Starting phenix.real_space_refine on Wed May 28 18:36:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tjs_41310/05_2025/8tjs_41310.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tjs_41310/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tjs_41310/05_2025/8tjs_41310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tjs_41310/05_2025/8tjs_41310.map" model { file = "/net/cci-nas-00/data/ceres_data/8tjs_41310/05_2025/8tjs_41310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tjs_41310/05_2025/8tjs_41310.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.69, per 1000 atoms: 0.58 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: 5.40 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.83 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: 7.35 Time building geometry restraints manager: 6.14 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: 0.00 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: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.010 Extract box with map and model: 0.800 Check model and map are aligned: 0.130 Set scattering table: 0.210 Process input model: 45.560 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.130 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.320 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.057 0.002 TRP P 103 HIS 0.009 0.001 HIS N 225 PHE 0.012 0.002 PHE N 53 TYR 0.036 0.002 TYR R 99 ARG 0.021 0.001 ARG R 64 Details of bonding type rmsd link_NAG-ASN : bond 0.00648 ( 48) link_NAG-ASN : angle 3.27105 ( 144) 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_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) hydrogen bonds : bond 0.24947 ( 587) hydrogen bonds : angle 9.92639 ( 1617) SS BOND : bond 0.04333 ( 41) SS BOND : angle 5.45442 ( 82) covalent geometry : bond 0.00606 (20593) covalent geometry : angle 0.94932 (27951) *********************** 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 : 2.059 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: 0.7145 (m-40) REVERT: G 476 THR cc_start: 0.8395 (p) cc_final: 0.8019 (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: 0.6740 (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: 0.7070 (mttt) outliers start: 15 outliers final: 2 residues processed: 320 average time/residue: 0.3271 time to fit residues: 158.9176 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 : 2.420 ------------------------------------------------------------------------------- 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 202 optimal weight: 20.0000 chunk 181 optimal weight: 0.3980 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 188 optimal weight: 9.9990 chunk 72 optimal weight: 0.0970 chunk 114 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 67 ASN G 137 ASN G 487 ASN N 82 GLN N 296 GLN N 357 GLN H 607 ASN ** H 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 656 ASN O 136 ASN Q 3 HIS T 38 GLN T 89 GLN S 37 GLN ** U 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.173022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.138087 restraints weight = 25365.658| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.10 r_work: 0.3283 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1250 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= 0.131 Angle : 0.627 9.800 28240 Z= 0.312 Chirality : 0.046 0.313 3336 Planarity : 0.004 0.049 3478 Dihedral : 10.780 97.100 4253 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.99 % Allowed : 7.30 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.16), residues: 2402 helix: -1.46 (0.25), residues: 389 sheet: -0.20 (0.20), residues: 685 loop : -1.77 (0.15), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP T 94 HIS 0.003 0.001 HIS G 383 PHE 0.011 0.001 PHE O 53 TYR 0.021 0.001 TYR R 99 ARG 0.004 0.000 ARG R 64 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 48) link_NAG-ASN : angle 1.94954 ( 144) link_ALPHA1-6 : bond 0.00490 ( 3) link_ALPHA1-6 : angle 2.01524 ( 9) link_BETA1-4 : bond 0.00412 ( 12) link_BETA1-4 : angle 1.62565 ( 36) link_ALPHA1-2 : bond 0.00984 ( 3) link_ALPHA1-2 : angle 3.29309 ( 9) link_ALPHA1-3 : bond 0.00746 ( 3) link_ALPHA1-3 : angle 2.81322 ( 9) hydrogen bonds : bond 0.04360 ( 587) hydrogen bonds : angle 6.40705 ( 1617) SS BOND : bond 0.00401 ( 41) SS BOND : angle 1.11869 ( 82) covalent geometry : bond 0.00299 (20593) covalent geometry : angle 0.60290 (27951) *********************** 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 291 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 270 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 365 ASN cc_start: 0.7496 (p0) cc_final: 0.7239 (p0) REVERT: I 515 ILE cc_start: 0.8205 (pt) cc_final: 0.7902 (pt) REVERT: Q 64 ARG cc_start: 0.8346 (ttm110) cc_final: 0.8039 (ttm110) outliers start: 21 outliers final: 12 residues processed: 285 average time/residue: 0.3427 time to fit residues: 144.8733 Evaluate side-chains 260 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 248 time to evaluate : 1.948 ------------------------------------------------------------------------------- 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 332 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 O residue 421 ASP 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 46 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 232 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 434 ASN ** H 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 HIS 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 = 0.3898 r_free = 0.3898 target = 0.166336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.134473 restraints weight = 25207.106| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.88 r_work: 0.3212 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20703 Z= 0.206 Angle : 0.668 10.453 28240 Z= 0.328 Chirality : 0.048 0.344 3336 Planarity : 0.004 0.050 3478 Dihedral : 9.457 96.357 4248 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.32 % Allowed : 9.98 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.16), residues: 2402 helix: -1.01 (0.26), residues: 399 sheet: -0.40 (0.20), residues: 659 loop : -1.52 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP Q 103 HIS 0.004 0.001 HIS N 339 PHE 0.015 0.002 PHE B 522 TYR 0.021 0.001 TYR R 99 ARG 0.008 0.001 ARG P 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 48) link_NAG-ASN : angle 1.98701 ( 144) link_ALPHA1-6 : bond 0.01127 ( 3) link_ALPHA1-6 : angle 2.03910 ( 9) link_BETA1-4 : bond 0.00489 ( 12) link_BETA1-4 : angle 1.44405 ( 36) link_ALPHA1-2 : bond 0.01302 ( 3) link_ALPHA1-2 : angle 3.37160 ( 9) link_ALPHA1-3 : bond 0.00965 ( 3) link_ALPHA1-3 : angle 1.90093 ( 9) hydrogen bonds : bond 0.03952 ( 587) hydrogen bonds : angle 5.81734 ( 1617) SS BOND : bond 0.00491 ( 41) SS BOND : angle 1.44963 ( 82) covalent geometry : bond 0.00493 (20593) covalent geometry : angle 0.64412 (27951) *********************** 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 285 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 257 time to evaluate : 1.970 Fit side-chains revert: symmetry clash REVERT: G 179 LEU cc_start: 0.8923 (mt) cc_final: 0.8573 (mp) REVERT: N 365 ASN cc_start: 0.7577 (p0) cc_final: 0.7323 (p0) REVERT: N 483 ASP cc_start: 0.6417 (t0) cc_final: 0.6192 (t0) REVERT: O 280 MET cc_start: 0.8421 (mmm) cc_final: 0.8221 (mmt) REVERT: I 515 ILE cc_start: 0.8194 (pt) cc_final: 0.7898 (pt) REVERT: Q 64 ARG cc_start: 0.8385 (ttm110) cc_final: 0.8079 (ttm110) REVERT: Q 72 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8102 (mt-10) REVERT: P 82 MET cc_start: 0.1420 (mmp) cc_final: 0.0830 (mtm) REVERT: P 100 ARG cc_start: 0.7948 (ttt90) cc_final: 0.7621 (ttt90) outliers start: 28 outliers final: 18 residues processed: 273 average time/residue: 0.3440 time to fit residues: 141.3067 Evaluate side-chains 261 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 243 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 449 GLN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain N residue 89 VAL 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 229 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 201 optimal weight: 20.0000 chunk 137 optimal weight: 0.7980 chunk 93 optimal weight: 8.9990 chunk 211 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 217 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN B 653 GLN ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 ASN N 341 ASN N 434 ASN ** H 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 HIS ** I 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 81 GLN T 89 GLN ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.159947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.122363 restraints weight = 25619.490| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.42 r_work: 0.3057 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 20703 Z= 0.367 Angle : 0.807 12.230 28240 Z= 0.397 Chirality : 0.053 0.430 3336 Planarity : 0.005 0.060 3478 Dihedral : 8.910 96.869 4248 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.26 % Allowed : 12.01 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.16), residues: 2402 helix: -1.09 (0.26), residues: 381 sheet: -0.51 (0.21), residues: 605 loop : -1.57 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP Q 103 HIS 0.007 0.002 HIS Q 32 PHE 0.024 0.002 PHE B 522 TYR 0.028 0.002 TYR R 99 ARG 0.009 0.001 ARG P 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00577 ( 48) link_NAG-ASN : angle 2.39546 ( 144) link_ALPHA1-6 : bond 0.00692 ( 3) link_ALPHA1-6 : angle 1.68073 ( 9) link_BETA1-4 : bond 0.00388 ( 12) link_BETA1-4 : angle 1.53431 ( 36) link_ALPHA1-2 : bond 0.01214 ( 3) link_ALPHA1-2 : angle 3.95497 ( 9) link_ALPHA1-3 : bond 0.00901 ( 3) link_ALPHA1-3 : angle 2.38467 ( 9) hydrogen bonds : bond 0.04180 ( 587) hydrogen bonds : angle 5.83674 ( 1617) SS BOND : bond 0.00630 ( 41) SS BOND : angle 1.87778 ( 82) covalent geometry : bond 0.00891 (20593) covalent geometry : angle 0.77931 (27951) *********************** 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 297 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 249 time to evaluate : 2.159 Fit side-chains revert: symmetry clash REVERT: G 139 THR cc_start: 0.7423 (m) cc_final: 0.7174 (m) REVERT: G 206 ASN cc_start: 0.8831 (t0) cc_final: 0.8524 (t0) REVERT: G 484 MET cc_start: 0.7468 (tpt) cc_final: 0.7221 (mtm) REVERT: N 365 ASN cc_start: 0.7520 (p0) cc_final: 0.7192 (p0) REVERT: N 501 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7213 (mt-10) REVERT: Q 64 ARG cc_start: 0.8360 (ttm110) cc_final: 0.8064 (ttm110) REVERT: Q 77 THR cc_start: 0.8535 (p) cc_final: 0.8295 (p) REVERT: Q 81 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6192 (mt0) REVERT: P 82 MET cc_start: 0.1420 (mmp) cc_final: 0.0789 (mtm) outliers start: 48 outliers final: 31 residues processed: 279 average time/residue: 0.3338 time to fit residues: 140.9572 Evaluate side-chains 266 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 233 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 207 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 270 LEU Chi-restraints excluded: chain N residue 334 ASP Chi-restraints excluded: chain N residue 386 ASN Chi-restraints excluded: chain N residue 501 GLU Chi-restraints excluded: chain N residue 508 THR Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 421 ASP 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 53 ILE Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain T residue 47 LEU 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 34 VAL Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain R residue 18 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 67 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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** I 625 ASN Q 81 GLN T 37 GLN T 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.163998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.127420 restraints weight = 25482.276| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.21 r_work: 0.3143 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20703 Z= 0.155 Angle : 0.645 10.173 28240 Z= 0.315 Chirality : 0.047 0.340 3336 Planarity : 0.004 0.050 3478 Dihedral : 8.111 91.821 4248 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.02 % Allowed : 13.70 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.16), residues: 2402 helix: -0.72 (0.27), residues: 388 sheet: -0.36 (0.21), residues: 610 loop : -1.44 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP T 94 HIS 0.004 0.001 HIS N 225 PHE 0.013 0.001 PHE B 522 TYR 0.022 0.001 TYR R 99 ARG 0.009 0.000 ARG R 64 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 48) link_NAG-ASN : angle 2.05527 ( 144) link_ALPHA1-6 : bond 0.00592 ( 3) link_ALPHA1-6 : angle 1.47105 ( 9) link_BETA1-4 : bond 0.00358 ( 12) link_BETA1-4 : angle 1.39024 ( 36) link_ALPHA1-2 : bond 0.01586 ( 3) link_ALPHA1-2 : angle 4.00539 ( 9) link_ALPHA1-3 : bond 0.01074 ( 3) link_ALPHA1-3 : angle 1.92618 ( 9) hydrogen bonds : bond 0.03363 ( 587) hydrogen bonds : angle 5.43751 ( 1617) SS BOND : bond 0.00452 ( 41) SS BOND : angle 1.43118 ( 82) covalent geometry : bond 0.00365 (20593) covalent geometry : angle 0.61898 (27951) *********************** 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 282 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 239 time to evaluate : 2.153 Fit side-chains revert: symmetry clash REVERT: G 206 ASN cc_start: 0.8805 (t0) cc_final: 0.8512 (t0) REVERT: G 484 MET cc_start: 0.7593 (tpt) cc_final: 0.7066 (mtm) REVERT: N 365 ASN cc_start: 0.7548 (p0) cc_final: 0.7220 (p0) REVERT: N 483 ASP cc_start: 0.6619 (t0) cc_final: 0.6417 (t0) REVERT: I 515 ILE cc_start: 0.8382 (pt) cc_final: 0.8132 (pt) REVERT: Q 64 ARG cc_start: 0.8314 (ttm110) cc_final: 0.8041 (ttm110) REVERT: Q 77 THR cc_start: 0.8636 (p) cc_final: 0.8381 (p) REVERT: Q 81 GLN cc_start: 0.6898 (OUTLIER) cc_final: 0.6568 (mt0) REVERT: Q 101 ASP cc_start: 0.8468 (m-30) cc_final: 0.8208 (m-30) REVERT: P 82 MET cc_start: 0.1556 (mmp) cc_final: 0.0858 (mtm) outliers start: 43 outliers final: 26 residues processed: 263 average time/residue: 0.3202 time to fit residues: 128.3191 Evaluate side-chains 249 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 222 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 449 GLN Chi-restraints excluded: chain N residue 89 VAL 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 592 LEU 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 636 SER Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain Q residue 81 GLN 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 168 optimal weight: 0.9990 chunk 204 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 114 GLN N 341 ASN N 434 ASN ** H 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.165806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.134835 restraints weight = 25485.975| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.91 r_work: 0.3176 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20703 Z= 0.145 Angle : 0.624 9.866 28240 Z= 0.304 Chirality : 0.046 0.309 3336 Planarity : 0.004 0.048 3478 Dihedral : 7.595 85.879 4248 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.88 % Allowed : 14.74 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.17), residues: 2402 helix: -0.51 (0.28), residues: 388 sheet: -0.36 (0.22), residues: 584 loop : -1.37 (0.15), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP T 94 HIS 0.004 0.001 HIS N 225 PHE 0.010 0.001 PHE O 391 TYR 0.018 0.001 TYR R 99 ARG 0.012 0.000 ARG R 64 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 48) link_NAG-ASN : angle 1.98433 ( 144) link_ALPHA1-6 : bond 0.00527 ( 3) link_ALPHA1-6 : angle 1.50395 ( 9) link_BETA1-4 : bond 0.00357 ( 12) link_BETA1-4 : angle 1.33499 ( 36) link_ALPHA1-2 : bond 0.01701 ( 3) link_ALPHA1-2 : angle 4.07327 ( 9) link_ALPHA1-3 : bond 0.01046 ( 3) link_ALPHA1-3 : angle 1.84075 ( 9) hydrogen bonds : bond 0.03199 ( 587) hydrogen bonds : angle 5.25035 ( 1617) SS BOND : bond 0.00446 ( 41) SS BOND : angle 1.34521 ( 82) covalent geometry : bond 0.00346 (20593) covalent geometry : angle 0.59873 (27951) *********************** 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 269 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 229 time to evaluate : 1.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 83 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7743 (tm-30) REVERT: G 206 ASN cc_start: 0.8764 (t0) cc_final: 0.8473 (t0) REVERT: G 484 MET cc_start: 0.7514 (tpt) cc_final: 0.7108 (mtm) REVERT: N 161 MET cc_start: 0.8558 (ttm) cc_final: 0.8195 (ttm) REVERT: N 365 ASN cc_start: 0.7503 (p0) cc_final: 0.7194 (p0) REVERT: N 483 ASP cc_start: 0.6538 (t0) cc_final: 0.6330 (t0) REVERT: I 515 ILE cc_start: 0.8405 (pt) cc_final: 0.8131 (pt) REVERT: Q 64 ARG cc_start: 0.8203 (ttm110) cc_final: 0.7987 (ttm110) REVERT: P 64 ARG cc_start: 0.8216 (ttm110) cc_final: 0.7959 (ttp-170) REVERT: P 82 MET cc_start: 0.1553 (mmp) cc_final: 0.1004 (mtm) outliers start: 40 outliers final: 32 residues processed: 253 average time/residue: 0.3200 time to fit residues: 123.0508 Evaluate side-chains 254 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 252 SER 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 126 CYS 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 592 LEU Chi-restraints excluded: chain H residue 599 SER 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 636 SER Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 53 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 106 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 231 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 201 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 212 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 434 ASN N 434 ASN ** H 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 81 GLN T 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.160457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121599 restraints weight = 25517.998| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.53 r_work: 0.3057 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 20703 Z= 0.282 Angle : 0.722 11.394 28240 Z= 0.353 Chirality : 0.050 0.384 3336 Planarity : 0.005 0.057 3478 Dihedral : 7.782 83.883 4246 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.26 % Allowed : 15.07 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.17), residues: 2402 helix: -0.70 (0.27), residues: 383 sheet: -0.38 (0.21), residues: 611 loop : -1.41 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP T 94 HIS 0.006 0.001 HIS O 383 PHE 0.019 0.002 PHE B 522 TYR 0.024 0.002 TYR R 99 ARG 0.012 0.001 ARG R 64 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 48) link_NAG-ASN : angle 2.25801 ( 144) link_ALPHA1-6 : bond 0.00450 ( 3) link_ALPHA1-6 : angle 1.57396 ( 9) link_BETA1-4 : bond 0.00355 ( 12) link_BETA1-4 : angle 1.37658 ( 36) link_ALPHA1-2 : bond 0.01635 ( 3) link_ALPHA1-2 : angle 4.18289 ( 9) link_ALPHA1-3 : bond 0.00967 ( 3) link_ALPHA1-3 : angle 1.88248 ( 9) hydrogen bonds : bond 0.03637 ( 587) hydrogen bonds : angle 5.40917 ( 1617) SS BOND : bond 0.00503 ( 41) SS BOND : angle 1.59004 ( 82) covalent geometry : bond 0.00681 (20593) covalent geometry : angle 0.69511 (27951) *********************** 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 287 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 239 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 83 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: G 484 MET cc_start: 0.7440 (tpt) cc_final: 0.7089 (mtm) REVERT: N 161 MET cc_start: 0.8489 (ttm) cc_final: 0.8081 (ttm) REVERT: N 365 ASN cc_start: 0.7474 (p0) cc_final: 0.7158 (p0) REVERT: H 657 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7352 (mp0) REVERT: Q 64 ARG cc_start: 0.8150 (ttm110) cc_final: 0.7942 (ttm110) REVERT: Q 72 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7823 (mt-10) REVERT: Q 79 TYR cc_start: 0.7996 (m-80) cc_final: 0.7584 (m-80) outliers start: 48 outliers final: 36 residues processed: 269 average time/residue: 0.3396 time to fit residues: 139.1422 Evaluate side-chains 264 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 227 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 182 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 449 GLN Chi-restraints excluded: chain B residue 528 SER 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 361 HIS 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 O residue 245 THR Chi-restraints excluded: chain O residue 329 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 Q residue 23 VAL Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain T residue 47 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 195 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 140 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 186 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** Q 81 GLN T 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.165623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.131677 restraints weight = 25671.166| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.09 r_work: 0.3147 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20703 Z= 0.133 Angle : 0.623 9.818 28240 Z= 0.302 Chirality : 0.046 0.308 3336 Planarity : 0.004 0.052 3478 Dihedral : 7.252 78.186 4246 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.93 % Allowed : 15.63 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.17), residues: 2402 helix: -0.38 (0.28), residues: 377 sheet: -0.20 (0.21), residues: 627 loop : -1.36 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP T 94 HIS 0.004 0.001 HIS N 225 PHE 0.014 0.001 PHE G 391 TYR 0.018 0.001 TYR R 99 ARG 0.012 0.000 ARG R 64 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 48) link_NAG-ASN : angle 2.01652 ( 144) link_ALPHA1-6 : bond 0.00438 ( 3) link_ALPHA1-6 : angle 1.52159 ( 9) link_BETA1-4 : bond 0.00351 ( 12) link_BETA1-4 : angle 1.33701 ( 36) link_ALPHA1-2 : bond 0.01854 ( 3) link_ALPHA1-2 : angle 4.27507 ( 9) link_ALPHA1-3 : bond 0.01046 ( 3) link_ALPHA1-3 : angle 1.54868 ( 9) hydrogen bonds : bond 0.03102 ( 587) hydrogen bonds : angle 5.16281 ( 1617) SS BOND : bond 0.00360 ( 41) SS BOND : angle 1.24528 ( 82) covalent geometry : bond 0.00313 (20593) covalent geometry : angle 0.59792 (27951) *********************** 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 272 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 231 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 83 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7779 (tm-30) REVERT: G 484 MET cc_start: 0.7480 (tpt) cc_final: 0.7012 (mtm) REVERT: N 161 MET cc_start: 0.8631 (ttm) cc_final: 0.8199 (ttm) REVERT: N 365 ASN cc_start: 0.7517 (p0) cc_final: 0.7246 (p0) REVERT: H 657 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7405 (mp0) REVERT: Q 101 ASP cc_start: 0.8349 (m-30) cc_final: 0.8091 (m-30) REVERT: P 64 ARG cc_start: 0.8168 (ttm110) cc_final: 0.7933 (ttp-170) REVERT: P 82 MET cc_start: 0.1103 (mmm) cc_final: -0.0035 (mtm) outliers start: 41 outliers final: 31 residues processed: 258 average time/residue: 0.3352 time to fit residues: 131.5750 Evaluate side-chains 257 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 332 ILE 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 334 ASP Chi-restraints excluded: chain N residue 361 HIS 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 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 53 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 205 optimal weight: 20.0000 chunk 130 optimal weight: 0.8980 chunk 226 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 214 optimal weight: 20.0000 chunk 126 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 chunk 12 optimal weight: 0.0670 chunk 139 optimal weight: 0.1980 chunk 17 optimal weight: 0.2980 chunk 175 optimal weight: 0.3980 overall best weight: 0.3718 ------------------------------------------------------------------------------- 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** N 434 ASN ** H 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.167950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.133570 restraints weight = 25580.163| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.11 r_work: 0.3191 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20703 Z= 0.106 Angle : 0.599 9.740 28240 Z= 0.290 Chirality : 0.045 0.254 3336 Planarity : 0.004 0.057 3478 Dihedral : 6.641 69.912 4246 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.88 % Allowed : 15.77 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.17), residues: 2402 helix: -0.28 (0.28), residues: 389 sheet: -0.06 (0.21), residues: 621 loop : -1.32 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP T 94 HIS 0.003 0.001 HIS N 225 PHE 0.012 0.001 PHE G 391 TYR 0.013 0.001 TYR R 33 ARG 0.015 0.000 ARG Q 64 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 48) link_NAG-ASN : angle 1.88043 ( 144) link_ALPHA1-6 : bond 0.00369 ( 3) link_ALPHA1-6 : angle 1.51481 ( 9) link_BETA1-4 : bond 0.00365 ( 12) link_BETA1-4 : angle 1.31504 ( 36) link_ALPHA1-2 : bond 0.01901 ( 3) link_ALPHA1-2 : angle 4.43997 ( 9) link_ALPHA1-3 : bond 0.01047 ( 3) link_ALPHA1-3 : angle 1.46238 ( 9) hydrogen bonds : bond 0.02922 ( 587) hydrogen bonds : angle 4.92970 ( 1617) SS BOND : bond 0.00347 ( 41) SS BOND : angle 1.11986 ( 82) covalent geometry : bond 0.00246 (20593) covalent geometry : angle 0.57510 (27951) *********************** 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 270 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 230 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 83 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7684 (tm-30) REVERT: G 484 MET cc_start: 0.7482 (tpt) cc_final: 0.6979 (mtm) REVERT: N 161 MET cc_start: 0.8561 (ttm) cc_final: 0.8124 (ttm) REVERT: N 336 ARG cc_start: 0.8117 (mtm110) cc_final: 0.7474 (mtm110) REVERT: N 365 ASN cc_start: 0.7481 (p0) cc_final: 0.7217 (p0) REVERT: N 483 ASP cc_start: 0.6732 (t0) cc_final: 0.6531 (t0) REVERT: H 535 MET cc_start: 0.8326 (mpp) cc_final: 0.7965 (mtt) REVERT: H 657 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7456 (mp0) REVERT: O 184 ILE cc_start: 0.8837 (tp) cc_final: 0.8637 (tp) REVERT: Q 101 ASP cc_start: 0.8328 (m-30) cc_final: 0.8080 (m-30) REVERT: T 89 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8410 (pp30) REVERT: P 64 ARG cc_start: 0.8203 (ttm110) cc_final: 0.7965 (ttp-170) REVERT: P 82 MET cc_start: 0.1099 (mmm) cc_final: 0.0130 (mtm) REVERT: R 82 MET cc_start: 0.6049 (mtt) cc_final: 0.5570 (mtt) outliers start: 40 outliers final: 29 residues processed: 257 average time/residue: 0.3702 time to fit residues: 145.9561 Evaluate side-chains 255 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain B residue 569 THR 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 334 ASP Chi-restraints excluded: chain N residue 361 HIS 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 599 SER Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 329 THR 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 Q residue 5 VAL Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain T residue 37 GLN 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 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 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 230 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 205 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 chunk 234 optimal weight: 0.0670 chunk 5 optimal weight: 3.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.164961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.127747 restraints weight = 25451.710| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.36 r_work: 0.3141 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3023 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= 0.141 Angle : 0.610 10.364 28240 Z= 0.296 Chirality : 0.045 0.282 3336 Planarity : 0.004 0.059 3478 Dihedral : 6.508 64.770 4246 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.65 % Allowed : 16.15 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.17), residues: 2402 helix: -0.16 (0.29), residues: 377 sheet: -0.17 (0.21), residues: 603 loop : -1.27 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP T 94 HIS 0.004 0.001 HIS N 225 PHE 0.011 0.001 PHE B 522 TYR 0.015 0.001 TYR R 99 ARG 0.014 0.000 ARG R 64 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 48) link_NAG-ASN : angle 1.90285 ( 144) link_ALPHA1-6 : bond 0.00356 ( 3) link_ALPHA1-6 : angle 1.55786 ( 9) link_BETA1-4 : bond 0.00352 ( 12) link_BETA1-4 : angle 1.29869 ( 36) link_ALPHA1-2 : bond 0.02021 ( 3) link_ALPHA1-2 : angle 4.54628 ( 9) link_ALPHA1-3 : bond 0.00990 ( 3) link_ALPHA1-3 : angle 1.49157 ( 9) hydrogen bonds : bond 0.03007 ( 587) hydrogen bonds : angle 4.92900 ( 1617) SS BOND : bond 0.00349 ( 41) SS BOND : angle 1.18006 ( 82) covalent geometry : bond 0.00339 (20593) covalent geometry : angle 0.58609 (27951) ********************** 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 257 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 222 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 83 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: G 206 ASN cc_start: 0.8584 (t0) cc_final: 0.8237 (t0) REVERT: G 484 MET cc_start: 0.7237 (tpt) cc_final: 0.7014 (mtm) REVERT: N 161 MET cc_start: 0.8339 (ttm) cc_final: 0.7902 (ttm) REVERT: N 336 ARG cc_start: 0.8007 (mtm110) cc_final: 0.7395 (mtm110) REVERT: N 365 ASN cc_start: 0.7416 (p0) cc_final: 0.7154 (p0) REVERT: H 657 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7426 (mp0) REVERT: Q 72 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7648 (mt-10) REVERT: Q 79 TYR cc_start: 0.7978 (m-80) cc_final: 0.7740 (m-80) REVERT: Q 101 ASP cc_start: 0.8196 (m-30) cc_final: 0.7941 (m-30) REVERT: T 89 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8348 (pp30) REVERT: P 64 ARG cc_start: 0.8214 (ttm110) cc_final: 0.7987 (ttp-170) REVERT: P 82 MET cc_start: 0.1060 (mmm) cc_final: 0.0116 (mtm) REVERT: R 82 MET cc_start: 0.6057 (mtt) cc_final: 0.5584 (mtt) REVERT: U 24 ARG cc_start: 0.8363 (ptp-110) cc_final: 0.8030 (mtm110) outliers start: 35 outliers final: 29 residues processed: 245 average time/residue: 0.3319 time to fit residues: 124.2651 Evaluate side-chains 251 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 252 SER 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 334 ASP Chi-restraints excluded: chain N residue 361 HIS 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 599 SER Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 329 THR 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 37 GLN 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 34 VAL Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain R residue 21 SER 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 35 optimal weight: 0.0050 chunk 120 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 206 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 224 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- 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 ** 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 = 0.3895 r_free = 0.3895 target = 0.166874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.131037 restraints weight = 25686.314| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.26 r_work: 0.3179 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3047 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= 0.128 Angle : 0.603 10.552 28240 Z= 0.292 Chirality : 0.045 0.295 3336 Planarity : 0.004 0.059 3478 Dihedral : 6.350 60.214 4246 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.60 % Allowed : 16.48 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.17), residues: 2402 helix: -0.11 (0.29), residues: 377 sheet: -0.08 (0.20), residues: 674 loop : -1.26 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP T 94 HIS 0.004 0.001 HIS N 225 PHE 0.011 0.001 PHE G 391 TYR 0.014 0.001 TYR R 99 ARG 0.014 0.000 ARG R 64 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 48) link_NAG-ASN : angle 1.87765 ( 144) link_ALPHA1-6 : bond 0.00364 ( 3) link_ALPHA1-6 : angle 1.55465 ( 9) link_BETA1-4 : bond 0.00344 ( 12) link_BETA1-4 : angle 1.29624 ( 36) link_ALPHA1-2 : bond 0.02068 ( 3) link_ALPHA1-2 : angle 4.61904 ( 9) link_ALPHA1-3 : bond 0.00971 ( 3) link_ALPHA1-3 : angle 1.41910 ( 9) hydrogen bonds : bond 0.02956 ( 587) hydrogen bonds : angle 4.86399 ( 1617) SS BOND : bond 0.00348 ( 41) SS BOND : angle 1.12109 ( 82) covalent geometry : bond 0.00305 (20593) covalent geometry : angle 0.57834 (27951) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10003.63 seconds wall clock time: 174 minutes 12.38 seconds (10452.38 seconds total)