Starting phenix.real_space_refine on Mon Aug 25 21:58:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tjs_41310/08_2025/8tjs_41310.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tjs_41310/08_2025/8tjs_41310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tjs_41310/08_2025/8tjs_41310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tjs_41310/08_2025/8tjs_41310.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tjs_41310/08_2025/8tjs_41310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tjs_41310/08_2025/8tjs_41310.map" } resolution = 3.31 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= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 13539 atoms to isotropic. 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 132 5.16 5 C 12609 2.51 5 N 3429 2.21 5 O 4023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20193 Number of models: 1 Model: "" Number of chains: 27 Chain: "G" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "N" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 3 Chain: "H" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "O" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 3 Chain: "I" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "Q" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 976 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "T" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "P" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 976 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "S" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "R" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 976 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "U" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "A" 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.72, per 1000 atoms: 0.23 Number of scatterers: 20193 At special positions: 0 Unit cell: (146.08, 141.93, 131.97, 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 132 16.00 O 4023 8.00 N 3429 7.00 C 12609 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 214 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 210 " - pdb=" SG CYS G 442 " distance=2.03 Simple disulfide: pdb=" SG CYS G 227 " - pdb=" SG CYS G 256 " distance=2.04 Simple disulfide: pdb=" SG CYS G 237 " - pdb=" SG CYS G 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 305 " - pdb=" SG CYS G 340 " distance=2.03 Simple disulfide: pdb=" SG CYS G 387 " - pdb=" SG CYS G 454 " distance=2.03 Simple disulfide: pdb=" SG CYS G 394 " - pdb=" SG CYS G 427 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS N 54 " - pdb=" SG CYS N 74 " distance=2.03 Simple disulfide: pdb=" SG CYS N 119 " - pdb=" SG CYS N 214 " distance=2.03 Simple disulfide: pdb=" SG CYS N 126 " - pdb=" SG CYS N 205 " distance=2.03 Simple disulfide: pdb=" SG CYS N 131 " - pdb=" SG CYS N 157 " distance=2.03 Simple disulfide: pdb=" SG CYS N 210 " - pdb=" SG CYS N 442 " distance=2.03 Simple disulfide: pdb=" SG CYS N 227 " - pdb=" SG CYS N 256 " distance=2.03 Simple disulfide: pdb=" SG CYS N 237 " - pdb=" SG CYS N 248 " distance=2.03 Simple disulfide: pdb=" SG CYS N 305 " - pdb=" SG CYS N 340 " distance=2.03 Simple disulfide: pdb=" SG CYS N 387 " - pdb=" SG CYS N 454 " distance=2.03 Simple disulfide: pdb=" SG CYS N 394 " - pdb=" SG CYS N 427 " distance=2.03 Simple disulfide: pdb=" SG CYS N 510 " - pdb=" SG CYS H 605 " distance=2.30 Simple disulfide: pdb=" SG CYS H 598 " - pdb=" SG CYS H 604 " distance=2.03 Simple disulfide: pdb=" SG CYS O 54 " - pdb=" SG CYS O 74 " distance=2.03 Simple disulfide: pdb=" SG CYS O 119 " - pdb=" SG CYS O 214 " distance=2.03 Simple disulfide: pdb=" SG CYS O 126 " - pdb=" SG CYS O 205 " distance=2.04 Simple disulfide: pdb=" SG CYS O 131 " - pdb=" SG CYS O 157 " distance=2.03 Simple disulfide: pdb=" SG CYS O 210 " - pdb=" SG CYS O 442 " distance=2.04 Simple disulfide: pdb=" SG CYS O 227 " - pdb=" SG CYS O 256 " distance=2.05 Simple disulfide: pdb=" SG CYS O 237 " - pdb=" SG CYS O 248 " distance=2.03 Simple disulfide: pdb=" SG CYS O 305 " - pdb=" SG CYS O 340 " distance=2.03 Simple disulfide: pdb=" SG CYS O 387 " - pdb=" SG CYS O 454 " distance=2.03 Simple disulfide: pdb=" SG CYS O 394 " - pdb=" SG CYS O 427 " distance=2.03 Simple disulfide: pdb=" SG CYS O 510 " - pdb=" SG CYS I 605 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.04 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 92 " distance=2.03 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 88 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN A 4 " - " MAN A 5 " " MAN E 4 " - " MAN E 5 " " MAN F 4 " - " MAN F 5 " ALPHA1-3 " BMA A 3 " - " MAN A 4 " " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " ALPHA1-6 " BMA A 3 " - " MAN A 6 " " BMA E 3 " - " MAN E 6 " " BMA F 3 " - " MAN F 6 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG G 601 " - " ASN G 243 " " NAG G 602 " - " ASN G 285 " " NAG G 603 " - " ASN G 348 " " NAG G 604 " - " ASN G 364 " " NAG G 605 " - " ASN G 372 " " NAG G 606 " - " ASN G 395 " " NAG G 607 " - " ASN G 401 " " NAG G 608 " - " ASN G 457 " " NAG G 609 " - " ASN G 156 " " NAG G 610 " - " ASN G 160 " " NAG G 611 " - " ASN G 304 " " NAG G 612 " - " ASN G 310 " " NAG G 613 " - " ASN G 88 " " NAG H 701 " - " ASN H 611 " " NAG H 702 " - " ASN H 618 " " NAG H 703 " - " ASN H 637 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 618 " " NAG I 703 " - " ASN I 637 " " NAG N 601 " - " ASN N 243 " " NAG N 602 " - " ASN N 285 " " NAG N 603 " - " ASN N 348 " " NAG N 604 " - " ASN N 364 " " NAG N 605 " - " ASN N 372 " " NAG N 606 " - " ASN N 395 " " NAG N 607 " - " ASN N 401 " " NAG N 608 " - " ASN N 457 " " NAG N 609 " - " ASN N 156 " " NAG N 610 " - " ASN N 160 " " NAG N 611 " - " ASN N 304 " " NAG N 612 " - " ASN N 310 " " NAG N 613 " - " ASN N 88 " " NAG O 601 " - " ASN O 243 " " NAG O 602 " - " ASN O 285 " " NAG O 603 " - " ASN O 348 " " NAG O 604 " - " ASN O 364 " " NAG O 605 " - " ASN O 372 " " NAG O 606 " - " ASN O 395 " " NAG O 607 " - " ASN O 401 " " NAG O 608 " - " ASN O 457 " " NAG O 609 " - " ASN O 156 " " NAG O 610 " - " ASN O 160 " " NAG O 611 " - " ASN O 304 " " NAG O 612 " - " ASN O 310 " " NAG O 613 " - " ASN O 88 " Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 964.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 44 sheets defined 17.0% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'G' and resid 98 through 115 removed outlier: 3.918A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.844A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 359 Processing helix chain 'G' and resid 377 through 382 Processing helix chain 'G' and resid 434 through 438 removed outlier: 3.960A pdb=" N GLN G 437 " --> pdb=" O ASN G 434 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG G 438 " --> pdb=" O MET G 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 434 through 438' Processing helix chain 'G' and resid 484 through 490 removed outlier: 3.593A pdb=" N TRP G 488 " --> pdb=" O MET G 484 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER G 490 " --> pdb=" O ASP G 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 538 through 543 removed outlier: 3.670A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 595 removed outlier: 3.651A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 636 through 639 removed outlier: 3.970A pdb=" N THR B 639 " --> pdb=" O SER B 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 636 through 639' Processing helix chain 'B' and resid 640 through 648 Processing helix chain 'B' and resid 650 through 664 removed outlier: 3.682A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 63 removed outlier: 3.569A pdb=" N THR N 63 " --> pdb=" O ALA N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 74 removed outlier: 5.828A pdb=" N HIS N 72 " --> pdb=" O TRP N 69 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA N 73 " --> pdb=" O ALA N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 115 removed outlier: 4.366A pdb=" N GLU N 102 " --> pdb=" O ASN N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 344 through 359 removed outlier: 3.577A pdb=" N GLN N 357 " --> pdb=" O LYS N 353 " (cutoff:3.500A) Processing helix chain 'N' and resid 434 through 438 removed outlier: 4.404A pdb=" N GLN N 437 " --> pdb=" O ASN N 434 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG N 438 " --> pdb=" O MET N 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 434 through 438' Processing helix chain 'N' and resid 484 through 490 removed outlier: 4.358A pdb=" N TRP N 488 " --> pdb=" O MET N 484 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER N 490 " --> pdb=" O ASP N 486 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 534 Processing helix chain 'H' and resid 536 through 543 removed outlier: 3.962A pdb=" N ASN H 543 " --> pdb=" O VAL H 539 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 587 Processing helix chain 'H' and resid 591 through 596 removed outlier: 4.009A pdb=" N TRP H 596 " --> pdb=" O LEU H 592 " (cutoff:3.500A) Processing helix chain 'H' and resid 627 through 635 Processing helix chain 'H' and resid 637 through 647 removed outlier: 4.285A pdb=" N ILE H 641 " --> pdb=" O ASN H 637 " (cutoff:3.500A) Processing helix chain 'H' and resid 653 through 661 removed outlier: 4.097A pdb=" N LEU H 661 " --> pdb=" O GLU H 657 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 64 removed outlier: 4.140A pdb=" N TYR O 61 " --> pdb=" O ASP O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 116 removed outlier: 4.050A pdb=" N GLU O 102 " --> pdb=" O ASN O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 122 through 126 removed outlier: 3.619A pdb=" N LEU O 125 " --> pdb=" O LEU O 122 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS O 126 " --> pdb=" O THR O 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 122 through 126' Processing helix chain 'O' and resid 344 through 362 removed outlier: 4.413A pdb=" N LYS O 360 " --> pdb=" O LYS O 356 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS O 361 " --> pdb=" O GLN O 357 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE O 362 " --> pdb=" O LEU O 358 " (cutoff:3.500A) Processing helix chain 'O' and resid 377 through 382 Processing helix chain 'O' and resid 484 through 490 removed outlier: 4.200A pdb=" N TRP O 488 " --> pdb=" O MET O 484 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER O 490 " --> pdb=" O ASP O 486 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 541 removed outlier: 3.538A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 573 through 595 removed outlier: 3.533A pdb=" N ALA I 578 " --> pdb=" O LYS I 574 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG I 579 " --> pdb=" O GLN I 575 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL I 583 " --> pdb=" O ARG I 579 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 636 Processing helix chain 'I' and resid 638 through 648 Processing helix chain 'I' and resid 650 through 659 removed outlier: 3.783A pdb=" N ASN I 656 " --> pdb=" O GLN I 652 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 87 removed outlier: 3.637A pdb=" N SER Q 87 " --> pdb=" O PRO Q 84 " (cutoff:3.500A) Processing helix chain 'T' and resid 50 through 52 No H-bonds generated for 'chain 'T' and resid 50 through 52' Processing helix chain 'T' and resid 79 through 83 removed outlier: 3.720A pdb=" N VAL T 83 " --> pdb=" O PRO T 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.610A pdb=" N SER P 87 " --> pdb=" O PRO P 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 83 removed outlier: 3.946A pdb=" N VAL S 83 " --> pdb=" O PRO S 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 83 removed outlier: 3.669A pdb=" N VAL U 83 " --> pdb=" O PRO U 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 503 through 508 removed outlier: 5.151A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.812A pdb=" N ILE G 234 " --> pdb=" O VAL G 254 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL G 251 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 75 through 76 removed outlier: 6.668A pdb=" N CYS G 54 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'G' and resid 169 through 177 removed outlier: 3.797A pdb=" N LYS G 198 " --> pdb=" O CYS G 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 211 through 212 removed outlier: 6.675A pdb=" N THR G 211 " --> pdb=" O TYR G 444 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 281 through 283 removed outlier: 11.566A pdb=" N VAL G 295 " --> pdb=" O THR G 464 " (cutoff:3.500A) removed outlier: 11.131A pdb=" N THR G 464 " --> pdb=" O VAL G 295 " (cutoff:3.500A) removed outlier: 12.432A pdb=" N PHE G 297 " --> pdb=" O ILE G 462 " (cutoff:3.500A) removed outlier: 12.400A pdb=" N ILE G 462 " --> pdb=" O PHE G 297 " (cutoff:3.500A) removed outlier: 10.588A pdb=" N THR G 299 " --> pdb=" O GLY G 460 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY G 460 " --> pdb=" O THR G 299 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE G 452 " --> pdb=" O ARG G 307 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASN G 309 " --> pdb=" O GLY G 450 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLY G 450 " --> pdb=" O ASN G 309 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE G 367 " --> pdb=" O GLU G 475 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N PHE G 477 " --> pdb=" O ILE G 367 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG G 369 " --> pdb=" O PHE G 477 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 281 through 283 removed outlier: 7.338A pdb=" N GLN G 302 " --> pdb=" O SER G 343 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER G 343 " --> pdb=" O GLN G 302 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS G 339 " --> pdb=" O THR G 306 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 313 through 317 Processing sheet with id=AB1, first strand: chain 'G' and resid 383 through 387 removed outlier: 3.638A pdb=" N PHE G 385 " --> pdb=" O PHE G 392 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 503 through 508 removed outlier: 5.380A pdb=" N VAL H 608 " --> pdb=" O VAL N 36 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL N 38 " --> pdb=" O THR H 606 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N THR H 606 " --> pdb=" O VAL N 38 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N TYR N 40 " --> pdb=" O CYS H 604 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N CYS H 604 " --> pdb=" O TYR N 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 45 through 47 removed outlier: 3.905A pdb=" N ILE N 234 " --> pdb=" O VAL N 254 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 91 through 93 removed outlier: 3.522A pdb=" N GLU N 91 " --> pdb=" O CYS N 248 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 169 through 177 removed outlier: 3.688A pdb=" N LYS N 198 " --> pdb=" O CYS N 131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 211 through 212 removed outlier: 6.679A pdb=" N THR N 211 " --> pdb=" O TYR N 444 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 268 through 269 removed outlier: 6.369A pdb=" N LEU N 269 " --> pdb=" O THR N 459 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE N 452 " --> pdb=" O ARG N 307 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS N 454 " --> pdb=" O CYS N 305 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY N 460 " --> pdb=" O THR N 299 " (cutoff:3.500A) removed outlier: 10.256A pdb=" N THR N 299 " --> pdb=" O GLY N 460 " (cutoff:3.500A) removed outlier: 11.928A pdb=" N ILE N 462 " --> pdb=" O PHE N 297 " (cutoff:3.500A) removed outlier: 11.817A pdb=" N PHE N 297 " --> pdb=" O ILE N 462 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N THR N 464 " --> pdb=" O VAL N 295 " (cutoff:3.500A) removed outlier: 11.455A pdb=" N VAL N 295 " --> pdb=" O THR N 464 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLN N 302 " --> pdb=" O SER N 343 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER N 343 " --> pdb=" O GLN N 302 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS N 339 " --> pdb=" O THR N 306 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA N 338 " --> pdb=" O CYS N 427 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 280 through 282 removed outlier: 11.455A pdb=" N VAL N 295 " --> pdb=" O THR N 464 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N THR N 464 " --> pdb=" O VAL N 295 " (cutoff:3.500A) removed outlier: 11.817A pdb=" N PHE N 297 " --> pdb=" O ILE N 462 " (cutoff:3.500A) removed outlier: 11.928A pdb=" N ILE N 462 " --> pdb=" O PHE N 297 " (cutoff:3.500A) removed outlier: 10.256A pdb=" N THR N 299 " --> pdb=" O GLY N 460 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY N 460 " --> pdb=" O THR N 299 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS N 454 " --> pdb=" O CYS N 305 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE N 452 " --> pdb=" O ARG N 307 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER N 402 " --> pdb=" O PHE N 370 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 310 through 321 removed outlier: 7.283A pdb=" N ASN N 310 " --> pdb=" O ILE N 331 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE N 331 " --> pdb=" O ASN N 310 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR N 312 " --> pdb=" O GLY N 330 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLN N 324 " --> pdb=" O ILE N 318 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 516 through 518 removed outlier: 3.552A pdb=" N THR R 12 " --> pdb=" O THR R 110 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 516 through 518 removed outlier: 7.062A pdb=" N MET R 34 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY R 50 " --> pdb=" O MET R 34 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TRP R 36 " --> pdb=" O VAL R 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 503 through 508 removed outlier: 4.908A pdb=" N VAL I 608 " --> pdb=" O VAL O 36 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL O 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR I 606 " --> pdb=" O VAL O 38 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N TYR O 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N CYS I 604 " --> pdb=" O TYR O 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 45 through 47 removed outlier: 3.718A pdb=" N ILE O 234 " --> pdb=" O VAL O 254 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL O 251 " --> pdb=" O LEU O 86 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 75 through 76 removed outlier: 7.042A pdb=" N CYS O 54 " --> pdb=" O VAL O 75 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 91 through 94 Processing sheet with id=AC7, first strand: chain 'O' and resid 169 through 177 removed outlier: 3.912A pdb=" N LYS O 198 " --> pdb=" O CYS O 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 268 through 269 removed outlier: 6.365A pdb=" N LEU O 269 " --> pdb=" O THR O 459 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N ARG O 453 " --> pdb=" O ILE O 303 " (cutoff:3.500A) removed outlier: 11.155A pdb=" N ILE O 303 " --> pdb=" O ARG O 453 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N VAL O 455 " --> pdb=" O VAL O 301 " (cutoff:3.500A) removed outlier: 10.731A pdb=" N VAL O 301 " --> pdb=" O VAL O 455 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N ASN O 457 " --> pdb=" O THR O 299 " (cutoff:3.500A) removed outlier: 10.259A pdb=" N THR O 299 " --> pdb=" O ASN O 457 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR O 459 " --> pdb=" O PHE O 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 293 through 306 current: chain 'O' and resid 368 through 370 removed outlier: 3.547A pdb=" N ILE O 368 " --> pdb=" O TRP O 404 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 280 through 282 removed outlier: 7.159A pdb=" N THR O 459 " --> pdb=" O PHE O 297 " (cutoff:3.500A) removed outlier: 10.259A pdb=" N THR O 299 " --> pdb=" O ASN O 457 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N ASN O 457 " --> pdb=" O THR O 299 " (cutoff:3.500A) removed outlier: 10.731A pdb=" N VAL O 301 " --> pdb=" O VAL O 455 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N VAL O 455 " --> pdb=" O VAL O 301 " (cutoff:3.500A) removed outlier: 11.155A pdb=" N ILE O 303 " --> pdb=" O ARG O 453 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N ARG O 453 " --> pdb=" O ILE O 303 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 453 through 465 current: chain 'O' and resid 422 through 427 Processing sheet with id=AD1, first strand: chain 'O' and resid 310 through 321 removed outlier: 6.477A pdb=" N ASN O 310 " --> pdb=" O ILE O 331 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE O 331 " --> pdb=" O ASN O 310 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR O 312 " --> pdb=" O GLY O 330 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN O 324 " --> pdb=" O ILE O 318 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 383 through 387 removed outlier: 3.649A pdb=" N GLU O 390 " --> pdb=" O CYS O 387 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 432 through 433 Processing sheet with id=AD4, first strand: chain 'Q' and resid 3 through 6 removed outlier: 3.708A pdb=" N LEU Q 20 " --> pdb=" O LEU Q 80 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR Q 77 " --> pdb=" O GLU Q 72 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 10 through 12 removed outlier: 5.770A pdb=" N GLY Q 10 " --> pdb=" O THR Q 110 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR Q 93 " --> pdb=" O HIS Q 35 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 10 through 12 removed outlier: 5.770A pdb=" N GLY Q 10 " --> pdb=" O THR Q 110 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'T' and resid 4 through 6 removed outlier: 3.713A pdb=" N THR T 5 " --> pdb=" O ARG T 24 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE T 71 " --> pdb=" O CYS T 23 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP T 70 " --> pdb=" O SER T 67 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER T 67 " --> pdb=" O ASP T 70 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'T' and resid 45 through 46 removed outlier: 3.678A pdb=" N VAL T 34 " --> pdb=" O GLN T 89 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN T 89 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR T 87 " --> pdb=" O TYR T 36 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN T 38 " --> pdb=" O VAL T 85 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY T 84 " --> pdb=" O VAL T 104 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'T' and resid 48 through 49 Processing sheet with id=AE1, first strand: chain 'P' and resid 4 through 8 Processing sheet with id=AE2, first strand: chain 'P' and resid 11 through 12 removed outlier: 3.541A pdb=" N THR P 12 " --> pdb=" O THR P 110 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL P 37 " --> pdb=" O TYR P 91 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N MET P 34 " --> pdb=" O GLY P 50 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLY P 50 " --> pdb=" O MET P 34 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP P 36 " --> pdb=" O VAL P 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 11 through 12 removed outlier: 3.541A pdb=" N THR P 12 " --> pdb=" O THR P 110 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 5 through 6 removed outlier: 4.260A pdb=" N THR S 5 " --> pdb=" O ARG S 24 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG S 24 " --> pdb=" O THR S 5 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP S 70 " --> pdb=" O SER S 67 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'S' and resid 53 through 54 removed outlier: 3.672A pdb=" N LYS S 53 " --> pdb=" O TYR S 49 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TRP S 35 " --> pdb=" O LEU S 47 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N TYR S 49 " --> pdb=" O LEU S 33 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU S 33 " --> pdb=" O TYR S 49 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 5 through 8 removed outlier: 3.508A pdb=" N VAL R 5 " --> pdb=" O VAL R 23 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER R 21 " --> pdb=" O SER R 7 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'U' and resid 4 through 6 removed outlier: 3.577A pdb=" N PHE U 71 " --> pdb=" O CYS U 23 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP U 70 " --> pdb=" O SER U 67 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER U 67 " --> pdb=" O ASP U 70 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'U' and resid 53 through 54 removed outlier: 5.762A pdb=" N VAL U 46 " --> pdb=" O GLN U 37 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLN U 37 " --> pdb=" O VAL U 46 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY U 84 " --> pdb=" O VAL U 104 " (cutoff:3.500A) 613 hydrogen bonds defined for protein. 1617 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: 3.67 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5360 1.33 - 1.46: 5851 1.46 - 1.59: 9205 1.59 - 1.72: 0 1.72 - 1.85: 177 Bond restraints: 20593 Sorted by residual: bond pdb=" C LYS N 117 " pdb=" N PRO N 118 " ideal model delta sigma weight residual 1.331 1.375 -0.043 7.90e-03 1.60e+04 2.98e+01 bond pdb=" C LYS O 117 " pdb=" N PRO O 118 " ideal model delta sigma weight residual 1.334 1.420 -0.086 2.34e-02 1.83e+03 1.35e+01 bond pdb=" N TRP U 94 " pdb=" CA TRP U 94 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.04e-02 9.25e+03 1.32e+01 bond pdb=" N ILE B 595 " pdb=" CA ILE B 595 " ideal model delta sigma weight residual 1.458 1.505 -0.047 1.32e-02 5.74e+03 1.25e+01 bond pdb=" N GLY U 99 " pdb=" CA GLY U 99 " ideal model delta sigma weight residual 1.445 1.477 -0.032 9.20e-03 1.18e+04 1.23e+01 ... (remaining 20588 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 27184 2.65 - 5.30: 670 5.30 - 7.95: 82 7.95 - 10.61: 13 10.61 - 13.26: 2 Bond angle restraints: 27951 Sorted by residual: angle pdb=" N TRP B 596 " pdb=" CA TRP B 596 " pdb=" C TRP B 596 " ideal model delta sigma weight residual 109.79 101.10 8.69 1.56e+00 4.11e-01 3.10e+01 angle pdb=" N ILE U 92 " pdb=" CA ILE U 92 " pdb=" C ILE U 92 " ideal model delta sigma weight residual 111.90 107.39 4.51 8.10e-01 1.52e+00 3.10e+01 angle pdb=" N PRO R 100 " pdb=" CA PRO R 100 " pdb=" C PRO R 100 " ideal model delta sigma weight residual 113.78 104.82 8.96 1.62e+00 3.81e-01 3.06e+01 angle pdb=" CB LYS Q 100E" pdb=" CG LYS Q 100E" pdb=" CD LYS Q 100E" ideal model delta sigma weight residual 111.30 123.24 -11.94 2.30e+00 1.89e-01 2.69e+01 angle pdb=" C ASN G 136 " pdb=" N ASN G 137 " pdb=" CA ASN G 137 " ideal model delta sigma weight residual 121.54 131.30 -9.76 1.91e+00 2.74e-01 2.61e+01 ... (remaining 27946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.85: 12480 23.85 - 47.70: 700 47.70 - 71.54: 123 71.54 - 95.39: 34 95.39 - 119.24: 20 Dihedral angle restraints: 13357 sinusoidal: 6339 harmonic: 7018 Sorted by residual: dihedral pdb=" CB CYS N 54 " pdb=" SG CYS N 54 " pdb=" SG CYS N 74 " pdb=" CB CYS N 74 " ideal model delta sinusoidal sigma weight residual -86.00 3.19 -89.19 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS O 119 " pdb=" SG CYS O 119 " pdb=" SG CYS O 214 " pdb=" CB CYS O 214 " ideal model delta sinusoidal sigma weight residual -86.00 -148.95 62.95 1 1.00e+01 1.00e-02 5.23e+01 dihedral pdb=" CB CYS T 23 " pdb=" SG CYS T 23 " pdb=" SG CYS T 88 " pdb=" CB CYS T 88 " ideal model delta sinusoidal sigma weight residual 93.00 152.96 -59.96 1 1.00e+01 1.00e-02 4.79e+01 ... (remaining 13354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2878 0.091 - 0.182: 421 0.182 - 0.272: 23 0.272 - 0.363: 8 0.363 - 0.454: 6 Chirality restraints: 3336 Sorted by residual: chirality pdb=" C1 NAG B 702 " pdb=" ND2 ASN B 618 " pdb=" C2 NAG B 702 " pdb=" O5 NAG B 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CA TYR R 99 " pdb=" N TYR R 99 " pdb=" C TYR R 99 " pdb=" CB TYR R 99 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" C1 NAG G 613 " pdb=" ND2 ASN G 88 " pdb=" C2 NAG G 613 " pdb=" O5 NAG G 613 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.29e+00 ... (remaining 3333 not shown) Planarity restraints: 3526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 613 " 0.318 2.00e-02 2.50e+03 2.69e-01 9.08e+02 pdb=" C7 NAG O 613 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG O 613 " 0.180 2.00e-02 2.50e+03 pdb=" N2 NAG O 613 " -0.470 2.00e-02 2.50e+03 pdb=" O7 NAG O 613 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 613 " 0.310 2.00e-02 2.50e+03 2.64e-01 8.72e+02 pdb=" C7 NAG G 613 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG G 613 " 0.172 2.00e-02 2.50e+03 pdb=" N2 NAG G 613 " -0.463 2.00e-02 2.50e+03 pdb=" O7 NAG G 613 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 613 " 0.293 2.00e-02 2.50e+03 2.50e-01 7.84e+02 pdb=" C7 NAG N 613 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG N 613 " 0.172 2.00e-02 2.50e+03 pdb=" N2 NAG N 613 " -0.437 2.00e-02 2.50e+03 pdb=" O7 NAG N 613 " 0.047 2.00e-02 2.50e+03 ... (remaining 3523 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4873 2.80 - 3.33: 16438 3.33 - 3.85: 32533 3.85 - 4.38: 37355 4.38 - 4.90: 65667 Nonbonded interactions: 156866 Sorted by model distance: nonbonded pdb=" O VAL O 36 " pdb=" OG1 THR I 606 " model vdw 2.280 3.040 nonbonded pdb=" O VAL G 36 " pdb=" OG1 THR B 606 " model vdw 2.308 3.040 nonbonded pdb=" OE1 GLU O 220 " pdb=" O6 NAG F 2 " model vdw 2.338 3.040 nonbonded pdb=" OG1 THR N 382 " pdb=" O CYS N 394 " model vdw 2.358 3.040 nonbonded pdb=" OG SER R 40 " pdb=" O ARG R 43 " model vdw 2.366 3.040 ... (remaining 156861 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.300 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5482 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 : 0.006 0.274 20703 Z= 0.369 Angle : 1.021 44.398 28240 Z= 0.564 Chirality : 0.062 0.454 3336 Planarity : 0.010 0.269 3478 Dihedral : 15.306 119.241 8722 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.71 % Allowed : 0.89 % Favored : 98.40 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.59 (0.15), residues: 2402 helix: -2.85 (0.19), residues: 378 sheet: -0.54 (0.21), residues: 644 loop : -2.01 (0.14), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG R 64 TYR 0.036 0.002 TYR R 99 PHE 0.012 0.002 PHE N 53 TRP 0.057 0.002 TRP P 103 HIS 0.009 0.001 HIS N 225 Details of bonding type rmsd covalent geometry : bond 0.00606 (20593) covalent geometry : angle 0.94932 (27951) SS BOND : bond 0.04333 ( 41) SS BOND : angle 5.45442 ( 82) hydrogen bonds : bond 0.24947 ( 587) hydrogen bonds : angle 9.92639 ( 1617) link_ALPHA1-2 : bond 0.00982 ( 3) link_ALPHA1-2 : angle 2.55323 ( 9) link_ALPHA1-3 : bond 0.00726 ( 3) link_ALPHA1-3 : angle 1.40349 ( 9) link_ALPHA1-6 : bond 0.00247 ( 3) link_ALPHA1-6 : angle 1.46436 ( 9) link_BETA1-4 : bond 0.00479 ( 12) link_BETA1-4 : angle 2.19351 ( 36) link_NAG-ASN : bond 0.00648 ( 48) link_NAG-ASN : angle 3.27105 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 310 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 67 ASN cc_start: 0.7362 (m110) cc_final: 0.7141 (m-40) REVERT: G 476 THR cc_start: 0.8395 (p) cc_final: 0.8018 (p) REVERT: N 365 ASN cc_start: 0.7291 (p0) cc_final: 0.7056 (p0) REVERT: H 542 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6742 (ptp-110) REVERT: I 515 ILE cc_start: 0.7732 (pt) cc_final: 0.7503 (pt) REVERT: I 655 LYS cc_start: 0.7379 (mttp) cc_final: 0.7042 (mttt) outliers start: 15 outliers final: 2 residues processed: 320 average time/residue: 0.1496 time to fit residues: 72.6540 Evaluate side-chains 266 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 263 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 119 CYS Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain H residue 542 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 30.0000 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 67 ASN G 212 GLN G 487 ASN N 82 GLN N 296 GLN ** N 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 357 GLN N 434 ASN H 607 ASN ** H 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 656 ASN O 136 ASN O 255 GLN Q 3 HIS T 89 GLN S 37 GLN ** U 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.168028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.134322 restraints weight = 25411.732| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.08 r_work: 0.3183 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 20703 Z= 0.236 Angle : 0.707 11.448 28240 Z= 0.350 Chirality : 0.049 0.397 3336 Planarity : 0.005 0.049 3478 Dihedral : 10.776 98.023 4253 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.18 % Allowed : 7.58 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.16), residues: 2402 helix: -1.70 (0.24), residues: 404 sheet: -0.36 (0.21), residues: 641 loop : -1.72 (0.15), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 64 TYR 0.027 0.002 TYR R 99 PHE 0.016 0.002 PHE B 522 TRP 0.023 0.002 TRP R 58 HIS 0.006 0.001 HIS G 339 Details of bonding type rmsd covalent geometry : bond 0.00566 (20593) covalent geometry : angle 0.68242 (27951) SS BOND : bond 0.00492 ( 41) SS BOND : angle 1.32543 ( 82) hydrogen bonds : bond 0.04235 ( 587) hydrogen bonds : angle 6.33611 ( 1617) link_ALPHA1-2 : bond 0.00547 ( 3) link_ALPHA1-2 : angle 3.29654 ( 9) link_ALPHA1-3 : bond 0.00593 ( 3) link_ALPHA1-3 : angle 3.26580 ( 9) link_ALPHA1-6 : bond 0.00436 ( 3) link_ALPHA1-6 : angle 1.95449 ( 9) link_BETA1-4 : bond 0.00345 ( 12) link_BETA1-4 : angle 1.69330 ( 36) link_NAG-ASN : bond 0.00384 ( 48) link_NAG-ASN : angle 2.09706 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 267 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 151 ARG cc_start: 0.8091 (mmp80) cc_final: 0.7846 (mmp-170) REVERT: N 365 ASN cc_start: 0.7453 (p0) cc_final: 0.7153 (p0) REVERT: I 515 ILE cc_start: 0.8105 (pt) cc_final: 0.7805 (pt) REVERT: Q 64 ARG cc_start: 0.8364 (ttm110) cc_final: 0.7992 (ttm110) REVERT: T 78 LEU cc_start: 0.7202 (mp) cc_final: 0.6901 (tt) REVERT: P 100 ARG cc_start: 0.8001 (ttt90) cc_final: 0.7541 (ttt90) REVERT: R 21 SER cc_start: 0.8026 (m) cc_final: 0.7443 (p) outliers start: 25 outliers final: 15 residues processed: 283 average time/residue: 0.1766 time to fit residues: 73.3726 Evaluate side-chains 262 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 247 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 449 GLN Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain N residue 386 ASN Chi-restraints excluded: chain N residue 508 THR Chi-restraints excluded: chain N residue 510 CYS Chi-restraints excluded: chain O residue 270 LEU Chi-restraints excluded: chain O residue 421 ASP Chi-restraints excluded: chain I residue 535 MET Chi-restraints excluded: chain Q residue 103 TRP Chi-restraints excluded: chain T residue 76 ASN Chi-restraints excluded: chain T residue 89 GLN Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain R residue 99 TYR Chi-restraints excluded: chain U residue 65 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 186 optimal weight: 9.9990 chunk 218 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 115 optimal weight: 0.0010 chunk 211 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 77 optimal weight: 0.0070 chunk 126 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 overall best weight: 0.7608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 GLN N 434 ASN H 591 GLN ** H 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 89 GLN ** U 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.168791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.136308 restraints weight = 25488.176| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.94 r_work: 0.3253 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20703 Z= 0.130 Angle : 0.614 10.066 28240 Z= 0.301 Chirality : 0.046 0.319 3336 Planarity : 0.004 0.057 3478 Dihedral : 9.657 94.883 4248 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.37 % Allowed : 10.50 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.16), residues: 2402 helix: -0.95 (0.26), residues: 398 sheet: -0.37 (0.21), residues: 651 loop : -1.54 (0.15), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 64 TYR 0.018 0.001 TYR R 99 PHE 0.013 0.001 PHE U 98 TRP 0.022 0.001 TRP Q 103 HIS 0.003 0.001 HIS O 225 Details of bonding type rmsd covalent geometry : bond 0.00303 (20593) covalent geometry : angle 0.59061 (27951) SS BOND : bond 0.00361 ( 41) SS BOND : angle 1.36216 ( 82) hydrogen bonds : bond 0.03661 ( 587) hydrogen bonds : angle 5.78909 ( 1617) link_ALPHA1-2 : bond 0.01392 ( 3) link_ALPHA1-2 : angle 3.31692 ( 9) link_ALPHA1-3 : bond 0.01008 ( 3) link_ALPHA1-3 : angle 1.93871 ( 9) link_ALPHA1-6 : bond 0.00798 ( 3) link_ALPHA1-6 : angle 1.77540 ( 9) link_BETA1-4 : bond 0.00433 ( 12) link_BETA1-4 : angle 1.41552 ( 36) link_NAG-ASN : bond 0.00291 ( 48) link_NAG-ASN : angle 1.89983 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 259 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: N 341 ASN cc_start: 0.8016 (p0) cc_final: 0.7760 (m-40) REVERT: N 365 ASN cc_start: 0.7514 (p0) cc_final: 0.7252 (p0) REVERT: N 483 ASP cc_start: 0.6402 (t0) cc_final: 0.6185 (t0) REVERT: H 542 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7947 (ptp-110) REVERT: O 280 MET cc_start: 0.8471 (mmm) cc_final: 0.8231 (mmt) REVERT: I 515 ILE cc_start: 0.8211 (pt) cc_final: 0.7881 (pt) REVERT: Q 64 ARG cc_start: 0.8345 (ttm110) cc_final: 0.8034 (ttm110) REVERT: T 78 LEU cc_start: 0.7311 (mp) cc_final: 0.6960 (tt) REVERT: P 100 ARG cc_start: 0.8021 (ttt90) cc_final: 0.7820 (ttt90) outliers start: 29 outliers final: 17 residues processed: 276 average time/residue: 0.1652 time to fit residues: 68.1370 Evaluate side-chains 259 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 241 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 449 GLN Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain N residue 386 ASN Chi-restraints excluded: chain N residue 508 THR Chi-restraints excluded: chain N residue 510 CYS Chi-restraints excluded: chain H residue 542 ARG Chi-restraints excluded: chain O residue 421 ASP Chi-restraints excluded: chain O residue 455 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 615 SER Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 76 ASN Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 89 GLN Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain R residue 32 HIS Chi-restraints excluded: chain R residue 72 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 55 optimal weight: 0.9980 chunk 184 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 105 optimal weight: 0.3980 chunk 98 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 153 optimal weight: 0.3980 chunk 40 optimal weight: 0.5980 chunk 220 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 434 ASN ** H 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.171032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.137302 restraints weight = 25592.551| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.07 r_work: 0.3233 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20703 Z= 0.112 Angle : 0.591 9.564 28240 Z= 0.287 Chirality : 0.045 0.271 3336 Planarity : 0.004 0.048 3478 Dihedral : 8.041 86.695 4248 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.65 % Allowed : 11.82 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.17), residues: 2402 helix: -0.52 (0.27), residues: 393 sheet: -0.21 (0.20), residues: 668 loop : -1.48 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 66 TYR 0.016 0.001 TYR R 99 PHE 0.014 0.001 PHE U 98 TRP 0.015 0.001 TRP T 94 HIS 0.003 0.001 HIS O 225 Details of bonding type rmsd covalent geometry : bond 0.00258 (20593) covalent geometry : angle 0.56737 (27951) SS BOND : bond 0.00311 ( 41) SS BOND : angle 1.26238 ( 82) hydrogen bonds : bond 0.03219 ( 587) hydrogen bonds : angle 5.36517 ( 1617) link_ALPHA1-2 : bond 0.01653 ( 3) link_ALPHA1-2 : angle 3.68659 ( 9) link_ALPHA1-3 : bond 0.01025 ( 3) link_ALPHA1-3 : angle 2.15446 ( 9) link_ALPHA1-6 : bond 0.00805 ( 3) link_ALPHA1-6 : angle 1.63529 ( 9) link_BETA1-4 : bond 0.00445 ( 12) link_BETA1-4 : angle 1.38534 ( 36) link_NAG-ASN : bond 0.00275 ( 48) link_NAG-ASN : angle 1.83602 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 254 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 365 ASN cc_start: 0.7361 (p0) cc_final: 0.7091 (p0) REVERT: H 542 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7801 (ptp-110) REVERT: I 515 ILE cc_start: 0.8098 (pt) cc_final: 0.7790 (pt) REVERT: Q 64 ARG cc_start: 0.8223 (ttm110) cc_final: 0.8006 (ttm110) REVERT: P 82 MET cc_start: 0.1439 (mmp) cc_final: 0.0526 (mtm) REVERT: P 100 ARG cc_start: 0.7874 (ttt90) cc_final: 0.7587 (ttt90) REVERT: R 82 MET cc_start: 0.6345 (mtm) cc_final: 0.5494 (mtm) outliers start: 35 outliers final: 24 residues processed: 276 average time/residue: 0.1305 time to fit residues: 54.3936 Evaluate side-chains 261 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 236 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 449 GLN Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain N residue 386 ASN Chi-restraints excluded: chain N residue 508 THR Chi-restraints excluded: chain N residue 510 CYS Chi-restraints excluded: chain H residue 542 ARG Chi-restraints excluded: chain O residue 421 ASP Chi-restraints excluded: chain O residue 455 VAL Chi-restraints excluded: chain I residue 535 MET Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 615 SER Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain T residue 76 ASN Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 89 GLN Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain R residue 32 HIS Chi-restraints excluded: chain R residue 72 GLU Chi-restraints excluded: chain R residue 99 TYR Chi-restraints excluded: chain U residue 65 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 237 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 154 optimal weight: 0.0370 chunk 27 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 chunk 217 optimal weight: 7.9990 chunk 130 optimal weight: 0.0470 chunk 19 optimal weight: 2.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 434 ASN ** H 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 651 ASN T 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.169041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.131604 restraints weight = 25464.432| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.25 r_work: 0.3197 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20703 Z= 0.124 Angle : 0.589 9.552 28240 Z= 0.285 Chirality : 0.045 0.270 3336 Planarity : 0.004 0.048 3478 Dihedral : 7.268 77.366 4246 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.65 % Allowed : 13.42 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.17), residues: 2402 helix: -0.34 (0.28), residues: 393 sheet: -0.10 (0.21), residues: 619 loop : -1.42 (0.15), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 64 TYR 0.016 0.001 TYR R 99 PHE 0.010 0.001 PHE U 98 TRP 0.013 0.001 TRP T 94 HIS 0.005 0.001 HIS O 383 Details of bonding type rmsd covalent geometry : bond 0.00291 (20593) covalent geometry : angle 0.56569 (27951) SS BOND : bond 0.00375 ( 41) SS BOND : angle 1.04499 ( 82) hydrogen bonds : bond 0.03105 ( 587) hydrogen bonds : angle 5.16118 ( 1617) link_ALPHA1-2 : bond 0.01841 ( 3) link_ALPHA1-2 : angle 4.13760 ( 9) link_ALPHA1-3 : bond 0.01123 ( 3) link_ALPHA1-3 : angle 1.93347 ( 9) link_ALPHA1-6 : bond 0.00588 ( 3) link_ALPHA1-6 : angle 1.48691 ( 9) link_BETA1-4 : bond 0.00421 ( 12) link_BETA1-4 : angle 1.33690 ( 36) link_NAG-ASN : bond 0.00280 ( 48) link_NAG-ASN : angle 1.82470 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 83 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7038 (tm-30) REVERT: G 280 MET cc_start: 0.8215 (mmm) cc_final: 0.8011 (mmm) REVERT: G 341 ASN cc_start: 0.7897 (p0) cc_final: 0.7562 (p0) REVERT: N 365 ASN cc_start: 0.7400 (p0) cc_final: 0.7111 (p0) REVERT: H 542 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7928 (ptp-110) REVERT: I 515 ILE cc_start: 0.8148 (pt) cc_final: 0.7841 (pt) REVERT: Q 64 ARG cc_start: 0.8208 (ttm110) cc_final: 0.7986 (ttm110) REVERT: Q 77 THR cc_start: 0.8588 (p) cc_final: 0.8375 (p) REVERT: T 78 LEU cc_start: 0.7051 (mp) cc_final: 0.6676 (tt) REVERT: P 64 ARG cc_start: 0.8214 (ttm110) cc_final: 0.7945 (ttp-170) REVERT: P 82 MET cc_start: 0.1457 (mmp) cc_final: 0.0565 (mtm) outliers start: 35 outliers final: 26 residues processed: 258 average time/residue: 0.1505 time to fit residues: 58.0809 Evaluate side-chains 257 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 229 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 449 GLN Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 367 ILE Chi-restraints excluded: chain N residue 386 ASN Chi-restraints excluded: chain N residue 508 THR Chi-restraints excluded: chain N residue 510 CYS Chi-restraints excluded: chain H residue 542 ARG Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 421 ASP Chi-restraints excluded: chain O residue 443 MET Chi-restraints excluded: chain O residue 455 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 615 SER Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain T residue 76 ASN Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 89 GLN Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain P residue 100 ARG Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain R residue 32 HIS Chi-restraints excluded: chain R residue 72 GLU Chi-restraints excluded: chain R residue 99 TYR Chi-restraints excluded: chain U residue 65 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 181 optimal weight: 0.0060 chunk 39 optimal weight: 0.9980 chunk 189 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 167 optimal weight: 0.6980 chunk 210 optimal weight: 8.9990 chunk 213 optimal weight: 0.3980 chunk 56 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 434 ASN ** H 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.169873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.133144 restraints weight = 25260.869| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.16 r_work: 0.3225 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20703 Z= 0.109 Angle : 0.575 9.557 28240 Z= 0.278 Chirality : 0.045 0.272 3336 Planarity : 0.004 0.049 3478 Dihedral : 6.769 64.354 4246 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.88 % Allowed : 13.42 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.17), residues: 2402 helix: -0.19 (0.28), residues: 393 sheet: -0.04 (0.21), residues: 621 loop : -1.35 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 64 TYR 0.014 0.001 TYR R 99 PHE 0.009 0.001 PHE O 391 TRP 0.013 0.001 TRP T 94 HIS 0.004 0.001 HIS O 339 Details of bonding type rmsd covalent geometry : bond 0.00254 (20593) covalent geometry : angle 0.55185 (27951) SS BOND : bond 0.00297 ( 41) SS BOND : angle 0.94201 ( 82) hydrogen bonds : bond 0.02958 ( 587) hydrogen bonds : angle 4.96640 ( 1617) link_ALPHA1-2 : bond 0.02030 ( 3) link_ALPHA1-2 : angle 4.40990 ( 9) link_ALPHA1-3 : bond 0.01086 ( 3) link_ALPHA1-3 : angle 1.90767 ( 9) link_ALPHA1-6 : bond 0.00485 ( 3) link_ALPHA1-6 : angle 1.49547 ( 9) link_BETA1-4 : bond 0.00383 ( 12) link_BETA1-4 : angle 1.33851 ( 36) link_NAG-ASN : bond 0.00263 ( 48) link_NAG-ASN : angle 1.77806 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 237 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 83 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7000 (tm-30) REVERT: G 341 ASN cc_start: 0.7818 (p0) cc_final: 0.7568 (p0) REVERT: N 365 ASN cc_start: 0.7394 (p0) cc_final: 0.7118 (p0) REVERT: N 435 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7573 (mtp) REVERT: H 542 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7926 (ptp-110) REVERT: I 515 ILE cc_start: 0.8118 (pt) cc_final: 0.7821 (pt) REVERT: T 32 ASP cc_start: 0.7279 (m-30) cc_final: 0.7067 (m-30) REVERT: T 78 LEU cc_start: 0.7056 (mp) cc_final: 0.6686 (tt) REVERT: P 64 ARG cc_start: 0.8237 (ttm110) cc_final: 0.7978 (ttp-170) REVERT: P 82 MET cc_start: 0.1427 (mmp) cc_final: 0.0555 (mtm) REVERT: P 100 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7279 (mtp180) REVERT: P 100 ARG cc_start: 0.7933 (ttt90) cc_final: 0.7520 (ttt90) outliers start: 40 outliers final: 25 residues processed: 261 average time/residue: 0.1424 time to fit residues: 55.7447 Evaluate side-chains 255 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 449 GLN Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 367 ILE Chi-restraints excluded: chain N residue 386 ASN Chi-restraints excluded: chain N residue 435 MET Chi-restraints excluded: chain N residue 508 THR Chi-restraints excluded: chain N residue 510 CYS Chi-restraints excluded: chain H residue 542 ARG Chi-restraints excluded: chain O residue 421 ASP Chi-restraints excluded: chain O residue 455 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 615 SER Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 89 GLN Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain P residue 100 ARG Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain R residue 32 HIS Chi-restraints excluded: chain R residue 72 GLU Chi-restraints excluded: chain R residue 99 TYR Chi-restraints excluded: chain U residue 65 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 147 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 209 optimal weight: 7.9990 chunk 198 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 186 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 156 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 212 GLN B 653 GLN ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 434 ASN ** H 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 HIS ** O 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 81 GLN T 37 GLN T 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.162136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127109 restraints weight = 25541.057| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.15 r_work: 0.3095 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 20703 Z= 0.322 Angle : 0.767 11.640 28240 Z= 0.376 Chirality : 0.052 0.396 3336 Planarity : 0.005 0.057 3478 Dihedral : 7.294 59.058 4246 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.21 % Allowed : 13.61 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.17), residues: 2402 helix: -0.71 (0.27), residues: 394 sheet: -0.29 (0.21), residues: 627 loop : -1.39 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 64 TYR 0.025 0.002 TYR R 99 PHE 0.023 0.002 PHE B 522 TRP 0.031 0.002 TRP Q 103 HIS 0.006 0.002 HIS O 225 Details of bonding type rmsd covalent geometry : bond 0.00783 (20593) covalent geometry : angle 0.74050 (27951) SS BOND : bond 0.00521 ( 41) SS BOND : angle 1.62339 ( 82) hydrogen bonds : bond 0.03858 ( 587) hydrogen bonds : angle 5.41035 ( 1617) link_ALPHA1-2 : bond 0.01875 ( 3) link_ALPHA1-2 : angle 4.72549 ( 9) link_ALPHA1-3 : bond 0.00984 ( 3) link_ALPHA1-3 : angle 2.20258 ( 9) link_ALPHA1-6 : bond 0.00371 ( 3) link_ALPHA1-6 : angle 1.62004 ( 9) link_BETA1-4 : bond 0.00352 ( 12) link_BETA1-4 : angle 1.44317 ( 36) link_NAG-ASN : bond 0.00510 ( 48) link_NAG-ASN : angle 2.27761 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 245 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 83 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: G 484 MET cc_start: 0.7804 (tpt) cc_final: 0.7101 (mtm) REVERT: N 99 ASN cc_start: 0.8452 (t0) cc_final: 0.8232 (t0) REVERT: N 365 ASN cc_start: 0.7522 (p0) cc_final: 0.7170 (p0) REVERT: N 435 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.8029 (mtm) REVERT: H 542 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8297 (ptp-110) REVERT: Q 81 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.6107 (mt0) REVERT: P 100 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7516 (mtp180) REVERT: R 82 MET cc_start: 0.7003 (mtm) cc_final: 0.5796 (mtm) outliers start: 47 outliers final: 35 residues processed: 272 average time/residue: 0.1326 time to fit residues: 54.5786 Evaluate side-chains 272 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 449 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 334 ASP Chi-restraints excluded: chain N residue 367 ILE Chi-restraints excluded: chain N residue 386 ASN Chi-restraints excluded: chain N residue 435 MET Chi-restraints excluded: chain N residue 508 THR Chi-restraints excluded: chain H residue 513 VAL Chi-restraints excluded: chain H residue 542 ARG Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 421 ASP Chi-restraints excluded: chain O residue 443 MET Chi-restraints excluded: chain O residue 455 VAL Chi-restraints excluded: chain I residue 535 MET Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 615 SER Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 89 GLN Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain P residue 100 ARG Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 32 HIS Chi-restraints excluded: chain R residue 72 GLU Chi-restraints excluded: chain R residue 99 TYR Chi-restraints excluded: chain U residue 37 GLN Chi-restraints excluded: chain U residue 65 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 180 optimal weight: 6.9990 chunk 188 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 212 GLN N 434 ASN ** H 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.166710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.134981 restraints weight = 25458.722| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.91 r_work: 0.3182 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 20703 Z= 0.133 Angle : 0.631 10.615 28240 Z= 0.307 Chirality : 0.046 0.302 3336 Planarity : 0.004 0.065 3478 Dihedral : 6.797 59.591 4246 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.93 % Allowed : 14.88 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.17), residues: 2402 helix: -0.35 (0.28), residues: 387 sheet: -0.16 (0.21), residues: 640 loop : -1.30 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 64 TYR 0.019 0.001 TYR R 99 PHE 0.014 0.001 PHE G 391 TRP 0.015 0.001 TRP T 94 HIS 0.004 0.001 HIS N 72 Details of bonding type rmsd covalent geometry : bond 0.00312 (20593) covalent geometry : angle 0.60422 (27951) SS BOND : bond 0.00376 ( 41) SS BOND : angle 1.33556 ( 82) hydrogen bonds : bond 0.03212 ( 587) hydrogen bonds : angle 5.08153 ( 1617) link_ALPHA1-2 : bond 0.02170 ( 3) link_ALPHA1-2 : angle 4.88387 ( 9) link_ALPHA1-3 : bond 0.01064 ( 3) link_ALPHA1-3 : angle 1.75877 ( 9) link_ALPHA1-6 : bond 0.00432 ( 3) link_ALPHA1-6 : angle 1.52700 ( 9) link_BETA1-4 : bond 0.00330 ( 12) link_BETA1-4 : angle 1.40179 ( 36) link_NAG-ASN : bond 0.00278 ( 48) link_NAG-ASN : angle 1.99053 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 239 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 83 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: G 341 ASN cc_start: 0.7981 (p0) cc_final: 0.7519 (p0) REVERT: G 484 MET cc_start: 0.7603 (tpt) cc_final: 0.7043 (mtm) REVERT: N 336 ARG cc_start: 0.8074 (mtm110) cc_final: 0.7449 (mtm110) REVERT: N 365 ASN cc_start: 0.7449 (p0) cc_final: 0.7120 (p0) REVERT: H 535 MET cc_start: 0.8301 (mpp) cc_final: 0.7962 (mtt) REVERT: H 542 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7986 (ptp-110) REVERT: H 657 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7475 (mp0) REVERT: T 32 ASP cc_start: 0.7521 (m-30) cc_final: 0.7289 (m-30) REVERT: T 89 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7928 (pp30) REVERT: P 64 ARG cc_start: 0.8495 (ttm110) cc_final: 0.8206 (ttp-170) REVERT: P 100 ARG cc_start: 0.7997 (ttt90) cc_final: 0.7539 (ttt90) REVERT: R 82 MET cc_start: 0.6658 (mtm) cc_final: 0.5499 (mtm) outliers start: 41 outliers final: 29 residues processed: 265 average time/residue: 0.1523 time to fit residues: 60.7371 Evaluate side-chains 263 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 449 GLN Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 CYS Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain N residue 367 ILE Chi-restraints excluded: chain N residue 386 ASN Chi-restraints excluded: chain N residue 508 THR Chi-restraints excluded: chain H residue 542 ARG Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 421 ASP Chi-restraints excluded: chain O residue 443 MET Chi-restraints excluded: chain O residue 455 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain T residue 76 ASN Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 89 GLN Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 32 HIS Chi-restraints excluded: chain R residue 72 GLU Chi-restraints excluded: chain R residue 99 TYR Chi-restraints excluded: chain U residue 37 GLN Chi-restraints excluded: chain U residue 65 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 66 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 193 optimal weight: 9.9990 chunk 189 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 164 optimal weight: 0.0870 chunk 95 optimal weight: 0.2980 chunk 47 optimal weight: 3.9990 overall best weight: 1.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 434 ASN ** H 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.165474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.130538 restraints weight = 25430.538| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.15 r_work: 0.3145 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20703 Z= 0.174 Angle : 0.645 11.121 28240 Z= 0.314 Chirality : 0.047 0.309 3336 Planarity : 0.004 0.059 3478 Dihedral : 6.668 59.548 4246 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.98 % Allowed : 14.97 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.17), residues: 2402 helix: -0.32 (0.28), residues: 387 sheet: -0.27 (0.21), residues: 615 loop : -1.29 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Q 64 TYR 0.018 0.001 TYR R 99 PHE 0.014 0.002 PHE B 522 TRP 0.014 0.001 TRP T 94 HIS 0.004 0.001 HIS N 225 Details of bonding type rmsd covalent geometry : bond 0.00419 (20593) covalent geometry : angle 0.61776 (27951) SS BOND : bond 0.00393 ( 41) SS BOND : angle 1.39023 ( 82) hydrogen bonds : bond 0.03191 ( 587) hydrogen bonds : angle 5.05189 ( 1617) link_ALPHA1-2 : bond 0.02040 ( 3) link_ALPHA1-2 : angle 4.85845 ( 9) link_ALPHA1-3 : bond 0.00958 ( 3) link_ALPHA1-3 : angle 1.76537 ( 9) link_ALPHA1-6 : bond 0.00370 ( 3) link_ALPHA1-6 : angle 1.56746 ( 9) link_BETA1-4 : bond 0.00313 ( 12) link_BETA1-4 : angle 1.36426 ( 36) link_NAG-ASN : bond 0.00313 ( 48) link_NAG-ASN : angle 2.01418 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 233 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 83 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: G 341 ASN cc_start: 0.8142 (p0) cc_final: 0.7725 (p0) REVERT: G 484 MET cc_start: 0.7622 (tpt) cc_final: 0.6975 (mtm) REVERT: N 365 ASN cc_start: 0.7458 (p0) cc_final: 0.7133 (p0) REVERT: N 483 ASP cc_start: 0.6604 (t0) cc_final: 0.6375 (t0) REVERT: H 535 MET cc_start: 0.8381 (mpp) cc_final: 0.8099 (mtt) REVERT: H 542 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8118 (ptp-110) REVERT: H 657 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7461 (mp0) REVERT: P 64 ARG cc_start: 0.8363 (ttm110) cc_final: 0.8043 (ttp-170) REVERT: R 82 MET cc_start: 0.6810 (mtm) cc_final: 0.5621 (mtm) REVERT: R 83 ARG cc_start: 0.7487 (ttm110) cc_final: 0.7257 (ttm110) outliers start: 42 outliers final: 37 residues processed: 262 average time/residue: 0.1643 time to fit residues: 64.1607 Evaluate side-chains 270 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 449 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 CYS Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain N residue 334 ASP Chi-restraints excluded: chain N residue 367 ILE Chi-restraints excluded: chain N residue 386 ASN Chi-restraints excluded: chain N residue 508 THR Chi-restraints excluded: chain H residue 513 VAL Chi-restraints excluded: chain H residue 542 ARG Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 421 ASP Chi-restraints excluded: chain O residue 443 MET Chi-restraints excluded: chain O residue 455 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain T residue 76 ASN Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 89 GLN Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 32 HIS Chi-restraints excluded: chain R residue 72 GLU Chi-restraints excluded: chain R residue 99 TYR Chi-restraints excluded: chain U residue 37 GLN Chi-restraints excluded: chain U residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 128 optimal weight: 0.9980 chunk 194 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 201 optimal weight: 20.0000 chunk 182 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 187 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 214 optimal weight: 50.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 114 GLN ** G 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 434 ASN ** H 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.163935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.129409 restraints weight = 25634.899| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.19 r_work: 0.3122 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20703 Z= 0.214 Angle : 0.673 10.966 28240 Z= 0.328 Chirality : 0.048 0.337 3336 Planarity : 0.004 0.061 3478 Dihedral : 6.740 59.656 4246 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.07 % Allowed : 15.16 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.17), residues: 2402 helix: -0.37 (0.28), residues: 382 sheet: -0.16 (0.21), residues: 637 loop : -1.32 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 64 TYR 0.020 0.002 TYR R 99 PHE 0.017 0.002 PHE B 522 TRP 0.013 0.001 TRP I 571 HIS 0.005 0.001 HIS G 383 Details of bonding type rmsd covalent geometry : bond 0.00520 (20593) covalent geometry : angle 0.64524 (27951) SS BOND : bond 0.00426 ( 41) SS BOND : angle 1.43430 ( 82) hydrogen bonds : bond 0.03304 ( 587) hydrogen bonds : angle 5.09914 ( 1617) link_ALPHA1-2 : bond 0.02007 ( 3) link_ALPHA1-2 : angle 4.89579 ( 9) link_ALPHA1-3 : bond 0.00955 ( 3) link_ALPHA1-3 : angle 1.77318 ( 9) link_ALPHA1-6 : bond 0.00353 ( 3) link_ALPHA1-6 : angle 1.59776 ( 9) link_BETA1-4 : bond 0.00313 ( 12) link_BETA1-4 : angle 1.37445 ( 36) link_NAG-ASN : bond 0.00362 ( 48) link_NAG-ASN : angle 2.10171 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4804 Ramachandran restraints generated. 2402 Oldfield, 0 Emsley, 2402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 238 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 83 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7774 (tm-30) REVERT: G 139 THR cc_start: 0.7547 (OUTLIER) cc_final: 0.7156 (m) REVERT: G 341 ASN cc_start: 0.8161 (p0) cc_final: 0.7781 (p0) REVERT: G 484 MET cc_start: 0.7668 (tpt) cc_final: 0.7025 (mtm) REVERT: N 336 ARG cc_start: 0.8107 (mtm110) cc_final: 0.7473 (mtm110) REVERT: N 365 ASN cc_start: 0.7486 (p0) cc_final: 0.7197 (p0) REVERT: H 535 MET cc_start: 0.8377 (mpp) cc_final: 0.8159 (mtt) REVERT: H 542 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8196 (ptp-110) REVERT: H 657 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7433 (mp0) REVERT: Q 79 TYR cc_start: 0.8064 (m-80) cc_final: 0.7764 (m-80) REVERT: P 100 ARG cc_start: 0.7999 (ttt90) cc_final: 0.7405 (ttt90) REVERT: R 82 MET cc_start: 0.6818 (mtm) cc_final: 0.5650 (mtm) REVERT: R 83 ARG cc_start: 0.7507 (ttm110) cc_final: 0.7274 (ttm110) outliers start: 44 outliers final: 34 residues processed: 270 average time/residue: 0.1703 time to fit residues: 68.3559 Evaluate side-chains 271 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 449 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 CYS Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain N residue 334 ASP Chi-restraints excluded: chain N residue 367 ILE Chi-restraints excluded: chain N residue 386 ASN Chi-restraints excluded: chain N residue 508 THR Chi-restraints excluded: chain H residue 513 VAL Chi-restraints excluded: chain H residue 542 ARG Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 329 THR Chi-restraints excluded: chain O residue 443 MET Chi-restraints excluded: chain O residue 455 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 89 GLN Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 32 HIS Chi-restraints excluded: chain R residue 72 GLU Chi-restraints excluded: chain R residue 99 TYR Chi-restraints excluded: chain U residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 48 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 72 optimal weight: 0.0570 chunk 21 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 114 GLN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 434 ASN ** H 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.165700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.129479 restraints weight = 25378.048| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.25 r_work: 0.3177 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20703 Z= 0.124 Angle : 0.608 10.968 28240 Z= 0.295 Chirality : 0.045 0.280 3336 Planarity : 0.004 0.060 3478 Dihedral : 6.415 58.188 4246 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.55 % Allowed : 15.63 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.17), residues: 2402 helix: -0.05 (0.29), residues: 369 sheet: -0.03 (0.21), residues: 636 loop : -1.26 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG Q 64 TYR 0.015 0.001 TYR R 99 PHE 0.012 0.001 PHE G 391 TRP 0.014 0.001 TRP T 94 HIS 0.004 0.001 HIS N 225 Details of bonding type rmsd covalent geometry : bond 0.00294 (20593) covalent geometry : angle 0.58125 (27951) SS BOND : bond 0.00336 ( 41) SS BOND : angle 1.17952 ( 82) hydrogen bonds : bond 0.02978 ( 587) hydrogen bonds : angle 4.91422 ( 1617) link_ALPHA1-2 : bond 0.02082 ( 3) link_ALPHA1-2 : angle 4.90214 ( 9) link_ALPHA1-3 : bond 0.00987 ( 3) link_ALPHA1-3 : angle 1.55427 ( 9) link_ALPHA1-6 : bond 0.00387 ( 3) link_ALPHA1-6 : angle 1.53714 ( 9) link_BETA1-4 : bond 0.00317 ( 12) link_BETA1-4 : angle 1.38479 ( 36) link_NAG-ASN : bond 0.00262 ( 48) link_NAG-ASN : angle 1.94986 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4673.89 seconds wall clock time: 81 minutes 1.68 seconds (4861.68 seconds total)