Starting phenix.real_space_refine on Fri Jul 3 14:52:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lok_23465/07_2026/7lok_23465.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lok_23465/07_2026/7lok_23465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lok_23465/07_2026/7lok_23465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lok_23465/07_2026/7lok_23465.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lok_23465/07_2026/7lok_23465.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lok_23465/07_2026/7lok_23465.cif" model { file = "/net/cci-nas-00/data/ceres_data/7lok_23465/07_2026/7lok_23465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lok_23465/07_2026/7lok_23465.cif" } resolution = 3.9 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= 0.003 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 84 5.16 5 C 9038 2.51 5 N 2558 2.21 5 O 2818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 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: 14498 Number of models: 1 Model: "" Number of chains: 25 Chain: "C" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2802 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 336} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 2832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2832 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 341} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 810 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Chain: "K" Number of atoms: 999 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 129, 996 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Conformer: "B" Number of residues, atoms: 129, 996 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} bond proxies already assigned to first conformer: 1014 Chain: "L" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 835 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "M" Number of atoms: 999 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 129, 996 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Conformer: "B" Number of residues, atoms: 129, 996 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} bond proxies already assigned to first conformer: 1014 Chain: "G" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 151 Unusual residues: {'MPT': 1} Classifications: {'peptide': 19, 'undetermined': 1} Link IDs: {'TRANS': 18, None: 1} Not linked: pdbres="MPT G 1 " pdbres="ASN G 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'MPT:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'U2X:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 151 Unusual residues: {'MPT': 1} Classifications: {'peptide': 19, 'undetermined': 1} Link IDs: {'TRANS': 18, None: 1} Not linked: pdbres="MPT H 1 " pdbres="ASN H 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'MPT:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'U2X:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 631 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 412 Unresolved non-hydrogen angles: 538 Unresolved non-hydrogen dihedrals: 352 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 12, 'ARG:plan': 5, 'ASN:plan1': 9, 'GLU:plan': 7, 'HIS:plan': 1, 'TRP:plan': 7, 'TYR:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 238 Chain: "E" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 1751 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 309} Link IDs: {'PTRANS': 21, 'TRANS': 331} Chain breaks: 4 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1080 Unresolved non-hydrogen angles: 1400 Unresolved non-hydrogen dihedrals: 911 Unresolved non-hydrogen chiralities: 106 Planarities with less than four sites: {'TRP:plan': 9, 'TYR:plan': 8, 'ASP:plan': 11, 'GLU:plan': 19, 'PHE:plan': 13, 'HIS:plan': 9, 'ASN:plan1': 25, 'GLN:plan1': 14, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 560 Chain: "I" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 97 Unusual residues: {'MPT': 1} Classifications: {'peptide': 19, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 18, None: 1} Not linked: pdbres="MPT I 1 " pdbres="ASN I 2 " Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'MPT:plan-1': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 51 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'U2X:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N LYS G 11 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS G 11 " occ=0.50 residue: pdb=" N LYS H 11 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS H 11 " occ=0.50 residue: pdb=" N LYS I 11 " occ=0.50 ... (3 atoms not shown) pdb=" CB LYS I 11 " occ=0.50 Time building chain proxies: 3.83, per 1000 atoms: 0.26 Number of scatterers: 14498 At special positions: 0 Unit cell: (135.792, 138, 149.04, 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 84 16.00 O 2818 8.00 N 2558 7.00 C 9038 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.05 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 385 " distance=2.01 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 418 " distance=2.29 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=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 24 " distance=2.03 Simple disulfide: pdb=" SG CYS G 10 " - pdb=" SG CYS G 26 " distance=2.03 Simple disulfide: pdb=" SG CYS H 6 " - pdb=" SG CYS H 24 " distance=2.03 Simple disulfide: pdb=" SG CYS H 10 " - pdb=" SG CYS H 26 " 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=7, symmetry=0 Links applied ALPHA1-3 " BMA N 3 " - " MAN N 6 " " MAN N 4 " - " MAN N 5 " " MAN O 4 " - " MAN O 5 " " BMA P 3 " - " MAN P 4 " ALPHA1-6 " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " BETA1-4 " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 332 " " NAG A 604 " - " ASN A 339 " " NAG A 605 " - " ASN A 448 " " NAG A 606 " - " ASN A 295 " " NAG C 601 " - " ASN C 448 " " NAG E 601 " - " ASN E 295 " " NAG N 1 " - " ASN C 262 " " NAG O 1 " - " ASN A 262 " " NAG P 1 " - " ASN E 262 " TRANS " DPR G 21 " - " ALA G 20 " " DPR H 21 " - " ALA H 20 " " DPR I 21 " - " ALA I 20 " Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 693.7 milliseconds 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPR G 21 " pdb=" CB DPR H 21 " pdb=" CB DPR I 21 " Number of C-beta restraints generated: 3710 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 39 sheets defined 21.3% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 99 through 116 removed outlier: 4.016A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 353 removed outlier: 4.250A pdb=" N LYS C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 390 removed outlier: 3.940A pdb=" N LEU C 390 " --> pdb=" O THR C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 387 through 390' Processing helix chain 'C' and resid 475 through 483 removed outlier: 3.872A pdb=" N ASN C 478 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ARG C 480 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER C 481 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 524 removed outlier: 4.355A pdb=" N LEU D 520 " --> pdb=" O GLY D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 544 removed outlier: 4.182A pdb=" N ARG D 542 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 577 Processing helix chain 'D' and resid 581 through 591 removed outlier: 3.846A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 596 Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.779A pdb=" N ILE D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 652 removed outlier: 3.916A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLN D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN D 651 " --> pdb=" O GLU D 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 337 through 351 removed outlier: 4.102A pdb=" N VAL A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 526 removed outlier: 3.796A pdb=" N LEU B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA B 525 " --> pdb=" O PHE B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 542 Processing helix chain 'B' and resid 562 through 567 removed outlier: 3.890A pdb=" N LEU B 566 " --> pdb=" O GLN B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 583 removed outlier: 4.584A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 593 removed outlier: 3.518A pdb=" N ARG B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.758A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 656 removed outlier: 3.598A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 103 through 107 Processing helix chain 'M' and resid 62 through 65 Processing helix chain 'G' and resid 2 through 12 Processing helix chain 'H' and resid 2 through 12 removed outlier: 3.666A pdb=" N ARG H 9 " --> pdb=" O PHE H 5 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS H 10 " --> pdb=" O CYS H 6 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER H 12 " --> pdb=" O LEU H 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 523 Processing helix chain 'F' and resid 529 through 543 removed outlier: 3.805A pdb=" N ALA F 533 " --> pdb=" O THR F 529 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL F 539 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG F 542 " --> pdb=" O THR F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 546 No H-bonds generated for 'chain 'F' and resid 544 through 546' Processing helix chain 'F' and resid 567 through 576 removed outlier: 4.467A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 596 removed outlier: 3.683A pdb=" N ARG F 585 " --> pdb=" O LEU F 581 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 624 removed outlier: 4.144A pdb=" N TRP F 623 " --> pdb=" O SER F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 4.629A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 650 removed outlier: 4.046A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 651 through 654 Processing helix chain 'E' and resid 65 through 70 Processing helix chain 'E' and resid 100 through 114 removed outlier: 4.057A pdb=" N MET E 104 " --> pdb=" O MET E 100 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE E 109 " --> pdb=" O HIS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 353 removed outlier: 3.764A pdb=" N LYS E 344 " --> pdb=" O GLU E 340 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL E 345 " --> pdb=" O THR E 341 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 476 through 481 Processing helix chain 'I' and resid 2 through 11 Processing helix chain 'I' and resid 12 through 14 No H-bonds generated for 'chain 'I' and resid 12 through 14' Processing sheet with id=AA1, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.715A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.682A pdb=" N SER C 243 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 92 removed outlier: 3.623A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 271 through 274 removed outlier: 3.641A pdb=" N MET C 271 " --> pdb=" O GLN C 287 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.714A pdb=" N CYS C 385 " --> pdb=" O HIS C 374 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.714A pdb=" N CYS C 385 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR C 297 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL C 292 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE C 449 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER C 447 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS C 296 " --> pdb=" O CYS C 445 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS C 445 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 359 through 360 removed outlier: 4.267A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 495 through 499 removed outlier: 4.938A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.677A pdb=" N VAL A 489 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AB2, first strand: chain 'A' and resid 92 through 94 removed outlier: 3.547A pdb=" N PHE A 93 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.754A pdb=" N ILE A 201 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 123 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER A 199 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 374 through 375 removed outlier: 3.875A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR A 297 " --> pdb=" O HIS A 330 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS A 296 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS A 445 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 394 through 395 removed outlier: 3.607A pdb=" N ILE A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 360 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.618A pdb=" N PHE J 71 " --> pdb=" O CYS J 23 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER J 63 " --> pdb=" O THR J 74 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.544A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR J 49 " --> pdb=" O THR J 53 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.647A pdb=" N TRP K 36 " --> pdb=" O GLY K 49 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL K 57 " --> pdb=" O ILE K 52 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AC2, first strand: chain 'K' and resid 68 through 72 removed outlier: 3.991A pdb=" N THR K 71 " --> pdb=" O TYR K 80 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.795A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.986A pdb=" N GLU L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.505A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR L 49 " --> pdb=" O THR L 53 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 3 through 6 removed outlier: 3.592A pdb=" N SER M 25 " --> pdb=" O GLN M 3 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.695A pdb=" N VAL M 99 " --> pdb=" O SER M 33 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE M 34 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ARG M 50 " --> pdb=" O PHE M 34 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG M 50 " --> pdb=" O HIS M 59 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 10 through 12 Processing sheet with id=AC9, first strand: chain 'M' and resid 18 through 20 removed outlier: 3.817A pdb=" N THR M 78 " --> pdb=" O ASP M 73 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 17 through 19 removed outlier: 3.906A pdb=" N ALA G 25 " --> pdb=" O ARG G 18 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 16 through 19 removed outlier: 4.298A pdb=" N LEU H 16 " --> pdb=" O VAL H 27 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA H 25 " --> pdb=" O ARG H 18 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 35 through 38 removed outlier: 3.886A pdb=" N THR E 37 " --> pdb=" O ALA E 497 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA E 497 " --> pdb=" O THR E 37 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.719A pdb=" N LYS E 490 " --> pdb=" O LYS E 46 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 84 through 85 Processing sheet with id=AD6, first strand: chain 'E' and resid 91 through 94 removed outlier: 4.098A pdb=" N PHE E 93 " --> pdb=" O GLY E 237 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 260 through 261 Processing sheet with id=AD8, first strand: chain 'E' and resid 296 through 297 Processing sheet with id=AD9, first strand: chain 'E' and resid 330 through 331 Processing sheet with id=AE1, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.736A pdb=" N HIS E 374 " --> pdb=" O CYS E 385 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS E 385 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 423 through 425 removed outlier: 4.132A pdb=" N ILE E 424 " --> pdb=" O ALA E 433 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 17 through 20 423 hydrogen bonds defined for protein. 1077 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2441 1.31 - 1.45: 3955 1.45 - 1.58: 8235 1.58 - 1.71: 2 1.71 - 1.85: 108 Bond restraints: 14741 Sorted by residual: bond pdb=" CD2 U2X I 23 " pdb=" CE2 U2X I 23 " ideal model delta sigma weight residual 1.390 1.513 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C1 NAG O 1 " pdb=" C2 NAG O 1 " ideal model delta sigma weight residual 1.532 1.651 -0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb=" N ILE A 277 " pdb=" CA ILE A 277 " ideal model delta sigma weight residual 1.459 1.510 -0.051 1.25e-02 6.40e+03 1.70e+01 bond pdb=" CD1 U2X I 23 " pdb=" CE1 U2X I 23 " ideal model delta sigma weight residual 1.384 1.466 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" N PRO A 253 " pdb=" CD PRO A 253 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 ... (remaining 14736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.71: 19903 3.71 - 7.42: 156 7.42 - 11.13: 10 11.13 - 14.84: 4 14.84 - 18.55: 2 Bond angle restraints: 20075 Sorted by residual: angle pdb=" N THR G 22 " pdb=" CA THR G 22 " pdb=" C THR G 22 " ideal model delta sigma weight residual 111.00 92.45 18.55 2.80e+00 1.28e-01 4.39e+01 angle pdb=" N THR H 22 " pdb=" CA THR H 22 " pdb=" C THR H 22 " ideal model delta sigma weight residual 111.00 92.65 18.35 2.80e+00 1.28e-01 4.29e+01 angle pdb=" C GLU E 275 " pdb=" N ASN E 276 " pdb=" CA ASN E 276 " ideal model delta sigma weight residual 121.90 114.31 7.59 1.26e+00 6.30e-01 3.62e+01 angle pdb=" N GLY E 343 " pdb=" CA GLY E 343 " pdb=" C GLY E 343 " ideal model delta sigma weight residual 114.66 107.41 7.25 1.24e+00 6.50e-01 3.42e+01 angle pdb=" C ASN A 276 " pdb=" N ILE A 277 " pdb=" CA ILE A 277 " ideal model delta sigma weight residual 121.97 132.26 -10.29 1.80e+00 3.09e-01 3.26e+01 ... (remaining 20070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7832 17.95 - 35.91: 640 35.91 - 53.86: 95 53.86 - 71.82: 21 71.82 - 89.77: 16 Dihedral angle restraints: 8604 sinusoidal: 2874 harmonic: 5730 Sorted by residual: dihedral pdb=" CB CYS G 6 " pdb=" SG CYS G 6 " pdb=" SG CYS G 24 " pdb=" CB CYS G 24 " ideal model delta sinusoidal sigma weight residual -86.00 -174.40 88.40 1 1.00e+01 1.00e-02 9.33e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual -86.00 -9.70 -76.30 1 1.00e+01 1.00e-02 7.33e+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 -86.00 -12.36 -73.64 1 1.00e+01 1.00e-02 6.90e+01 ... (remaining 8601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.092: 2396 1.092 - 2.183: 1 2.183 - 3.275: 0 3.275 - 4.366: 0 4.366 - 5.458: 3 Chirality restraints: 2400 Sorted by residual: chirality pdb=" C1 MAN N 6 " pdb=" O3 BMA N 3 " pdb=" C2 MAN N 6 " pdb=" O5 MAN N 6 " both_signs ideal model delta sigma weight residual False 2.40 1.05 1.35 2.00e-02 2.50e+03 4.53e+03 chirality pdb=" CA DPR H 21 " pdb=" N DPR H 21 " pdb=" C DPR H 21 " pdb=" CB DPR H 21 " both_signs ideal model delta sigma weight residual False 2.72 -2.74 5.46 2.00e-01 2.50e+01 7.45e+02 chirality pdb=" CA DPR G 21 " pdb=" N DPR G 21 " pdb=" C DPR G 21 " pdb=" CB DPR G 21 " both_signs ideal model delta sigma weight residual False 2.72 -2.73 5.45 2.00e-01 2.50e+01 7.43e+02 ... (remaining 2397 not shown) Planarity restraints: 2592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 605 " 0.340 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG A 605 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A 605 " 0.073 2.00e-02 2.50e+03 pdb=" N2 NAG A 605 " -0.521 2.00e-02 2.50e+03 pdb=" O7 NAG A 605 " 0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 1 " 0.263 2.00e-02 2.50e+03 2.22e-01 6.15e+02 pdb=" C7 NAG O 1 " -0.068 2.00e-02 2.50e+03 pdb=" C8 NAG O 1 " 0.173 2.00e-02 2.50e+03 pdb=" N2 NAG O 1 " -0.377 2.00e-02 2.50e+03 pdb=" O7 NAG O 1 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " -0.247 2.00e-02 2.50e+03 2.12e-01 5.64e+02 pdb=" C7 NAG N 2 " 0.053 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " 0.025 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " 0.355 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " -0.186 2.00e-02 2.50e+03 ... (remaining 2589 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.96: 11 1.96 - 2.70: 704 2.70 - 3.43: 19773 3.43 - 4.17: 30067 4.17 - 4.90: 52109 Nonbonded interactions: 102664 Sorted by model distance: nonbonded pdb=" O DPR G 21 " pdb=" N U2X G 23 " model vdw 1.226 3.120 nonbonded pdb=" O DPR H 21 " pdb=" N U2X H 23 " model vdw 1.263 3.120 nonbonded pdb=" C DPR H 21 " pdb=" N U2X H 23 " model vdw 1.451 3.350 nonbonded pdb=" C DPR G 21 " pdb=" N U2X G 23 " model vdw 1.453 3.350 nonbonded pdb=" CB LEU F 523 " pdb=" CB PRO E 43 " model vdw 1.510 3.072 ... (remaining 102659 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 34 through 40 and (name N or name CA or name C or name O \ or name CB )) or resid 41 or (resid 42 through 123 and (name N or name CA or nam \ e C or name O or name CB )) or resid 124 or (resid 125 and (name N or name CA or \ name C or name O or name CB )) or (resid 197 through 221 and (name N or name CA \ or name C or name O or name CB )) or resid 222 or (resid 223 through 234 and (n \ ame N or name CA or name C or name O or name CB )) or resid 235 or (resid 236 an \ d (name N or name CA or name C or name O or name CB )) or resid 237 or (resid 23 \ 8 through 249 and (name N or name CA or name C or name O or name CB )) or resid \ 250 or (resid 251 through 261 and (name N or name CA or name C or name O or name \ CB )) or resid 262 through 263 or (resid 264 through 294 and (name N or name CA \ or name C or name O or name CB )) or resid 295 or (resid 296 through 342 and (n \ ame N or name CA or name C or name O or name CB )) or resid 343 or (resid 344 th \ rough 353 and (name N or name CA or name C or name O or name CB )) or resid 354 \ or (resid 355 through 365 and (name N or name CA or name C or name O or name CB \ )) or resid 366 through 367 or (resid 368 through 378 and (name N or name CA or \ name C or name O or name CB )) or (resid 379 through 388 and (name N or name CA \ or name C or name O or name CB )) or resid 389 or (resid 390 through 430 and (na \ me N or name CA or name C or name O or name CB )) or resid 431 or (resid 432 thr \ ough 440 and (name N or name CA or name C or name O or name CB )) or resid 441 o \ r (resid 442 through 450 and (name N or name CA or name C or name O or name CB ) \ ) or resid 451 or (resid 452 through 457 and (name N or name CA or name C or nam \ e O or name CB )) or resid 458 or (resid 464 through 470 and (name N or name CA \ or name C or name O or name CB )) or resid 471 through 473 or (resid 474 through \ 494 and (name N or name CA or name C or name O or name CB )) or resid 495 or (r \ esid 496 through 499 and (name N or name CA or name C or name O or name CB )) or \ resid 606)) selection = (chain 'C' and ((resid 34 through 40 and (name N or name CA or name C or name O \ or name CB )) or resid 41 or (resid 42 through 123 and (name N or name CA or nam \ e C or name O or name CB )) or resid 124 or (resid 125 and (name N or name CA or \ name C or name O or name CB )) or (resid 197 through 221 and (name N or name CA \ or name C or name O or name CB )) or resid 222 or (resid 223 through 234 and (n \ ame N or name CA or name C or name O or name CB )) or resid 235 or (resid 236 an \ d (name N or name CA or name C or name O or name CB )) or resid 237 or (resid 23 \ 8 through 249 and (name N or name CA or name C or name O or name CB )) or resid \ 250 or (resid 251 through 261 and (name N or name CA or name C or name O or name \ CB )) or resid 262 through 263 or (resid 264 through 294 and (name N or name CA \ or name C or name O or name CB )) or resid 295 or (resid 296 through 300 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 326 through 342 and \ (name N or name CA or name C or name O or name CB )) or resid 343 or (resid 344 \ through 353 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 54 or (resid 355 through 365 and (name N or name CA or name C or name O or name \ CB )) or resid 366 through 367 or (resid 368 through 378 and (name N or name CA \ or name C or name O or name CB )) or resid 379 through 380 or (resid 381 through \ 388 and (name N or name CA or name C or name O or name CB )) or resid 389 or (r \ esid 390 through 430 and (name N or name CA or name C or name O or name CB )) or \ resid 431 or (resid 432 through 440 and (name N or name CA or name C or name O \ or name CB )) or resid 441 or (resid 442 through 450 and (name N or name CA or n \ ame C or name O or name CB )) or resid 451 or (resid 452 through 457 and (name N \ or name CA or name C or name O or name CB )) or resid 458 or (resid 464 through \ 470 and (name N or name CA or name C or name O or name CB )) or resid 471 throu \ gh 473 or (resid 474 through 494 and (name N or name CA or name C or name O or n \ ame CB )) or resid 495 or (resid 496 through 499 and (name N or name CA or name \ C or name O or name CB )) or resid 601)) selection = (chain 'E' and (resid 34 through 458 or resid 464 through 601)) } ncs_group { reference = (chain 'B' and ((resid 519 through 520 and (name N or name CA or name C or name \ O or name CB )) or resid 521 or (resid 522 through 523 and (name N or name CA or \ name C or name O or name CB )) or (resid 524 through 530 and (name N or name CA \ or name C or name O or name CB )) or (resid 531 through 542 and (name N or name \ CA or name C or name O or name CB )) or (resid 563 through 571 and (name N or n \ ame CA or name C or name O or name CB )) or resid 572 or (resid 573 through 593 \ and (name N or name CA or name C or name O or name CB )) or resid 594 or (resid \ 595 through 596 and (name N or name CA or name C or name O or name CB )) or resi \ d 597 or (resid 598 through 599 and (name N or name CA or name C or name O or na \ me CB )) or resid 600 or (resid 601 through 643 and (name N or name CA or name C \ or name O or name CB )) or resid 644 or (resid 645 through 655 and (name N or n \ ame CA or name C or name O or name CB )))) selection = (chain 'D' and ((resid 519 through 520 and (name N or name CA or name C or name \ O or name CB )) or resid 521 or (resid 522 through 523 and (name N or name CA or \ name C or name O or name CB )) or (resid 524 through 530 and (name N or name CA \ or name C or name O or name CB )) or (resid 531 through 542 and (name N or name \ CA or name C or name O or name CB )) or (resid 563 through 571 and (name N or n \ ame CA or name C or name O or name CB )) or resid 572 or (resid 573 through 593 \ and (name N or name CA or name C or name O or name CB )) or resid 594 or (resid \ 595 through 596 and (name N or name CA or name C or name O or name CB )) or resi \ d 597 or (resid 598 through 599 and (name N or name CA or name C or name O or na \ me CB )) or resid 600 or (resid 601 through 643 and (name N or name CA or name C \ or name O or name CB )) or resid 644 or (resid 645 through 655 and (name N or n \ ame CA or name C or name O or name CB )))) selection = (chain 'F' and (resid 519 through 542 or resid 563 through 655)) } ncs_group { reference = (chain 'G' and ((resid 1 and (name CA or name C or name O or name CB )) or (resi \ d 2 through 13 and (name N or name CA or name C or name O or name CB )) or resid \ 14 or (resid 15 through 16 and (name N or name CA or name C or name O or name C \ B )) or resid 17 or (resid 18 through 20 and (name N or name CA or name C or nam \ e O or name CB )) or resid 21 or (resid 22 and (name N or name CA or name C or n \ ame O or name CB )) or resid 23 or (resid 24 through 27 and (name N or name CA o \ r name C or name O or name CB )) or resid 28)) selection = (chain 'H' and ((resid 1 and (name CA or name C or name O or name CB )) or (resi \ d 2 through 13 and (name N or name CA or name C or name O or name CB )) or resid \ 14 or (resid 15 through 16 and (name N or name CA or name C or name O or name C \ B )) or resid 17 or (resid 18 through 20 and (name N or name CA or name C or nam \ e O or name CB )) or resid 21 or (resid 22 and (name N or name CA or name C or n \ ame O or name CB )) or resid 23 or (resid 24 through 27 and (name N or name CA o \ r name C or name O or name CB )) or resid 28)) selection = chain 'I' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 3 through 108) } ncs_group { reference = (chain 'K' and (resid 1 through 42 or resid 44 through 129)) selection = (chain 'M' and (resid 1 through 42 or resid 44 through 129)) } 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=0.50 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: 1.010 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.820 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 0.007 0.258 14802 Z= 0.387 Angle : 1.019 26.876 20209 Z= 0.544 Chirality : 0.205 5.458 2400 Planarity : 0.012 0.295 2578 Dihedral : 13.681 89.770 4801 Min Nonbonded Distance : 1.226 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.86 % Favored : 87.99 % Rotamer: Outliers : 0.39 % Allowed : 8.99 % Favored : 90.62 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.60 % 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: -5.60 (0.14), residues: 1931 helix: -3.94 (0.15), residues: 385 sheet: -3.11 (0.20), residues: 505 loop : -4.05 (0.14), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 54 TYR 0.014 0.002 TYR D 586 PHE 0.018 0.001 PHE A 53 TRP 0.034 0.002 TRP C 112 HIS 0.007 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.36 (14741) covalent geometry : angle 0.93076 / 0.52 (20075) SS BOND : bond 0.04925 / 1.52 ( 28) SS BOND : angle 5.34810 / 4.58 ( 56) hydrogen bonds : bond 0.29631 / 20.10 ( 402) hydrogen bonds : angle 10.53726 / 7.48 ( 1077) Misc. bond : bond 0.04857 / 2.57 ( 7) link_ALPHA1-3 : bond 0.00575 / 0.29 ( 4) link_ALPHA1-3 : angle 6.14457 / 3.83 ( 12) link_ALPHA1-6 : bond 0.00152 / 0.07 ( 2) link_ALPHA1-6 : angle 1.80650 / 1.37 ( 6) link_BETA1-4 : bond 0.01703 / 0.85 ( 6) link_BETA1-4 : angle 4.82411 / 2.03 ( 18) link_NAG-ASN : bond 0.02004 / 1.44 ( 11) link_NAG-ASN : angle 5.73508 / 4.01 ( 33) link_TRANS : bond 0.01139 / 0.57 ( 3) link_TRANS : angle 1.25052 / 0.93 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 238 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 591 GLN cc_start: 0.8958 (tp40) cc_final: 0.8736 (tp40) REVERT: D 648 GLU cc_start: 0.8470 (mp0) cc_final: 0.8206 (mp0) REVERT: B 621 GLU cc_start: 0.8266 (pp20) cc_final: 0.7863 (pp20) REVERT: B 622 ILE cc_start: 0.9031 (mt) cc_final: 0.8654 (mm) REVERT: J 58 VAL cc_start: 0.8199 (t) cc_final: 0.7992 (t) REVERT: K 81 LEU cc_start: 0.8819 (tt) cc_final: 0.8172 (tt) REVERT: M 120 GLN cc_start: 0.8127 (pp30) cc_final: 0.7914 (pp30) outliers start: 5 outliers final: 1 residues processed: 242 average time/residue: 0.1239 time to fit residues: 43.0510 Evaluate side-chains 169 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.0010 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 279 ASN C 352 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN D 543 ASN D 630 GLN A 33 ASN A 66 HIS A 72 HIS A 258 GLN B 630 GLN ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN L 37 GLN M 65 GLN H 4 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.108406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.084320 restraints weight = 60032.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.084226 restraints weight = 42707.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.085157 restraints weight = 36985.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.086041 restraints weight = 25410.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.086229 restraints weight = 23196.224| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14802 Z= 0.209 Angle : 0.804 16.729 20209 Z= 0.395 Chirality : 0.049 0.347 2400 Planarity : 0.005 0.052 2578 Dihedral : 6.084 65.705 2119 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.01 % Favored : 90.94 % Rotamer: Outliers : 2.42 % Allowed : 16.73 % Favored : 80.84 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.60 % 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: -4.53 (0.16), residues: 1931 helix: -2.71 (0.21), residues: 400 sheet: -2.60 (0.22), residues: 486 loop : -3.41 (0.16), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 24 TYR 0.017 0.002 TYR C 384 PHE 0.014 0.002 PHE A 53 TRP 0.030 0.002 TRP C 96 HIS 0.004 0.001 HIS K 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 (14741) covalent geometry : angle 0.76077 / 0.38 (20075) SS BOND : bond 0.00676 / 0.34 ( 28) SS BOND : angle 3.58285 / 2.55 ( 56) hydrogen bonds : bond 0.06134 / 4.03 ( 402) hydrogen bonds : angle 7.27176 / 5.12 ( 1077) Misc. bond : bond 0.00223 / 0.16 ( 7) link_ALPHA1-3 : bond 0.01519 / 0.80 ( 4) link_ALPHA1-3 : angle 3.86768 / 2.71 ( 12) link_ALPHA1-6 : bond 0.00873 / 0.43 ( 2) link_ALPHA1-6 : angle 0.94530 / 0.72 ( 6) link_BETA1-4 : bond 0.00667 / 0.33 ( 6) link_BETA1-4 : angle 3.00245 / 1.62 ( 18) link_NAG-ASN : bond 0.00402 / 0.25 ( 11) link_NAG-ASN : angle 3.36491 / 2.20 ( 33) link_TRANS : bond 0.00500 / 0.25 ( 3) link_TRANS : angle 1.04821 / 0.78 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 265 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8266 (pp) REVERT: D 634 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8247 (tp30) REVERT: A 40 TYR cc_start: 0.9008 (t80) cc_final: 0.8785 (t80) REVERT: B 621 GLU cc_start: 0.8198 (pp20) cc_final: 0.7884 (pp20) REVERT: B 622 ILE cc_start: 0.8942 (mt) cc_final: 0.8473 (mm) REVERT: J 45 ARG cc_start: 0.6420 (ttt90) cc_final: 0.6219 (ttp80) REVERT: J 58 VAL cc_start: 0.8504 (t) cc_final: 0.8170 (t) REVERT: J 70 GLU cc_start: 0.7371 (pm20) cc_final: 0.7025 (pm20) REVERT: K 115 LEU cc_start: 0.8870 (mt) cc_final: 0.8613 (mp) REVERT: L 27 GLU cc_start: 0.7503 (mp0) cc_final: 0.7189 (mp0) REVERT: M 120 GLN cc_start: 0.8190 (pp30) cc_final: 0.7764 (pp30) outliers start: 31 outliers final: 18 residues processed: 214 average time/residue: 0.1206 time to fit residues: 38.4299 Evaluate side-chains 184 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain K residue 65 GLN Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain H residue 4 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 132 optimal weight: 3.9990 chunk 176 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 175 optimal weight: 50.0000 chunk 8 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 279 ASN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.106681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.079479 restraints weight = 54284.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.080938 restraints weight = 29373.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.081852 restraints weight = 19898.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.082146 restraints weight = 19229.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.082214 restraints weight = 15917.095| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 14802 Z= 0.214 Angle : 0.760 16.210 20209 Z= 0.372 Chirality : 0.048 0.294 2400 Planarity : 0.004 0.056 2578 Dihedral : 5.762 64.419 2119 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.22 % Favored : 90.73 % Rotamer: Outliers : 4.14 % Allowed : 18.14 % Favored : 77.72 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.95 (0.17), residues: 1931 helix: -1.94 (0.23), residues: 409 sheet: -2.25 (0.22), residues: 490 loop : -3.16 (0.16), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 18 TYR 0.016 0.002 TYR D 586 PHE 0.015 0.001 PHE A 53 TRP 0.014 0.001 TRP C 479 HIS 0.016 0.001 HIS H 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 (14741) covalent geometry : angle 0.71707 / 0.36 (20075) SS BOND : bond 0.00699 / 0.30 ( 28) SS BOND : angle 3.42561 / 2.44 ( 56) hydrogen bonds : bond 0.05199 / 3.36 ( 402) hydrogen bonds : angle 6.46040 / 4.58 ( 1077) Misc. bond : bond 0.00091 / 0.06 ( 7) link_ALPHA1-3 : bond 0.01120 / 0.59 ( 4) link_ALPHA1-3 : angle 3.63962 / 2.86 ( 12) link_ALPHA1-6 : bond 0.00556 / 0.27 ( 2) link_ALPHA1-6 : angle 1.19830 / 0.74 ( 6) link_BETA1-4 : bond 0.00628 / 0.31 ( 6) link_BETA1-4 : angle 3.10325 / 1.69 ( 18) link_NAG-ASN : bond 0.00380 / 0.22 ( 11) link_NAG-ASN : angle 3.15480 / 2.11 ( 33) link_TRANS : bond 0.00381 / 0.19 ( 3) link_TRANS : angle 1.19237 / 0.88 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 175 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 265 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8191 (pp) REVERT: D 620 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8739 (p) REVERT: D 634 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8323 (tp30) REVERT: D 648 GLU cc_start: 0.8380 (mp0) cc_final: 0.8105 (mp0) REVERT: A 100 MET cc_start: 0.8909 (mtp) cc_final: 0.8676 (mtm) REVERT: A 104 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8623 (ttm) REVERT: B 621 GLU cc_start: 0.8281 (pp20) cc_final: 0.7857 (pp20) REVERT: B 622 ILE cc_start: 0.8840 (mt) cc_final: 0.8337 (mm) REVERT: J 4 MET cc_start: 0.7318 (mmm) cc_final: 0.6689 (mmm) REVERT: J 45 ARG cc_start: 0.6677 (ttt90) cc_final: 0.6376 (ttp80) REVERT: J 58 VAL cc_start: 0.8480 (t) cc_final: 0.8123 (t) REVERT: J 70 GLU cc_start: 0.7515 (pm20) cc_final: 0.7197 (pm20) REVERT: J 107 GLU cc_start: 0.7323 (pt0) cc_final: 0.7118 (tp30) REVERT: K 115 LEU cc_start: 0.9043 (mt) cc_final: 0.8802 (mp) REVERT: L 27 GLU cc_start: 0.7486 (mp0) cc_final: 0.7001 (mp0) REVERT: L 75 ILE cc_start: 0.8246 (tp) cc_final: 0.7533 (tp) REVERT: M 120 GLN cc_start: 0.8112 (pp30) cc_final: 0.7694 (pp30) outliers start: 53 outliers final: 32 residues processed: 215 average time/residue: 0.1199 time to fit residues: 38.0751 Evaluate side-chains 197 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 83 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 38 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 117 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 170 optimal weight: 40.0000 chunk 159 optimal weight: 20.0000 chunk 175 optimal weight: 50.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 279 ASN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.106113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.078096 restraints weight = 40799.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.080171 restraints weight = 23527.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.081507 restraints weight = 16818.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.082329 restraints weight = 13737.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.082757 restraints weight = 12169.608| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (14 function evaluations) r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 14802 Z= 0.260 Angle : 0.789 16.621 20209 Z= 0.385 Chirality : 0.049 0.324 2400 Planarity : 0.004 0.045 2578 Dihedral : 5.832 59.599 2119 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.34 % Favored : 88.61 % Rotamer: Outliers : 5.39 % Allowed : 18.92 % Favored : 75.68 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.69 (0.17), residues: 1931 helix: -1.66 (0.24), residues: 410 sheet: -2.10 (0.23), residues: 484 loop : -3.03 (0.17), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 18 TYR 0.024 0.002 TYR L 49 PHE 0.018 0.002 PHE A 53 TRP 0.019 0.002 TRP C 479 HIS 0.007 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.26 (14741) covalent geometry : angle 0.74695 / 0.37 (20075) SS BOND : bond 0.00804 / 0.36 ( 28) SS BOND : angle 3.49537 / 2.48 ( 56) hydrogen bonds : bond 0.04994 / 3.20 ( 402) hydrogen bonds : angle 6.30162 / 4.45 ( 1077) Misc. bond : bond 0.00171 / 0.09 ( 7) link_ALPHA1-3 : bond 0.00848 / 0.44 ( 4) link_ALPHA1-3 : angle 3.67226 / 3.10 ( 12) link_ALPHA1-6 : bond 0.00357 / 0.18 ( 2) link_ALPHA1-6 : angle 1.39530 / 0.88 ( 6) link_BETA1-4 : bond 0.00596 / 0.29 ( 6) link_BETA1-4 : angle 3.41544 / 1.92 ( 18) link_NAG-ASN : bond 0.00408 / 0.25 ( 11) link_NAG-ASN : angle 3.04574 / 2.04 ( 33) link_TRANS : bond 0.00405 / 0.20 ( 3) link_TRANS : angle 1.07123 / 0.81 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 165 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.7953 (t70) REVERT: C 265 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8212 (pp) REVERT: D 634 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8331 (tp30) REVERT: D 648 GLU cc_start: 0.8319 (mp0) cc_final: 0.8058 (mp0) REVERT: A 100 MET cc_start: 0.8740 (mtp) cc_final: 0.8492 (mtm) REVERT: A 104 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8489 (ttm) REVERT: B 621 GLU cc_start: 0.8222 (pp20) cc_final: 0.7902 (pp20) REVERT: J 4 MET cc_start: 0.7335 (mmm) cc_final: 0.6813 (mmm) REVERT: J 17 GLU cc_start: 0.6459 (tm-30) cc_final: 0.6200 (tm-30) REVERT: J 45 ARG cc_start: 0.6796 (ttt90) cc_final: 0.6457 (ttp80) REVERT: J 58 VAL cc_start: 0.8458 (t) cc_final: 0.8088 (t) REVERT: J 70 GLU cc_start: 0.7586 (pm20) cc_final: 0.7254 (pm20) REVERT: J 82 ASP cc_start: 0.7538 (m-30) cc_final: 0.7304 (m-30) REVERT: J 107 GLU cc_start: 0.7311 (pt0) cc_final: 0.7090 (tp30) REVERT: K 115 LEU cc_start: 0.9000 (mt) cc_final: 0.8746 (mp) REVERT: L 27 GLU cc_start: 0.7629 (mp0) cc_final: 0.7128 (mp0) REVERT: M 120 GLN cc_start: 0.8184 (pp30) cc_final: 0.7737 (pp30) REVERT: G 8 LEU cc_start: 0.9115 (tt) cc_final: 0.8905 (mp) outliers start: 69 outliers final: 45 residues processed: 219 average time/residue: 0.1052 time to fit residues: 34.5690 Evaluate side-chains 204 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain G residue 16 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 169 optimal weight: 30.0000 chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 171 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 chunk 91 optimal weight: 0.2980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 279 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS A 99 ASN ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.108538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.079872 restraints weight = 62463.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.083602 restraints weight = 31677.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.084196 restraints weight = 17035.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.084703 restraints weight = 14507.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.084755 restraints weight = 13432.269| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14802 Z= 0.136 Angle : 0.693 15.822 20209 Z= 0.334 Chirality : 0.047 0.311 2400 Planarity : 0.004 0.042 2578 Dihedral : 5.385 58.892 2119 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.47 % Favored : 93.47 % Rotamer: Outliers : 3.91 % Allowed : 21.34 % Favored : 74.75 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.30 (0.18), residues: 1931 helix: -1.27 (0.25), residues: 410 sheet: -1.84 (0.23), residues: 489 loop : -2.82 (0.17), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 50 TYR 0.021 0.001 TYR L 49 PHE 0.009 0.001 PHE C 53 TRP 0.016 0.001 TRP C 479 HIS 0.005 0.001 HIS K 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (14741) covalent geometry : angle 0.64970 / 0.32 (20075) SS BOND : bond 0.00682 / 0.28 ( 28) SS BOND : angle 3.31228 / 2.34 ( 56) hydrogen bonds : bond 0.04038 / 2.55 ( 402) hydrogen bonds : angle 5.77459 / 4.07 ( 1077) Misc. bond : bond 0.00086 / 0.06 ( 7) link_ALPHA1-3 : bond 0.00723 / 0.37 ( 4) link_ALPHA1-3 : angle 3.21054 / 2.65 ( 12) link_ALPHA1-6 : bond 0.00633 / 0.32 ( 2) link_ALPHA1-6 : angle 1.50012 / 0.93 ( 6) link_BETA1-4 : bond 0.00723 / 0.36 ( 6) link_BETA1-4 : angle 3.21525 / 1.70 ( 18) link_NAG-ASN : bond 0.00403 / 0.25 ( 11) link_NAG-ASN : angle 2.89641 / 1.93 ( 33) link_TRANS : bond 0.00474 / 0.24 ( 3) link_TRANS : angle 1.01654 / 0.75 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 177 time to evaluate : 0.378 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 265 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8257 (pp) REVERT: D 620 SER cc_start: 0.9152 (OUTLIER) cc_final: 0.8736 (p) REVERT: D 634 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8319 (tp30) REVERT: D 648 GLU cc_start: 0.8246 (mp0) cc_final: 0.7941 (mp0) REVERT: A 100 MET cc_start: 0.8594 (mtp) cc_final: 0.8346 (mtm) REVERT: A 104 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8166 (tpp) REVERT: A 217 TYR cc_start: 0.8833 (m-80) cc_final: 0.8529 (m-80) REVERT: A 479 TRP cc_start: 0.8055 (m-90) cc_final: 0.7616 (m-90) REVERT: B 621 GLU cc_start: 0.8234 (pp20) cc_final: 0.7905 (pp20) REVERT: J 4 MET cc_start: 0.7261 (mmm) cc_final: 0.6667 (mmm) REVERT: J 45 ARG cc_start: 0.6822 (ttt90) cc_final: 0.6584 (ttp-170) REVERT: J 58 VAL cc_start: 0.8401 (t) cc_final: 0.8033 (t) REVERT: J 70 GLU cc_start: 0.7622 (pm20) cc_final: 0.7286 (pm20) REVERT: J 82 ASP cc_start: 0.7366 (m-30) cc_final: 0.7123 (m-30) REVERT: K 115 LEU cc_start: 0.9092 (mt) cc_final: 0.8768 (mp) REVERT: L 27 GLU cc_start: 0.7551 (mp0) cc_final: 0.6961 (mp0) REVERT: M 120 GLN cc_start: 0.7836 (pp30) cc_final: 0.7445 (pp30) REVERT: G 8 LEU cc_start: 0.9195 (tt) cc_final: 0.8919 (mp) REVERT: H 13 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8463 (tt) outliers start: 50 outliers final: 26 residues processed: 216 average time/residue: 0.1030 time to fit residues: 33.7559 Evaluate side-chains 195 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain H residue 13 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 81 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 134 optimal weight: 10.0000 chunk 180 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 141 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 79 optimal weight: 0.0170 chunk 188 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN C 279 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.109663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.081952 restraints weight = 63100.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.084266 restraints weight = 31085.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.086138 restraints weight = 18593.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.086232 restraints weight = 16056.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.086126 restraints weight = 13575.842| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14802 Z= 0.116 Angle : 0.656 15.210 20209 Z= 0.318 Chirality : 0.046 0.284 2400 Planarity : 0.003 0.043 2578 Dihedral : 5.080 59.134 2119 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.94 % Favored : 93.01 % Rotamer: Outliers : 4.69 % Allowed : 20.80 % Favored : 74.51 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.60 % 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: -2.96 (0.18), residues: 1931 helix: -0.93 (0.26), residues: 408 sheet: -1.71 (0.24), residues: 475 loop : -2.58 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 50 TYR 0.028 0.001 TYR L 49 PHE 0.011 0.001 PHE C 53 TRP 0.015 0.001 TRP A 45 HIS 0.004 0.001 HIS K 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (14741) covalent geometry : angle 0.61433 / 0.30 (20075) SS BOND : bond 0.00669 / 0.29 ( 28) SS BOND : angle 3.16589 / 2.25 ( 56) hydrogen bonds : bond 0.03626 / 2.29 ( 402) hydrogen bonds : angle 5.42437 / 3.82 ( 1077) Misc. bond : bond 0.00085 / 0.06 ( 7) link_ALPHA1-3 : bond 0.00770 / 0.39 ( 4) link_ALPHA1-3 : angle 2.79718 / 2.31 ( 12) link_ALPHA1-6 : bond 0.00792 / 0.40 ( 2) link_ALPHA1-6 : angle 1.56347 / 0.96 ( 6) link_BETA1-4 : bond 0.00676 / 0.33 ( 6) link_BETA1-4 : angle 3.06074 / 1.60 ( 18) link_NAG-ASN : bond 0.00420 / 0.26 ( 11) link_NAG-ASN : angle 2.85651 / 1.91 ( 33) link_TRANS : bond 0.00494 / 0.25 ( 3) link_TRANS : angle 0.95120 / 0.72 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 178 time to evaluate : 0.564 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 107 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7707 (t70) REVERT: D 620 SER cc_start: 0.9183 (OUTLIER) cc_final: 0.8823 (p) REVERT: D 634 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8230 (tp30) REVERT: D 648 GLU cc_start: 0.8202 (mp0) cc_final: 0.7928 (mp0) REVERT: A 479 TRP cc_start: 0.7982 (m-90) cc_final: 0.7419 (m-90) REVERT: B 621 GLU cc_start: 0.8218 (pp20) cc_final: 0.7874 (pp20) REVERT: J 4 MET cc_start: 0.7335 (mmm) cc_final: 0.6865 (mmm) REVERT: J 17 GLU cc_start: 0.6496 (tm-30) cc_final: 0.6235 (tm-30) REVERT: J 27 GLU cc_start: 0.8153 (pt0) cc_final: 0.7529 (pm20) REVERT: J 45 ARG cc_start: 0.6646 (ttt90) cc_final: 0.6246 (ttp-110) REVERT: J 58 VAL cc_start: 0.8428 (t) cc_final: 0.8013 (t) REVERT: J 70 GLU cc_start: 0.7698 (pm20) cc_final: 0.7369 (pm20) REVERT: J 81 GLU cc_start: 0.7146 (pm20) cc_final: 0.6920 (pm20) REVERT: J 82 ASP cc_start: 0.7549 (m-30) cc_final: 0.7261 (m-30) REVERT: K 6 GLU cc_start: 0.5849 (mt-10) cc_final: 0.5577 (mt-10) REVERT: K 115 LEU cc_start: 0.9045 (mt) cc_final: 0.8788 (mp) REVERT: L 27 GLU cc_start: 0.7500 (mp0) cc_final: 0.6964 (mp0) REVERT: M 120 GLN cc_start: 0.7711 (pp30) cc_final: 0.7318 (pp30) REVERT: H 13 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8444 (tt) outliers start: 60 outliers final: 38 residues processed: 226 average time/residue: 0.1087 time to fit residues: 37.1608 Evaluate side-chains 206 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 102 GLN Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain H residue 13 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 125 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 161 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 279 ASN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 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 = 0.3738 r_free = 0.3738 target = 0.108850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.080730 restraints weight = 62447.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.083126 restraints weight = 31174.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.084294 restraints weight = 19051.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.084802 restraints weight = 15416.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.084716 restraints weight = 13990.585| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14802 Z= 0.153 Angle : 0.693 15.359 20209 Z= 0.334 Chirality : 0.046 0.284 2400 Planarity : 0.003 0.045 2578 Dihedral : 5.133 58.829 2119 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.25 % Favored : 92.70 % Rotamer: Outliers : 4.53 % Allowed : 21.42 % Favored : 74.04 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.60 % 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: -2.88 (0.18), residues: 1931 helix: -0.77 (0.26), residues: 408 sheet: -1.61 (0.25), residues: 458 loop : -2.59 (0.17), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 18 TYR 0.025 0.001 TYR L 49 PHE 0.016 0.001 PHE L 100 TRP 0.017 0.001 TRP C 479 HIS 0.012 0.001 HIS K 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (14741) covalent geometry : angle 0.65369 / 0.32 (20075) SS BOND : bond 0.00674 / 0.28 ( 28) SS BOND : angle 3.20414 / 2.27 ( 56) hydrogen bonds : bond 0.03784 / 2.40 ( 402) hydrogen bonds : angle 5.40991 / 3.81 ( 1077) Misc. bond : bond 0.00076 / 0.06 ( 7) link_ALPHA1-3 : bond 0.00590 / 0.30 ( 4) link_ALPHA1-3 : angle 2.80562 / 2.38 ( 12) link_ALPHA1-6 : bond 0.00548 / 0.28 ( 2) link_ALPHA1-6 : angle 1.54310 / 0.95 ( 6) link_BETA1-4 : bond 0.00633 / 0.31 ( 6) link_BETA1-4 : angle 3.08936 / 1.65 ( 18) link_NAG-ASN : bond 0.00394 / 0.24 ( 11) link_NAG-ASN : angle 2.82864 / 1.90 ( 33) link_TRANS : bond 0.00470 / 0.24 ( 3) link_TRANS : angle 0.93055 / 0.70 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 174 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7823 (t70) REVERT: D 620 SER cc_start: 0.9207 (OUTLIER) cc_final: 0.8845 (p) REVERT: D 634 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8336 (tp30) REVERT: D 648 GLU cc_start: 0.8217 (mp0) cc_final: 0.7918 (mp0) REVERT: A 100 MET cc_start: 0.8689 (mtp) cc_final: 0.8386 (mtp) REVERT: A 104 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8292 (tpp) REVERT: A 217 TYR cc_start: 0.8677 (m-80) cc_final: 0.8475 (m-80) REVERT: B 621 GLU cc_start: 0.8285 (pp20) cc_final: 0.7901 (pp20) REVERT: J 4 MET cc_start: 0.7324 (mmm) cc_final: 0.6798 (mmm) REVERT: J 27 GLU cc_start: 0.8155 (pt0) cc_final: 0.7498 (pm20) REVERT: J 37 GLN cc_start: 0.8042 (tt0) cc_final: 0.7335 (pt0) REVERT: J 45 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6530 (ttt180) REVERT: J 58 VAL cc_start: 0.8400 (t) cc_final: 0.8196 (t) REVERT: J 70 GLU cc_start: 0.7710 (pm20) cc_final: 0.7382 (pm20) REVERT: J 82 ASP cc_start: 0.7445 (m-30) cc_final: 0.7149 (m-30) REVERT: K 6 GLU cc_start: 0.5847 (mt-10) cc_final: 0.5475 (mt-10) REVERT: K 120 GLN cc_start: 0.8050 (pm20) cc_final: 0.7727 (pm20) REVERT: L 4 MET cc_start: 0.6335 (OUTLIER) cc_final: 0.6114 (ptt) REVERT: L 27 GLU cc_start: 0.7561 (mp0) cc_final: 0.7022 (mp0) REVERT: M 120 GLN cc_start: 0.7803 (pp30) cc_final: 0.7381 (pp30) REVERT: G 8 LEU cc_start: 0.9105 (pp) cc_final: 0.8850 (mp) REVERT: H 13 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8464 (tt) outliers start: 58 outliers final: 46 residues processed: 218 average time/residue: 0.1092 time to fit residues: 35.8268 Evaluate side-chains 221 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 169 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain K residue 65 GLN Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain H residue 13 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 90 optimal weight: 0.9990 chunk 89 optimal weight: 0.0270 chunk 31 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 154 optimal weight: 10.0000 chunk 0 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 279 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 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 = 0.3771 r_free = 0.3771 target = 0.111035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.084409 restraints weight = 45450.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.085897 restraints weight = 27367.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.087529 restraints weight = 18826.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.087817 restraints weight = 15668.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.087792 restraints weight = 13560.259| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14802 Z= 0.103 Angle : 0.659 14.614 20209 Z= 0.316 Chirality : 0.045 0.256 2400 Planarity : 0.003 0.052 2578 Dihedral : 4.862 58.289 2119 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.64 % Favored : 94.30 % Rotamer: Outliers : 3.44 % Allowed : 23.06 % Favored : 73.49 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.60 % 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: -2.61 (0.19), residues: 1931 helix: -0.53 (0.26), residues: 412 sheet: -1.41 (0.24), residues: 483 loop : -2.45 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 18 TYR 0.025 0.001 TYR L 49 PHE 0.013 0.001 PHE L 100 TRP 0.013 0.001 TRP C 479 HIS 0.008 0.001 HIS K 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (14741) covalent geometry : angle 0.62191 / 0.30 (20075) SS BOND : bond 0.00579 / 0.23 ( 28) SS BOND : angle 3.03779 / 2.16 ( 56) hydrogen bonds : bond 0.03296 / 2.08 ( 402) hydrogen bonds : angle 5.11981 / 3.61 ( 1077) Misc. bond : bond 0.00094 / 0.07 ( 7) link_ALPHA1-3 : bond 0.00673 / 0.34 ( 4) link_ALPHA1-3 : angle 2.45170 / 2.00 ( 12) link_ALPHA1-6 : bond 0.00759 / 0.38 ( 2) link_ALPHA1-6 : angle 1.68544 / 1.05 ( 6) link_BETA1-4 : bond 0.00792 / 0.39 ( 6) link_BETA1-4 : angle 3.00433 / 1.52 ( 18) link_NAG-ASN : bond 0.00439 / 0.27 ( 11) link_NAG-ASN : angle 2.69879 / 1.80 ( 33) link_TRANS : bond 0.00513 / 0.26 ( 3) link_TRANS : angle 0.90453 / 0.68 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7687 (t70) REVERT: D 620 SER cc_start: 0.8990 (OUTLIER) cc_final: 0.8755 (p) REVERT: D 634 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8124 (tp30) REVERT: D 648 GLU cc_start: 0.7985 (mp0) cc_final: 0.7690 (mp0) REVERT: A 104 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8276 (tpp) REVERT: A 475 MET cc_start: 0.8657 (tpp) cc_final: 0.8147 (tpp) REVERT: A 479 TRP cc_start: 0.7941 (m-90) cc_final: 0.7621 (m-90) REVERT: B 621 GLU cc_start: 0.8232 (pp20) cc_final: 0.7878 (pp20) REVERT: B 622 ILE cc_start: 0.9076 (mt) cc_final: 0.8651 (pt) REVERT: J 4 MET cc_start: 0.7202 (mmm) cc_final: 0.6732 (mmm) REVERT: J 17 GLU cc_start: 0.6552 (tm-30) cc_final: 0.6274 (tm-30) REVERT: J 27 GLU cc_start: 0.8200 (pt0) cc_final: 0.7724 (pm20) REVERT: J 32 ASP cc_start: 0.7939 (m-30) cc_final: 0.7431 (m-30) REVERT: J 37 GLN cc_start: 0.7910 (tt0) cc_final: 0.7318 (pt0) REVERT: J 45 ARG cc_start: 0.6627 (OUTLIER) cc_final: 0.6034 (ttt180) REVERT: J 46 LEU cc_start: 0.8181 (mt) cc_final: 0.7932 (mp) REVERT: J 70 GLU cc_start: 0.7709 (pm20) cc_final: 0.7403 (pm20) REVERT: J 82 ASP cc_start: 0.7602 (m-30) cc_final: 0.7332 (m-30) REVERT: J 93 ASN cc_start: 0.7832 (p0) cc_final: 0.7595 (p0) REVERT: K 6 GLU cc_start: 0.5786 (mt-10) cc_final: 0.5467 (mt-10) REVERT: K 120 GLN cc_start: 0.8061 (pm20) cc_final: 0.7790 (pm20) REVERT: L 4 MET cc_start: 0.6012 (OUTLIER) cc_final: 0.5779 (ptt) REVERT: L 27 GLU cc_start: 0.7606 (mp0) cc_final: 0.7109 (mp0) REVERT: M 120 GLN cc_start: 0.7724 (pp30) cc_final: 0.7278 (pp30) REVERT: H 13 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8554 (tt) outliers start: 44 outliers final: 31 residues processed: 219 average time/residue: 0.1158 time to fit residues: 38.2062 Evaluate side-chains 208 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 1 GLU Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain H residue 13 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 30 optimal weight: 9.9990 chunk 125 optimal weight: 20.0000 chunk 119 optimal weight: 7.9990 chunk 155 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 161 optimal weight: 20.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 279 ASN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** 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 = 0.3711 r_free = 0.3711 target = 0.107095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.078800 restraints weight = 66102.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.081453 restraints weight = 33226.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.081604 restraints weight = 19500.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.082095 restraints weight = 19494.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.082224 restraints weight = 16580.732| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 14802 Z= 0.238 Angle : 0.772 15.681 20209 Z= 0.372 Chirality : 0.049 0.303 2400 Planarity : 0.004 0.044 2578 Dihedral : 5.301 58.284 2119 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.48 % Favored : 90.47 % Rotamer: Outliers : 4.14 % Allowed : 22.91 % Favored : 72.95 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.60 % 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: -2.76 (0.19), residues: 1931 helix: -0.51 (0.26), residues: 408 sheet: -1.61 (0.24), residues: 481 loop : -2.55 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 18 TYR 0.026 0.002 TYR L 49 PHE 0.017 0.002 PHE A 53 TRP 0.019 0.002 TRP C 479 HIS 0.013 0.001 HIS K 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.24 (14741) covalent geometry : angle 0.73420 / 0.36 (20075) SS BOND : bond 0.00760 / 0.34 ( 28) SS BOND : angle 3.32920 / 2.36 ( 56) hydrogen bonds : bond 0.04332 / 2.74 ( 402) hydrogen bonds : angle 5.52853 / 3.89 ( 1077) Misc. bond : bond 0.00063 / 0.04 ( 7) link_ALPHA1-3 : bond 0.00578 / 0.30 ( 4) link_ALPHA1-3 : angle 3.00720 / 2.67 ( 12) link_ALPHA1-6 : bond 0.00332 / 0.17 ( 2) link_ALPHA1-6 : angle 1.60509 / 1.00 ( 6) link_BETA1-4 : bond 0.00569 / 0.28 ( 6) link_BETA1-4 : angle 3.27469 / 1.82 ( 18) link_NAG-ASN : bond 0.00412 / 0.24 ( 11) link_NAG-ASN : angle 2.84469 / 1.93 ( 33) link_TRANS : bond 0.00429 / 0.22 ( 3) link_TRANS : angle 0.94247 / 0.71 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 169 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.8003 (t70) REVERT: D 620 SER cc_start: 0.9178 (OUTLIER) cc_final: 0.8819 (p) REVERT: D 634 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8468 (tp30) REVERT: D 648 GLU cc_start: 0.8270 (mp0) cc_final: 0.7974 (mp0) REVERT: A 104 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8469 (tpp) REVERT: J 4 MET cc_start: 0.7470 (mmm) cc_final: 0.6786 (mmm) REVERT: J 17 GLU cc_start: 0.6745 (tm-30) cc_final: 0.6377 (tm-30) REVERT: J 37 GLN cc_start: 0.7960 (tt0) cc_final: 0.7465 (pt0) REVERT: J 45 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6400 (ttt180) REVERT: J 70 GLU cc_start: 0.7756 (pm20) cc_final: 0.7440 (pm20) REVERT: J 82 ASP cc_start: 0.7534 (m-30) cc_final: 0.7249 (m-30) REVERT: J 93 ASN cc_start: 0.7962 (p0) cc_final: 0.7707 (p0) REVERT: L 4 MET cc_start: 0.6265 (OUTLIER) cc_final: 0.5985 (ptt) REVERT: L 27 GLU cc_start: 0.7747 (mp0) cc_final: 0.7201 (mp0) REVERT: M 120 GLN cc_start: 0.7824 (pp30) cc_final: 0.7444 (pp30) REVERT: H 13 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8569 (tt) outliers start: 53 outliers final: 39 residues processed: 208 average time/residue: 0.1109 time to fit residues: 34.9539 Evaluate side-chains 210 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 165 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain K residue 13 LYS Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain H residue 13 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 100 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 158 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 135 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 177 optimal weight: 30.0000 chunk 48 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 279 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** 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 = 0.3745 r_free = 0.3745 target = 0.109257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.080538 restraints weight = 72941.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.083962 restraints weight = 34079.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.084654 restraints weight = 18092.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.085044 restraints weight = 17320.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.085000 restraints weight = 14607.088| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14802 Z= 0.124 Angle : 0.686 14.972 20209 Z= 0.329 Chirality : 0.046 0.293 2400 Planarity : 0.004 0.055 2578 Dihedral : 5.033 57.039 2119 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.16 % Favored : 93.79 % Rotamer: Outliers : 3.44 % Allowed : 23.22 % Favored : 73.34 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.60 % 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: -2.56 (0.19), residues: 1931 helix: -0.36 (0.26), residues: 413 sheet: -1.37 (0.24), residues: 485 loop : -2.50 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG J 18 TYR 0.024 0.001 TYR L 49 PHE 0.012 0.001 PHE L 100 TRP 0.016 0.001 TRP C 479 HIS 0.006 0.001 HIS K 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (14741) covalent geometry : angle 0.64836 / 0.32 (20075) SS BOND : bond 0.00638 / 0.26 ( 28) SS BOND : angle 3.12541 / 2.23 ( 56) hydrogen bonds : bond 0.03558 / 2.24 ( 402) hydrogen bonds : angle 5.21426 / 3.66 ( 1077) Misc. bond : bond 0.00077 / 0.06 ( 7) link_ALPHA1-3 : bond 0.00599 / 0.31 ( 4) link_ALPHA1-3 : angle 2.64688 / 2.28 ( 12) link_ALPHA1-6 : bond 0.00635 / 0.32 ( 2) link_ALPHA1-6 : angle 1.65022 / 1.03 ( 6) link_BETA1-4 : bond 0.00716 / 0.35 ( 6) link_BETA1-4 : angle 3.16666 / 1.64 ( 18) link_NAG-ASN : bond 0.00402 / 0.25 ( 11) link_NAG-ASN : angle 2.72451 / 1.83 ( 33) link_TRANS : bond 0.00508 / 0.25 ( 3) link_TRANS : angle 0.88008 / 0.65 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7892 (t70) REVERT: D 634 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8342 (tp30) REVERT: D 648 GLU cc_start: 0.8119 (mp0) cc_final: 0.7817 (mp0) REVERT: A 104 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8362 (tpp) REVERT: A 479 TRP cc_start: 0.7960 (m-90) cc_final: 0.7564 (m-90) REVERT: B 591 GLN cc_start: 0.8962 (tm-30) cc_final: 0.8573 (tm-30) REVERT: J 4 MET cc_start: 0.7518 (mmm) cc_final: 0.6855 (mmm) REVERT: J 27 GLU cc_start: 0.8139 (pt0) cc_final: 0.7619 (pm20) REVERT: J 37 GLN cc_start: 0.7923 (tt0) cc_final: 0.7491 (pt0) REVERT: J 45 ARG cc_start: 0.6407 (OUTLIER) cc_final: 0.5901 (ttt180) REVERT: J 82 ASP cc_start: 0.7536 (m-30) cc_final: 0.7277 (m-30) REVERT: J 93 ASN cc_start: 0.7917 (p0) cc_final: 0.7672 (p0) REVERT: K 6 GLU cc_start: 0.5884 (mt-10) cc_final: 0.5563 (mt-10) REVERT: K 120 GLN cc_start: 0.7994 (pm20) cc_final: 0.7711 (pm20) REVERT: L 4 MET cc_start: 0.6017 (OUTLIER) cc_final: 0.5740 (ptt) REVERT: L 27 GLU cc_start: 0.7771 (mp0) cc_final: 0.7200 (mp0) REVERT: M 120 GLN cc_start: 0.7688 (pp30) cc_final: 0.7316 (pp30) REVERT: H 13 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8571 (tt) outliers start: 44 outliers final: 36 residues processed: 204 average time/residue: 0.1088 time to fit residues: 33.3987 Evaluate side-chains 207 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain H residue 13 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 20 optimal weight: 2.9990 chunk 163 optimal weight: 40.0000 chunk 103 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 155 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 279 ASN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** 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 = 0.3721 r_free = 0.3721 target = 0.107693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.082209 restraints weight = 45400.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.082145 restraints weight = 26318.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.082852 restraints weight = 19308.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.083223 restraints weight = 17592.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.083325 restraints weight = 15742.810| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14802 Z= 0.190 Angle : 0.728 15.405 20209 Z= 0.350 Chirality : 0.047 0.305 2400 Planarity : 0.004 0.056 2578 Dihedral : 5.177 57.075 2119 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.96 % Favored : 90.99 % Rotamer: Outliers : 3.75 % Allowed : 23.06 % Favored : 73.18 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.60 % 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: -2.58 (0.19), residues: 1931 helix: -0.28 (0.26), residues: 407 sheet: -1.49 (0.24), residues: 482 loop : -2.48 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 18 TYR 0.023 0.002 TYR L 49 PHE 0.014 0.001 PHE A 53 TRP 0.019 0.001 TRP C 479 HIS 0.008 0.001 HIS K 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (14741) covalent geometry : angle 0.69061 / 0.34 (20075) SS BOND : bond 0.00698 / 0.29 ( 28) SS BOND : angle 3.23892 / 2.30 ( 56) hydrogen bonds : bond 0.03987 / 2.52 ( 402) hydrogen bonds : angle 5.37091 / 3.76 ( 1077) Misc. bond : bond 0.00065 / 0.05 ( 7) link_ALPHA1-3 : bond 0.00590 / 0.31 ( 4) link_ALPHA1-3 : angle 2.85161 / 2.54 ( 12) link_ALPHA1-6 : bond 0.00464 / 0.23 ( 2) link_ALPHA1-6 : angle 1.62031 / 1.01 ( 6) link_BETA1-4 : bond 0.00602 / 0.29 ( 6) link_BETA1-4 : angle 3.24060 / 1.75 ( 18) link_NAG-ASN : bond 0.00395 / 0.24 ( 11) link_NAG-ASN : angle 2.76475 / 1.86 ( 33) link_TRANS : bond 0.00455 / 0.23 ( 3) link_TRANS : angle 0.90105 / 0.68 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2582.11 seconds wall clock time: 45 minutes 25.70 seconds (2725.70 seconds total)