER cc_start: 0.7514 (t) cc_final: 0.7295 (m) REVERT: B 631 TRP cc_start: 0.7873 (t-100) cc_final: 0.7276 (t-100) REVERT: B 636 SER cc_start: 0.7590 (p) cc_final: 0.7109 (m) outliers start: 55 outliers final: 34 residues processed: 260 average time/residue: 0.1155 time to fit residues: 45.3875 Evaluate side-chains 233 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 614 TRP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 595 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN A 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.131324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.103974 restraints weight = 27282.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.106481 restraints weight = 22118.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.107549 restraints weight = 14070.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.108189 restraints weight = 12186.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.108736 restraints weight = 11403.717| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16230 Z= 0.182 Angle : 0.713 10.551 22238 Z= 0.343 Chirality : 0.047 0.368 2775 Planarity : 0.004 0.067 2696 Dihedral : 4.954 32.669 2036 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.88 % Allowed : 11.83 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.20), residues: 1669 helix: 1.28 (0.26), residues: 420 sheet: 0.53 (0.23), residues: 451 loop : -0.23 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 480 TYR 0.014 0.001 TYR A 40 PHE 0.019 0.002 PHE A 53 TRP 0.024 0.002 TRP F 610 HIS 0.003 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (16111) covalent geometry : angle 0.65872 / 0.33 (21914) SS BOND : bond 0.00575 / 0.35 ( 33) SS BOND : angle 2.20797 / 1.68 ( 66) hydrogen bonds : bond 0.05015 / 3.26 ( 541) hydrogen bonds : angle 5.01616 / 3.51 ( 1452) link_ALPHA1-3 : bond 0.00832 / 0.41 ( 3) link_ALPHA1-3 : angle 1.25161 / 0.79 ( 9) link_ALPHA1-6 : bond 0.00458 / 0.23 ( 3) link_ALPHA1-6 : angle 1.53753 / 1.03 ( 9) link_BETA1-4 : bond 0.00550 / 0.32 ( 17) link_BETA1-4 : angle 1.67511 / 1.13 ( 51) link_NAG-ASN : bond 0.00458 / 0.29 ( 63) link_NAG-ASN : angle 2.63170 / 1.88 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 211 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 LEU cc_start: 0.8294 (mp) cc_final: 0.7869 (mp) REVERT: D 588 ARG cc_start: 0.8362 (ttp80) cc_final: 0.7799 (ttm-80) REVERT: E 419 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8295 (mtp85) REVERT: F 591 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8160 (tt0) REVERT: A 325 ASP cc_start: 0.7853 (t0) cc_final: 0.7365 (t0) REVERT: B 530 MET cc_start: 0.7109 (mtt) cc_final: 0.6215 (mtt) REVERT: B 548 ILE cc_start: 0.7406 (OUTLIER) cc_final: 0.6746 (mt) REVERT: B 616 ASN cc_start: 0.7202 (OUTLIER) cc_final: 0.6770 (m-40) REVERT: B 631 TRP cc_start: 0.7587 (t-100) cc_final: 0.7264 (t-100) outliers start: 59 outliers final: 36 residues processed: 253 average time/residue: 0.1184 time to fit residues: 44.9035 Evaluate side-chains 224 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 419 ARG Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 614 TRP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 616 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 172 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 105 HIS C 114 GLN ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.124333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.097067 restraints weight = 27698.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.099356 restraints weight = 19719.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.100812 restraints weight = 13201.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.101309 restraints weight = 11093.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.101458 restraints weight = 10678.377| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 16230 Z= 0.349 Angle : 0.924 10.384 22238 Z= 0.441 Chirality : 0.054 0.407 2775 Planarity : 0.005 0.072 2696 Dihedral : 5.608 36.632 2036 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.27 % Allowed : 13.07 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.19), residues: 1669 helix: 0.85 (0.26), residues: 421 sheet: -0.10 (0.23), residues: 451 loop : -0.73 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 480 TYR 0.031 0.003 TYR C 217 PHE 0.019 0.003 PHE A 53 TRP 0.047 0.002 TRP F 610 HIS 0.007 0.002 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00833 / 0.35 (16111) covalent geometry : angle 0.87590 / 0.43 (21914) SS BOND : bond 0.00860 / 0.48 ( 33) SS BOND : angle 2.27744 / 1.77 ( 66) hydrogen bonds : bond 0.06160 / 4.04 ( 541) hydrogen bonds : angle 5.55693 / 3.87 ( 1452) link_ALPHA1-3 : bond 0.01018 / 0.51 ( 3) link_ALPHA1-3 : angle 1.31751 / 0.78 ( 9) link_ALPHA1-6 : bond 0.00264 / 0.13 ( 3) link_ALPHA1-6 : angle 1.69346 / 1.12 ( 9) link_BETA1-4 : bond 0.00612 / 0.34 ( 17) link_BETA1-4 : angle 1.99689 / 1.40 ( 51) link_NAG-ASN : bond 0.00622 / 0.38 ( 63) link_NAG-ASN : angle 2.90861 / 2.06 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 209 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 GLN cc_start: 0.7766 (tm-30) cc_final: 0.7510 (mm110) REVERT: C 99 ASN cc_start: 0.8324 (t0) cc_final: 0.7893 (t0) REVERT: C 475 MET cc_start: 0.7987 (mmm) cc_final: 0.7750 (mmt) REVERT: D 588 ARG cc_start: 0.8383 (ttp80) cc_final: 0.7847 (ttm-80) REVERT: D 623 TRP cc_start: 0.8119 (m100) cc_final: 0.7685 (m100) REVERT: E 108 ILE cc_start: 0.9047 (mt) cc_final: 0.8841 (mm) REVERT: E 125 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8885 (tt) REVERT: E 161 MET cc_start: 0.8446 (tpp) cc_final: 0.7961 (ttm) REVERT: E 199 SER cc_start: 0.9457 (p) cc_final: 0.8851 (m) REVERT: E 233 PHE cc_start: 0.8614 (t80) cc_final: 0.7927 (t80) REVERT: E 419 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8278 (mtp85) REVERT: F 591 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8244 (tt0) REVERT: F 599 SER cc_start: 0.8670 (p) cc_final: 0.8443 (t) REVERT: F 631 TRP cc_start: 0.8614 (t-100) cc_final: 0.8370 (t-100) REVERT: A 161 MET cc_start: 0.8765 (tpt) cc_final: 0.8375 (tpt) REVERT: A 166 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7334 (mmp80) REVERT: B 530 MET cc_start: 0.7241 (mtt) cc_final: 0.6099 (mtt) REVERT: B 548 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7069 (mt) REVERT: B 616 ASN cc_start: 0.7542 (OUTLIER) cc_final: 0.6846 (m-40) REVERT: B 631 TRP cc_start: 0.7685 (t-100) cc_final: 0.7125 (t-100) REVERT: B 636 SER cc_start: 0.7608 (p) cc_final: 0.7196 (m) outliers start: 65 outliers final: 40 residues processed: 257 average time/residue: 0.1061 time to fit residues: 41.3480 Evaluate side-chains 222 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 419 ARG Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 614 TRP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 616 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 85 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 176 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 137 ASN F 577 GLN A 195 ASN A 425 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.140721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.115356 restraints weight = 25661.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.117815 restraints weight = 19449.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119072 restraints weight = 14227.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119566 restraints weight = 11112.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.119883 restraints weight = 10717.042| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.5619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16230 Z= 0.139 Angle : 0.694 10.105 22238 Z= 0.333 Chirality : 0.046 0.369 2775 Planarity : 0.004 0.054 2696 Dihedral : 5.102 33.429 2036 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.35 % Allowed : 14.91 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.20), residues: 1669 helix: 1.10 (0.26), residues: 421 sheet: 0.03 (0.23), residues: 453 loop : -0.59 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 504 TYR 0.013 0.001 TYR E 191 PHE 0.018 0.002 PHE A 53 TRP 0.042 0.001 TRP F 610 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (16111) covalent geometry : angle 0.63934 / 0.32 (21914) SS BOND : bond 0.00609 / 0.35 ( 33) SS BOND : angle 2.11898 / 1.60 ( 66) hydrogen bonds : bond 0.04769 / 3.12 ( 541) hydrogen bonds : angle 4.95295 / 3.44 ( 1452) link_ALPHA1-3 : bond 0.00807 / 0.40 ( 3) link_ALPHA1-3 : angle 1.30882 / 0.89 ( 9) link_ALPHA1-6 : bond 0.00481 / 0.24 ( 3) link_ALPHA1-6 : angle 1.48015 / 0.96 ( 9) link_BETA1-4 : bond 0.00515 / 0.31 ( 17) link_BETA1-4 : angle 1.41345 / 0.99 ( 51) link_NAG-ASN : bond 0.00547 / 0.38 ( 63) link_NAG-ASN : angle 2.65511 / 1.89 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 ASN cc_start: 0.8384 (t0) cc_final: 0.7950 (t0) REVERT: C 164 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7980 (pm20) REVERT: D 588 ARG cc_start: 0.8249 (ttp80) cc_final: 0.7843 (ttm-80) REVERT: E 233 PHE cc_start: 0.8516 (t80) cc_final: 0.7958 (t80) REVERT: E 419 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8289 (mtp85) REVERT: F 591 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8174 (tt0) REVERT: A 166 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7101 (mmp80) REVERT: B 530 MET cc_start: 0.6981 (mtt) cc_final: 0.6045 (mtt) REVERT: B 548 ILE cc_start: 0.7390 (OUTLIER) cc_final: 0.6808 (mt) REVERT: B 616 ASN cc_start: 0.7205 (OUTLIER) cc_final: 0.6746 (m-40) REVERT: B 631 TRP cc_start: 0.7385 (t-100) cc_final: 0.7043 (t-100) REVERT: B 636 SER cc_start: 0.7230 (p) cc_final: 0.6762 (m) REVERT: B 638 TYR cc_start: 0.5437 (OUTLIER) cc_final: 0.4355 (m-80) REVERT: B 655 LYS cc_start: 0.8058 (tptt) cc_final: 0.7596 (tptt) outliers start: 51 outliers final: 33 residues processed: 232 average time/residue: 0.1135 time to fit residues: 40.5699 Evaluate side-chains 215 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 419 ARG Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 614 TRP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 638 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 32 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 154 optimal weight: 0.0970 chunk 87 optimal weight: 6.9990 chunk 99 optimal weight: 0.0040 chunk 135 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 543 ASN B 658 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.139311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.113922 restraints weight = 25881.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.116803 restraints weight = 19169.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117650 restraints weight = 12933.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.118836 restraints weight = 11265.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119110 restraints weight = 10359.418| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.5795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16230 Z= 0.179 Angle : 0.703 14.798 22238 Z= 0.335 Chirality : 0.047 0.369 2775 Planarity : 0.004 0.057 2696 Dihedral : 5.002 33.389 2036 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.94 % Allowed : 15.51 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.20), residues: 1669 helix: 1.20 (0.26), residues: 420 sheet: -0.02 (0.23), residues: 452 loop : -0.65 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 504 TYR 0.015 0.002 TYR C 217 PHE 0.015 0.002 PHE A 53 TRP 0.030 0.001 TRP F 610 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (16111) covalent geometry : angle 0.65631 / 0.32 (21914) SS BOND : bond 0.00594 / 0.35 ( 33) SS BOND : angle 1.91584 / 1.39 ( 66) hydrogen bonds : bond 0.04762 / 3.13 ( 541) hydrogen bonds : angle 4.90453 / 3.41 ( 1452) link_ALPHA1-3 : bond 0.00826 / 0.41 ( 3) link_ALPHA1-3 : angle 1.24335 / 0.81 ( 9) link_ALPHA1-6 : bond 0.00364 / 0.18 ( 3) link_ALPHA1-6 : angle 1.52814 / 1.00 ( 9) link_BETA1-4 : bond 0.00485 / 0.28 ( 17) link_BETA1-4 : angle 1.43930 / 1.01 ( 51) link_NAG-ASN : bond 0.00475 / 0.30 ( 63) link_NAG-ASN : angle 2.48291 / 1.75 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 185 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 ASN cc_start: 0.8426 (t0) cc_final: 0.8011 (t0) REVERT: D 523 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8763 (mt) REVERT: D 588 ARG cc_start: 0.8249 (ttp80) cc_final: 0.7888 (ttm-80) REVERT: E 188 ASN cc_start: 0.7646 (p0) cc_final: 0.7357 (p0) REVERT: E 233 PHE cc_start: 0.8580 (t80) cc_final: 0.8051 (t80) REVERT: E 419 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8297 (mtp85) REVERT: F 591 GLN cc_start: 0.8653 (tt0) cc_final: 0.8199 (tt0) REVERT: F 599 SER cc_start: 0.8549 (p) cc_final: 0.8287 (t) REVERT: A 150 MET cc_start: 0.7659 (tpt) cc_final: 0.7408 (tpt) REVERT: A 166 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7122 (mmp80) REVERT: A 424 ILE cc_start: 0.9364 (mm) cc_final: 0.9141 (mm) REVERT: B 530 MET cc_start: 0.6958 (mtt) cc_final: 0.5804 (mtt) REVERT: B 548 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.6778 (mt) REVERT: B 631 TRP cc_start: 0.7273 (t-100) cc_final: 0.6935 (t-100) REVERT: B 636 SER cc_start: 0.7336 (p) cc_final: 0.6863 (m) REVERT: B 638 TYR cc_start: 0.5338 (OUTLIER) cc_final: 0.4359 (m-80) outliers start: 60 outliers final: 31 residues processed: 231 average time/residue: 0.1138 time to fit residues: 40.7224 Evaluate side-chains 209 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 419 ARG Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 614 TRP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 638 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 0.0970 chunk 183 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 181 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 625 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.130039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.106020 restraints weight = 26561.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.108496 restraints weight = 23648.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.109088 restraints weight = 18320.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.109514 restraints weight = 15344.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.109644 restraints weight = 14067.807| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16230 Z= 0.140 Angle : 0.672 13.147 22238 Z= 0.322 Chirality : 0.045 0.364 2775 Planarity : 0.004 0.060 2696 Dihedral : 4.967 35.201 2036 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.89 % Allowed : 16.69 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.20), residues: 1669 helix: 1.23 (0.26), residues: 422 sheet: 0.10 (0.23), residues: 447 loop : -0.66 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 504 TYR 0.011 0.001 TYR E 39 PHE 0.015 0.002 PHE B 522 TRP 0.028 0.001 TRP F 610 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (16111) covalent geometry : angle 0.62339 / 0.31 (21914) SS BOND : bond 0.00468 / 0.25 ( 33) SS BOND : angle 2.00737 / 1.47 ( 66) hydrogen bonds : bond 0.04399 / 2.89 ( 541) hydrogen bonds : angle 4.76577 / 3.32 ( 1452) link_ALPHA1-3 : bond 0.00768 / 0.38 ( 3) link_ALPHA1-3 : angle 1.28830 / 0.87 ( 9) link_ALPHA1-6 : bond 0.00400 / 0.20 ( 3) link_ALPHA1-6 : angle 1.47234 / 0.96 ( 9) link_BETA1-4 : bond 0.00482 / 0.29 ( 17) link_BETA1-4 : angle 1.29155 / 0.91 ( 51) link_NAG-ASN : bond 0.00454 / 0.30 ( 63) link_NAG-ASN : angle 2.46049 / 1.78 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 181 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 ASN cc_start: 0.8419 (t0) cc_final: 0.7972 (t0) REVERT: C 164 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.8013 (pm20) REVERT: D 588 ARG cc_start: 0.8275 (ttp80) cc_final: 0.7881 (ttm-80) REVERT: E 188 ASN cc_start: 0.7588 (p0) cc_final: 0.7338 (p0) REVERT: E 199 SER cc_start: 0.9507 (p) cc_final: 0.8901 (m) REVERT: E 233 PHE cc_start: 0.8592 (t80) cc_final: 0.8102 (t80) REVERT: F 591 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8187 (tt0) REVERT: A 166 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7182 (mmp80) REVERT: A 424 ILE cc_start: 0.9295 (mm) cc_final: 0.9090 (mm) REVERT: B 530 MET cc_start: 0.7079 (mtt) cc_final: 0.5805 (mtt) REVERT: B 631 TRP cc_start: 0.7287 (t-100) cc_final: 0.6918 (t-100) REVERT: B 636 SER cc_start: 0.7204 (p) cc_final: 0.6753 (m) REVERT: B 638 TYR cc_start: 0.5356 (OUTLIER) cc_final: 0.4387 (m-80) outliers start: 44 outliers final: 33 residues processed: 211 average time/residue: 0.1210 time to fit residues: 38.3289 Evaluate side-chains 214 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 614 TRP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 638 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 177 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 543 ASN D 607 ASN F 585 HIS A 188 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.134194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.108219 restraints weight = 26161.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.112164 restraints weight = 20137.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.113061 restraints weight = 12789.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.113524 restraints weight = 10523.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.113747 restraints weight = 10089.006| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.6089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16230 Z= 0.222 Angle : 0.740 13.160 22238 Z= 0.352 Chirality : 0.048 0.368 2775 Planarity : 0.004 0.058 2696 Dihedral : 5.128 33.357 2036 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.89 % Allowed : 17.28 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.20), residues: 1669 helix: 1.21 (0.26), residues: 420 sheet: 0.01 (0.23), residues: 441 loop : -0.72 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 350 TYR 0.017 0.002 TYR C 217 PHE 0.021 0.002 PHE C 468 TRP 0.026 0.002 TRP F 610 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.22 (16111) covalent geometry : angle 0.69507 / 0.34 (21914) SS BOND : bond 0.00574 / 0.35 ( 33) SS BOND : angle 2.18474 / 1.58 ( 66) hydrogen bonds : bond 0.04890 / 3.22 ( 541) hydrogen bonds : angle 4.98071 / 3.46 ( 1452) link_ALPHA1-3 : bond 0.00841 / 0.42 ( 3) link_ALPHA1-3 : angle 1.24141 / 0.80 ( 9) link_ALPHA1-6 : bond 0.00322 / 0.16 ( 3) link_ALPHA1-6 : angle 1.56071 / 1.02 ( 9) link_BETA1-4 : bond 0.00471 / 0.27 ( 17) link_BETA1-4 : angle 1.45061 / 1.03 ( 51) link_NAG-ASN : bond 0.00460 / 0.28 ( 63) link_NAG-ASN : angle 2.45668 / 1.74 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 ASN cc_start: 0.8463 (t0) cc_final: 0.7991 (t0) REVERT: D 588 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7881 (ttm-80) REVERT: E 199 SER cc_start: 0.9481 (p) cc_final: 0.8857 (m) REVERT: E 233 PHE cc_start: 0.8649 (t80) cc_final: 0.8137 (t80) REVERT: F 591 GLN cc_start: 0.8688 (tt0) cc_final: 0.8237 (tt0) REVERT: F 599 SER cc_start: 0.8556 (p) cc_final: 0.8289 (t) REVERT: A 150 MET cc_start: 0.7678 (tpt) cc_final: 0.7401 (tpt) REVERT: A 166 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7110 (mmp80) REVERT: B 631 TRP cc_start: 0.7325 (t-100) cc_final: 0.6971 (t-100) REVERT: B 638 TYR cc_start: 0.5359 (OUTLIER) cc_final: 0.4369 (m-80) outliers start: 44 outliers final: 34 residues processed: 219 average time/residue: 0.1186 time to fit residues: 39.4892 Evaluate side-chains 209 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 614 TRP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 638 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 86 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 157 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 185 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 GLN ** A 188 ASN ** 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 = 0.3677 r_free = 0.3677 target = 0.136574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.111615 restraints weight = 26120.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114762 restraints weight = 20795.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.115928 restraints weight = 14173.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.116326 restraints weight = 11135.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.116557 restraints weight = 11146.486| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.6186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16230 Z= 0.177 Angle : 0.729 13.280 22238 Z= 0.346 Chirality : 0.047 0.363 2775 Planarity : 0.004 0.081 2696 Dihedral : 5.104 36.601 2036 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.76 % Allowed : 17.67 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.20), residues: 1669 helix: 1.28 (0.26), residues: 415 sheet: 0.01 (0.24), residues: 439 loop : -0.70 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 166 TYR 0.015 0.002 TYR B 638 PHE 0.016 0.002 PHE B 522 TRP 0.027 0.001 TRP F 610 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (16111) covalent geometry : angle 0.68453 / 0.34 (21914) SS BOND : bond 0.00494 / 0.28 ( 33) SS BOND : angle 1.98046 / 1.44 ( 66) hydrogen bonds : bond 0.04657 / 3.07 ( 541) hydrogen bonds : angle 4.93078 / 3.43 ( 1452) link_ALPHA1-3 : bond 0.00821 / 0.41 ( 3) link_ALPHA1-3 : angle 1.27859 / 0.85 ( 9) link_ALPHA1-6 : bond 0.00354 / 0.18 ( 3) link_ALPHA1-6 : angle 1.51167 / 0.98 ( 9) link_BETA1-4 : bond 0.00456 / 0.27 ( 17) link_BETA1-4 : angle 1.33945 / 0.95 ( 51) link_NAG-ASN : bond 0.00781 / 0.35 ( 63) link_NAG-ASN : angle 2.49569 / 1.74 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 ASN cc_start: 0.8460 (t0) cc_final: 0.7979 (t0) REVERT: D 588 ARG cc_start: 0.8254 (ttp80) cc_final: 0.7870 (ttm-80) REVERT: E 199 SER cc_start: 0.9480 (p) cc_final: 0.8900 (m) REVERT: E 233 PHE cc_start: 0.8634 (t80) cc_final: 0.8138 (t80) REVERT: F 591 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: A 150 MET cc_start: 0.7660 (tpt) cc_final: 0.7388 (tpt) REVERT: A 166 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7147 (mmp80) REVERT: B 530 MET cc_start: 0.6817 (mtt) cc_final: 0.6227 (mtt) REVERT: B 631 TRP cc_start: 0.7311 (t-100) cc_final: 0.7030 (t-100) REVERT: B 636 SER cc_start: 0.7544 (p) cc_final: 0.7301 (m) outliers start: 42 outliers final: 34 residues processed: 205 average time/residue: 0.1197 time to fit residues: 37.1664 Evaluate side-chains 209 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 614 TRP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 606 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 134 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 185 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.138280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.113399 restraints weight = 26092.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.116117 restraints weight = 20672.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.117568 restraints weight = 13859.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118214 restraints weight = 11405.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118444 restraints weight = 10546.512| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.6286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16230 Z= 0.139 Angle : 0.666 10.906 22238 Z= 0.320 Chirality : 0.045 0.355 2775 Planarity : 0.004 0.072 2696 Dihedral : 4.850 29.896 2036 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.56 % Allowed : 17.54 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.20), residues: 1669 helix: 1.49 (0.26), residues: 416 sheet: 0.10 (0.24), residues: 432 loop : -0.73 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 166 TYR 0.009 0.001 TYR E 191 PHE 0.015 0.001 PHE C 53 TRP 0.034 0.002 TRP D 631 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (16111) covalent geometry : angle 0.62323 / 0.31 (21914) SS BOND : bond 0.00469 / 0.26 ( 33) SS BOND : angle 1.99739 / 1.41 ( 66) hydrogen bonds : bond 0.04274 / 2.82 ( 541) hydrogen bonds : angle 4.76544 / 3.31 ( 1452) link_ALPHA1-3 : bond 0.00778 / 0.39 ( 3) link_ALPHA1-3 : angle 1.30303 / 0.87 ( 9) link_ALPHA1-6 : bond 0.00371 / 0.19 ( 3) link_ALPHA1-6 : angle 1.44334 / 0.94 ( 9) link_BETA1-4 : bond 0.00465 / 0.28 ( 17) link_BETA1-4 : angle 1.19840 / 0.85 ( 51) link_NAG-ASN : bond 0.00546 / 0.29 ( 63) link_NAG-ASN : angle 2.28067 / 1.59 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2416.19 seconds wall clock time: 42 minutes 46.95 seconds (2566.95 seconds total)