Starting phenix.real_space_refine on Mon Aug 25 15:55:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tjr_41309/08_2025/8tjr_41309.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tjr_41309/08_2025/8tjr_41309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tjr_41309/08_2025/8tjr_41309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tjr_41309/08_2025/8tjr_41309.map" model { file = "/net/cci-nas-00/data/ceres_data/8tjr_41309/08_2025/8tjr_41309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tjr_41309/08_2025/8tjr_41309.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.031 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 13531 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 124 5.16 5 C 11422 2.51 5 N 3075 2.21 5 O 3662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18283 Number of models: 1 Model: "" Number of chains: 25 Chain: "J" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 893 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "K" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "A" Number of atoms: 3551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3551 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Chain: "D" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "B" 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: "E" 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: "H" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 893 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "L" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "C" 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: "F" 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: "P" 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "X" 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" 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: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" 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: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.96, per 1000 atoms: 0.22 Number of scatterers: 18283 At special positions: 0 Unit cell: (127.828, 152.011, 145.965, 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 124 16.00 O 3662 8.00 N 3075 7.00 C 11422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 98 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 93 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 214 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 442 " distance=2.05 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 427 " distance=2.03 Simple disulfide: pdb=" SG CYS A 510 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 214 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 210 " - pdb=" SG CYS B 442 " distance=2.03 Simple disulfide: pdb=" SG CYS B 227 " - pdb=" SG CYS B 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 305 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 427 " distance=2.03 Simple disulfide: pdb=" SG CYS B 510 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 210 " - pdb=" SG CYS C 442 " distance=2.03 Simple disulfide: pdb=" SG CYS C 227 " - pdb=" SG CYS C 256 " distance=2.04 Simple disulfide: pdb=" SG CYS C 237 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS C 305 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 427 " distance=2.03 Simple disulfide: pdb=" SG CYS C 510 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN P 4 " - " MAN P 5 " " MAN U 4 " - " MAN U 5 " " MAN X 4 " - " MAN X 5 " ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA U 3 " - " MAN U 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA P 3 " - " MAN P 6 " " BMA U 3 " - " MAN U 6 " " BMA X 3 " - " MAN X 6 " BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG A 601 " - " ASN A 243 " " NAG A 602 " - " ASN A 285 " " NAG A 603 " - " ASN A 348 " " NAG A 604 " - " ASN A 364 " " NAG A 605 " - " ASN A 372 " " NAG A 606 " - " ASN A 395 " " NAG A 607 " - " ASN A 401 " " NAG A 608 " - " ASN A 457 " " NAG A 609 " - " ASN A 156 " " NAG A 610 " - " ASN A 160 " " NAG A 611 " - " ASN A 304 " " NAG A 612 " - " ASN A 310 " " NAG A 613 " - " ASN A 88 " " NAG B 601 " - " ASN B 243 " " NAG B 602 " - " ASN B 285 " " NAG B 603 " - " ASN B 348 " " NAG B 604 " - " ASN B 364 " " NAG B 605 " - " ASN B 372 " " NAG B 606 " - " ASN B 395 " " NAG B 607 " - " ASN B 401 " " NAG B 608 " - " ASN B 457 " " NAG B 609 " - " ASN B 156 " " NAG B 610 " - " ASN B 160 " " NAG B 611 " - " ASN B 304 " " NAG B 612 " - " ASN B 310 " " NAG B 613 " - " ASN B 88 " " NAG C 601 " - " ASN C 243 " " NAG C 602 " - " ASN C 285 " " NAG C 603 " - " ASN C 348 " " NAG C 604 " - " ASN C 364 " " NAG C 605 " - " ASN C 372 " " NAG C 606 " - " ASN C 395 " " NAG C 607 " - " ASN C 401 " " NAG C 608 " - " ASN C 457 " " NAG C 609 " - " ASN C 156 " " NAG C 610 " - " ASN C 160 " " NAG C 611 " - " ASN C 304 " " NAG C 612 " - " ASN C 310 " " NAG C 613 " - " ASN C 88 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 618 " " NAG E 703 " - " ASN E 637 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 668.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4070 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 35 sheets defined 16.6% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.603A pdb=" N ASP J 31 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'J' and resid 89 through 93 removed outlier: 4.208A pdb=" N THR J 93 " --> pdb=" O THR J 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.230A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 4.086A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 344 through 363 removed outlier: 4.241A pdb=" N LYS A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N HIS A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.508A pdb=" N THR A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 490 removed outlier: 3.762A pdb=" N TRP A 488 " --> pdb=" O MET A 484 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 490 " --> pdb=" O ASP A 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.528A pdb=" N ALA D 526 " --> pdb=" O LEU D 523 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 523 through 527' Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.972A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 596 removed outlier: 4.128A pdb=" N VAL D 580 " --> pdb=" O LEU D 576 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY D 594 " --> pdb=" O GLN D 590 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.518A pdb=" N ASP D 632 " --> pdb=" O TRP D 628 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 660 removed outlier: 3.552A pdb=" N GLU D 657 " --> pdb=" O GLN D 653 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN D 658 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP D 659 " --> pdb=" O LYS D 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.710A pdb=" N LYS B 97 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN B 98 " --> pdb=" O MET B 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 94 through 98' Processing helix chain 'B' and resid 99 through 114 removed outlier: 3.958A pdb=" N MET B 104 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.873A pdb=" N LEU B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 122 through 126' Processing helix chain 'B' and resid 344 through 353 removed outlier: 3.658A pdb=" N ASN B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 358 Processing helix chain 'B' and resid 358 through 363 removed outlier: 3.807A pdb=" N PHE B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 489 removed outlier: 3.765A pdb=" N TRP B 488 " --> pdb=" O MET B 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 removed outlier: 3.530A pdb=" N SER E 534 " --> pdb=" O MET E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 542 removed outlier: 4.261A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 546 removed outlier: 3.893A pdb=" N SER E 546 " --> pdb=" O ASN E 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 543 through 546' Processing helix chain 'E' and resid 573 through 595 removed outlier: 3.713A pdb=" N ARG E 588 " --> pdb=" O GLU E 584 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 632 Processing helix chain 'E' and resid 638 through 643 removed outlier: 3.785A pdb=" N ILE E 642 " --> pdb=" O TYR E 638 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 655 removed outlier: 3.724A pdb=" N LYS E 655 " --> pdb=" O ASN E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 662 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.507A pdb=" N ASP H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'C' and resid 98 through 115 removed outlier: 4.017A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS C 105 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.845A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 126' Processing helix chain 'C' and resid 344 through 362 removed outlier: 3.690A pdb=" N LYS C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS C 360 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N HIS C 361 " --> pdb=" O GLN C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 487 removed outlier: 3.660A pdb=" N ASP C 486 " --> pdb=" O ASP C 483 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.907A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 596 removed outlier: 4.214A pdb=" N GLY F 594 " --> pdb=" O GLN F 590 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.568A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 651 through 664 Processing sheet with id=AA1, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.965A pdb=" N LYS J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER J 25 " --> pdb=" O LYS J 3 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU J 18 " --> pdb=" O MET J 85 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU J 20 " --> pdb=" O LEU J 83 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU J 83 " --> pdb=" O LEU J 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.543A pdb=" N VAL J 108 " --> pdb=" O TYR J 96 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL J 110 " --> pdb=" O ALA J 94 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA J 94 " --> pdb=" O VAL J 110 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE J 34 " --> pdb=" O LEU J 50 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 5 through 6 Processing sheet with id=AA4, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.568A pdb=" N LEU K 11 " --> pdb=" O GLU K 110 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR K 107 " --> pdb=" O TYR K 91 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER K 90 " --> pdb=" O LEU K 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 67 through 68 Processing sheet with id=AA6, first strand: chain 'A' and resid 503 through 508 removed outlier: 4.740A pdb=" N VAL A 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.916A pdb=" N ILE A 234 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 66 through 67 removed outlier: 7.180A pdb=" N HIS A 66 " --> pdb=" O SER A 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.779A pdb=" N GLU A 91 " --> pdb=" O CYS A 248 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 169 through 177 removed outlier: 3.559A pdb=" N LYS A 198 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 268 through 270 removed outlier: 5.737A pdb=" N LEU A 269 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 303 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 301 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLN A 302 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER A 343 " --> pdb=" O GLN A 302 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A 339 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 390 " --> pdb=" O CYS A 387 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 280 through 282 removed outlier: 6.472A pdb=" N ARG A 369 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 368 " --> pdb=" O TRP A 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 402 " --> pdb=" O PHE A 370 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 313 through 321 removed outlier: 6.667A pdb=" N GLN A 324 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 432 through 433 removed outlier: 4.188A pdb=" N ILE A 433 " --> pdb=" O MET A 443 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 503 through 508 removed outlier: 4.563A pdb=" N VAL B 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.231A pdb=" N ILE B 234 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL B 251 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 91 through 93 Processing sheet with id=AB9, first strand: chain 'B' and resid 169 through 177 removed outlier: 3.698A pdb=" N LYS B 198 " --> pdb=" O CYS B 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 268 through 270 removed outlier: 5.861A pdb=" N LEU B 269 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY B 450 " --> pdb=" O ASN B 309 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASN B 309 " --> pdb=" O GLY B 450 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE B 452 " --> pdb=" O ARG B 307 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLY B 460 " --> pdb=" O THR B 299 " (cutoff:3.500A) removed outlier: 10.674A pdb=" N THR B 299 " --> pdb=" O GLY B 460 " (cutoff:3.500A) removed outlier: 12.030A pdb=" N ILE B 462 " --> pdb=" O PHE B 297 " (cutoff:3.500A) removed outlier: 12.248A pdb=" N PHE B 297 " --> pdb=" O ILE B 462 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N THR B 464 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 11.157A pdb=" N VAL B 295 " --> pdb=" O THR B 464 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLN B 302 " --> pdb=" O SER B 343 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N SER B 343 " --> pdb=" O GLN B 302 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS B 339 " --> pdb=" O THR B 306 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 430 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE B 391 " --> pdb=" O LYS B 430 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 390 " --> pdb=" O CYS B 387 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 280 through 282 removed outlier: 11.157A pdb=" N VAL B 295 " --> pdb=" O THR B 464 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N THR B 464 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 12.248A pdb=" N PHE B 297 " --> pdb=" O ILE B 462 " (cutoff:3.500A) removed outlier: 12.030A pdb=" N ILE B 462 " --> pdb=" O PHE B 297 " (cutoff:3.500A) removed outlier: 10.674A pdb=" N THR B 299 " --> pdb=" O GLY B 460 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLY B 460 " --> pdb=" O THR B 299 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE B 452 " --> pdb=" O ARG B 307 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASN B 309 " --> pdb=" O GLY B 450 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY B 450 " --> pdb=" O ASN B 309 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 368 " --> pdb=" O TRP B 404 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 313 through 321 removed outlier: 6.628A pdb=" N GLN B 324 " --> pdb=" O ILE B 318 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 432 through 433 Processing sheet with id=AC5, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.825A pdb=" N LYS H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER H 25 " --> pdb=" O LYS H 3 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.608A pdb=" N VAL H 12 " --> pdb=" O THR H 111 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL H 108 " --> pdb=" O TYR H 96 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE H 34 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.535A pdb=" N LEU L 78 " --> pdb=" O MET L 21 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.878A pdb=" N GLU L 110 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU L 38 " --> pdb=" O HIS L 54 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N HIS L 54 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 503 through 508 removed outlier: 4.999A pdb=" N VAL C 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.528A pdb=" N ILE C 234 " --> pdb=" O VAL C 254 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.747A pdb=" N GLU C 91 " --> pdb=" O CYS C 248 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.654A pdb=" N LYS C 198 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 154 through 159 Processing sheet with id=AD5, first strand: chain 'C' and resid 211 through 212 removed outlier: 6.429A pdb=" N THR C 211 " --> pdb=" O TYR C 444 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 268 through 270 removed outlier: 5.747A pdb=" N LEU C 269 " --> pdb=" O THR C 459 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N GLY C 450 " --> pdb=" O ASN C 309 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ASN C 309 " --> pdb=" O GLY C 450 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE C 452 " --> pdb=" O ARG C 307 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG C 307 " --> pdb=" O ILE C 452 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 301 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLN C 302 " --> pdb=" O SER C 343 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER C 343 " --> pdb=" O GLN C 302 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS C 339 " --> pdb=" O THR C 306 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA C 338 " --> pdb=" O CYS C 427 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 430 " --> pdb=" O PHE C 391 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE C 391 " --> pdb=" O LYS C 430 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 280 through 282 removed outlier: 3.597A pdb=" N MET C 280 " --> pdb=" O GLN C 296 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ARG C 369 " --> pdb=" O PHE C 477 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 368 " --> pdb=" O TRP C 404 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 402 " --> pdb=" O PHE C 370 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 313 through 321 removed outlier: 6.411A pdb=" N GLN C 324 " --> pdb=" O ILE C 318 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5786 1.34 - 1.47: 4538 1.47 - 1.59: 8147 1.59 - 1.72: 0 1.72 - 1.84: 168 Bond restraints: 18639 Sorted by residual: bond pdb=" C1 NAG F 702 " pdb=" O5 NAG F 702 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" N VAL K 63 " pdb=" CA VAL K 63 " ideal model delta sigma weight residual 1.462 1.494 -0.032 8.70e-03 1.32e+04 1.36e+01 bond pdb=" N VAL K 56 " pdb=" CA VAL K 56 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.12e+01 bond pdb=" N GLU D 621 " pdb=" CA GLU D 621 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.18e-02 7.18e+03 9.77e+00 bond pdb=" N VAL A 254 " pdb=" CA VAL A 254 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.14e-02 7.69e+03 9.74e+00 ... (remaining 18634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 24547 2.10 - 4.19: 647 4.19 - 6.29: 76 6.29 - 8.39: 22 8.39 - 10.49: 1 Bond angle restraints: 25293 Sorted by residual: angle pdb=" CA VAL F 570 " pdb=" C VAL F 570 " pdb=" O VAL F 570 " ideal model delta sigma weight residual 121.58 117.35 4.23 1.00e+00 1.00e+00 1.79e+01 angle pdb=" CA ASP K 55 " pdb=" C ASP K 55 " pdb=" O ASP K 55 " ideal model delta sigma weight residual 122.03 117.18 4.85 1.17e+00 7.31e-01 1.72e+01 angle pdb=" N GLN D 640 " pdb=" CA GLN D 640 " pdb=" C GLN D 640 " ideal model delta sigma weight residual 114.56 109.36 5.20 1.27e+00 6.20e-01 1.67e+01 angle pdb=" C TYR J 56 " pdb=" N THR J 57 " pdb=" CA THR J 57 " ideal model delta sigma weight residual 121.54 128.68 -7.14 1.91e+00 2.74e-01 1.40e+01 angle pdb=" C TYR H 56 " pdb=" N THR H 57 " pdb=" CA THR H 57 " ideal model delta sigma weight residual 121.54 128.40 -6.86 1.91e+00 2.74e-01 1.29e+01 ... (remaining 25288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.45: 11464 25.45 - 50.89: 625 50.89 - 76.34: 85 76.34 - 101.79: 36 101.79 - 127.24: 9 Dihedral angle restraints: 12219 sinusoidal: 5907 harmonic: 6312 Sorted by residual: dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual -86.00 -0.17 -85.83 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual -86.00 -9.99 -76.01 1 1.00e+01 1.00e-02 7.28e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 214 " pdb=" CB CYS A 214 " ideal model delta sinusoidal sigma weight residual -86.00 -156.80 70.80 1 1.00e+01 1.00e-02 6.44e+01 ... (remaining 12216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2922 0.111 - 0.223: 124 0.223 - 0.334: 8 0.334 - 0.446: 1 0.446 - 0.557: 1 Chirality restraints: 3056 Sorted by residual: chirality pdb=" C1 NAG F 703 " pdb=" ND2 ASN F 637 " pdb=" C2 NAG F 703 " pdb=" O5 NAG F 703 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" C1 NAG D 702 " pdb=" ND2 ASN D 618 " pdb=" C2 NAG D 702 " pdb=" O5 NAG D 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 3053 not shown) Planarity restraints: 3180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR L 14 " -0.069 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO L 15 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO L 15 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO L 15 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 611 " -0.000 2.00e-02 2.50e+03 3.29e-02 1.35e+01 pdb=" CG ASN E 611 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN E 611 " -0.040 2.00e-02 2.50e+03 pdb=" ND2 ASN E 611 " 0.034 2.00e-02 2.50e+03 pdb=" C1 NAG E 701 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 304 " 0.001 2.00e-02 2.50e+03 2.38e-02 7.09e+00 pdb=" CG ASN B 304 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN B 304 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN B 304 " -0.032 2.00e-02 2.50e+03 pdb=" C1 NAG B 611 " 0.026 2.00e-02 2.50e+03 ... (remaining 3177 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1080 2.74 - 3.28: 15716 3.28 - 3.82: 26835 3.82 - 4.36: 32230 4.36 - 4.90: 57608 Nonbonded interactions: 133469 Sorted by model distance: nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 508 " model vdw 2.196 3.040 nonbonded pdb=" OH TYR C 61 " pdb=" O CYS C 74 " model vdw 2.219 3.040 nonbonded pdb=" O LEU C 378 " pdb=" OG1 THR C 382 " model vdw 2.251 3.040 nonbonded pdb=" OD2 ASP A 466 " pdb=" OG1 THR A 476 " model vdw 2.275 3.040 nonbonded pdb=" O LEU A 378 " pdb=" OG1 THR A 382 " model vdw 2.284 3.040 ... (remaining 133464 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 'B' and (resid 32 through 140 or resid 150 through 613)) selection = (chain 'C' and (resid 32 through 140 or resid 150 through 613)) } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 519 through 703) selection = (chain 'F' and resid 519 through 703) } ncs_group { reference = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'X' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.620 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 18748 Z= 0.303 Angle : 0.822 17.012 25580 Z= 0.429 Chirality : 0.053 0.557 3056 Planarity : 0.005 0.105 3132 Dihedral : 15.514 127.236 8029 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.10 % Allowed : 0.67 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.10 (0.17), residues: 2154 helix: -2.48 (0.24), residues: 370 sheet: -0.38 (0.22), residues: 616 loop : -1.57 (0.16), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 542 TYR 0.011 0.001 TYR D 586 PHE 0.010 0.001 PHE B 53 TRP 0.032 0.001 TRP C 488 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00524 (18639) covalent geometry : angle 0.76630 (25293) SS BOND : bond 0.00501 ( 40) SS BOND : angle 1.80034 ( 80) hydrogen bonds : bond 0.24437 ( 477) hydrogen bonds : angle 8.70015 ( 1344) link_ALPHA1-2 : bond 0.00943 ( 3) link_ALPHA1-2 : angle 2.13504 ( 9) link_ALPHA1-3 : bond 0.00661 ( 3) link_ALPHA1-3 : angle 1.73817 ( 9) link_ALPHA1-6 : bond 0.00395 ( 3) link_ALPHA1-6 : angle 1.44945 ( 9) link_BETA1-4 : bond 0.00392 ( 12) link_BETA1-4 : angle 1.57438 ( 36) link_NAG-ASN : bond 0.00685 ( 48) link_NAG-ASN : angle 3.72551 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 304 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 7 THR cc_start: 0.2942 (OUTLIER) cc_final: 0.2636 (m) REVERT: A 114 GLN cc_start: 0.8303 (tt0) cc_final: 0.7997 (tt0) REVERT: A 341 ASN cc_start: 0.7022 (p0) cc_final: 0.6503 (p0) REVERT: D 655 LYS cc_start: 0.8205 (ttmt) cc_final: 0.7853 (ttpt) REVERT: B 365 ASN cc_start: 0.8523 (m-40) cc_final: 0.7610 (p0) REVERT: E 636 SER cc_start: 0.7612 (t) cc_final: 0.7230 (p) REVERT: E 647 GLU cc_start: 0.8113 (tt0) cc_final: 0.7841 (tt0) REVERT: E 655 LYS cc_start: 0.7533 (pttp) cc_final: 0.7096 (tttt) REVERT: E 660 LEU cc_start: 0.7580 (tp) cc_final: 0.7354 (tt) REVERT: C 199 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7466 (mm-30) REVERT: C 241 LYS cc_start: 0.7971 (tppt) cc_final: 0.7769 (mtmm) REVERT: C 276 GLU cc_start: 0.8012 (mp0) cc_final: 0.7725 (mp0) REVERT: C 367 ILE cc_start: 0.7681 (mm) cc_final: 0.7438 (mm) REVERT: C 513 ARG cc_start: 0.7529 (mtt180) cc_final: 0.6878 (mmt90) REVERT: F 621 GLU cc_start: 0.7364 (pt0) cc_final: 0.7121 (pt0) REVERT: F 653 GLN cc_start: 0.7556 (tp40) cc_final: 0.7336 (tp40) outliers start: 2 outliers final: 0 residues processed: 306 average time/residue: 0.1393 time to fit residues: 63.6552 Evaluate side-chains 217 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 7 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 0.0270 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.0870 chunk 212 optimal weight: 0.3980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 47 GLN A 137 ASN C 302 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.147142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.107082 restraints weight = 24235.217| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.14 r_work: 0.3098 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18748 Z= 0.108 Angle : 0.632 14.009 25580 Z= 0.303 Chirality : 0.046 0.515 3056 Planarity : 0.004 0.082 3132 Dihedral : 11.603 109.121 3967 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.19 % Allowed : 7.47 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.18), residues: 2154 helix: -1.79 (0.26), residues: 376 sheet: -0.02 (0.21), residues: 646 loop : -1.51 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 513 TYR 0.010 0.001 TYR H 103 PHE 0.013 0.001 PHE A 391 TRP 0.011 0.001 TRP D 610 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00234 (18639) covalent geometry : angle 0.58281 (25293) SS BOND : bond 0.00273 ( 40) SS BOND : angle 1.41793 ( 80) hydrogen bonds : bond 0.04424 ( 477) hydrogen bonds : angle 5.80404 ( 1344) link_ALPHA1-2 : bond 0.01355 ( 3) link_ALPHA1-2 : angle 3.34427 ( 9) link_ALPHA1-3 : bond 0.00810 ( 3) link_ALPHA1-3 : angle 2.18640 ( 9) link_ALPHA1-6 : bond 0.00683 ( 3) link_ALPHA1-6 : angle 1.70265 ( 9) link_BETA1-4 : bond 0.00342 ( 12) link_BETA1-4 : angle 1.57319 ( 36) link_NAG-ASN : bond 0.00522 ( 48) link_NAG-ASN : angle 2.87545 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 35 TYR cc_start: 0.7795 (m-80) cc_final: 0.7396 (m-80) REVERT: A 114 GLN cc_start: 0.8338 (tt0) cc_final: 0.8026 (tt0) REVERT: D 542 ARG cc_start: 0.8532 (mtp85) cc_final: 0.8268 (mtt90) REVERT: D 655 LYS cc_start: 0.8325 (ttmt) cc_final: 0.7974 (ttpt) REVERT: B 365 ASN cc_start: 0.8525 (m-40) cc_final: 0.7753 (p0) REVERT: E 620 SER cc_start: 0.9067 (m) cc_final: 0.8647 (p) REVERT: E 636 SER cc_start: 0.7768 (t) cc_final: 0.7359 (p) REVERT: E 655 LYS cc_start: 0.7629 (pttp) cc_final: 0.7110 (tttt) REVERT: L 23 CYS cc_start: 0.6925 (t) cc_final: 0.6628 (t) REVERT: C 100 MET cc_start: 0.8230 (mtp) cc_final: 0.7812 (mtp) REVERT: C 241 LYS cc_start: 0.8125 (tppt) cc_final: 0.7866 (mtmm) REVERT: C 367 ILE cc_start: 0.7798 (mm) cc_final: 0.7594 (mm) REVERT: C 484 MET cc_start: 0.8627 (tpp) cc_final: 0.8372 (tpp) REVERT: C 513 ARG cc_start: 0.7747 (mtt180) cc_final: 0.7310 (mmt90) outliers start: 23 outliers final: 9 residues processed: 240 average time/residue: 0.1385 time to fit residues: 49.7924 Evaluate side-chains 221 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 212 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 655 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 176 optimal weight: 0.0670 chunk 151 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 0.0050 chunk 160 optimal weight: 5.9990 overall best weight: 1.0336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 ASN C 271 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.142303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.102181 restraints weight = 24482.872| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.14 r_work: 0.3025 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18748 Z= 0.139 Angle : 0.644 14.259 25580 Z= 0.307 Chirality : 0.047 0.487 3056 Planarity : 0.004 0.072 3132 Dihedral : 9.771 104.850 3966 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.82 % Allowed : 9.29 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.18), residues: 2154 helix: -1.53 (0.27), residues: 385 sheet: -0.14 (0.21), residues: 678 loop : -1.46 (0.17), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 542 TYR 0.009 0.001 TYR A 40 PHE 0.016 0.001 PHE K 76 TRP 0.009 0.001 TRP F 571 HIS 0.003 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00325 (18639) covalent geometry : angle 0.59633 (25293) SS BOND : bond 0.00294 ( 40) SS BOND : angle 1.61642 ( 80) hydrogen bonds : bond 0.04452 ( 477) hydrogen bonds : angle 5.16320 ( 1344) link_ALPHA1-2 : bond 0.01782 ( 3) link_ALPHA1-2 : angle 3.47220 ( 9) link_ALPHA1-3 : bond 0.01085 ( 3) link_ALPHA1-3 : angle 1.23619 ( 9) link_ALPHA1-6 : bond 0.00906 ( 3) link_ALPHA1-6 : angle 1.46804 ( 9) link_BETA1-4 : bond 0.00515 ( 12) link_BETA1-4 : angle 1.42312 ( 36) link_NAG-ASN : bond 0.00489 ( 48) link_NAG-ASN : angle 2.85930 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 27 GLN cc_start: 0.8510 (tt0) cc_final: 0.7756 (mt0) REVERT: A 114 GLN cc_start: 0.8262 (tt0) cc_final: 0.7906 (tt0) REVERT: D 542 ARG cc_start: 0.8596 (mtp85) cc_final: 0.8247 (mtt90) REVERT: D 621 GLU cc_start: 0.8242 (pt0) cc_final: 0.7536 (pm20) REVERT: E 620 SER cc_start: 0.9124 (m) cc_final: 0.8660 (p) REVERT: E 625 ASN cc_start: 0.8804 (m-40) cc_final: 0.8532 (m110) REVERT: E 636 SER cc_start: 0.7972 (t) cc_final: 0.7569 (p) REVERT: E 655 LYS cc_start: 0.7788 (pttp) cc_final: 0.7199 (tttt) REVERT: C 178 ARG cc_start: 0.8650 (tmm-80) cc_final: 0.8184 (ttp80) REVERT: C 241 LYS cc_start: 0.8154 (tppt) cc_final: 0.7878 (mtmm) REVERT: C 341 ASN cc_start: 0.7984 (p0) cc_final: 0.7651 (p0) REVERT: C 484 MET cc_start: 0.8695 (tpp) cc_final: 0.8230 (tpp) REVERT: C 513 ARG cc_start: 0.7814 (mtt180) cc_final: 0.7143 (mmt90) REVERT: F 543 ASN cc_start: 0.8503 (m-40) cc_final: 0.8282 (m-40) outliers start: 35 outliers final: 25 residues processed: 241 average time/residue: 0.1391 time to fit residues: 50.1053 Evaluate side-chains 232 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 640 GLN Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 655 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 138 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 34 optimal weight: 0.0970 chunk 62 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 61 ASN D 543 ASN B 67 ASN F 658 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.137943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.098128 restraints weight = 24620.563| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.12 r_work: 0.2968 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18748 Z= 0.167 Angle : 0.680 13.381 25580 Z= 0.325 Chirality : 0.048 0.497 3056 Planarity : 0.004 0.082 3132 Dihedral : 8.369 102.333 3966 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.23 % Allowed : 10.79 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.18), residues: 2154 helix: -1.28 (0.28), residues: 372 sheet: -0.09 (0.21), residues: 679 loop : -1.55 (0.17), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 513 TYR 0.009 0.001 TYR H 96 PHE 0.013 0.002 PHE B 392 TRP 0.011 0.001 TRP F 571 HIS 0.004 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00400 (18639) covalent geometry : angle 0.62935 (25293) SS BOND : bond 0.00399 ( 40) SS BOND : angle 1.83436 ( 80) hydrogen bonds : bond 0.04398 ( 477) hydrogen bonds : angle 4.95266 ( 1344) link_ALPHA1-2 : bond 0.02179 ( 3) link_ALPHA1-2 : angle 4.54848 ( 9) link_ALPHA1-3 : bond 0.00980 ( 3) link_ALPHA1-3 : angle 1.72896 ( 9) link_ALPHA1-6 : bond 0.00678 ( 3) link_ALPHA1-6 : angle 1.84597 ( 9) link_BETA1-4 : bond 0.00371 ( 12) link_BETA1-4 : angle 1.57341 ( 36) link_NAG-ASN : bond 0.00465 ( 48) link_NAG-ASN : angle 2.89228 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 227 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 27 GLN cc_start: 0.8460 (tt0) cc_final: 0.7838 (mt0) REVERT: K 94 MET cc_start: 0.5738 (mtm) cc_final: 0.5447 (mtt) REVERT: A 114 GLN cc_start: 0.8223 (tt0) cc_final: 0.7968 (tt0) REVERT: A 214 CYS cc_start: 0.7480 (OUTLIER) cc_final: 0.6643 (m) REVERT: D 621 GLU cc_start: 0.8266 (pt0) cc_final: 0.7385 (pm20) REVERT: D 624 ASP cc_start: 0.8708 (m-30) cc_final: 0.8497 (m-30) REVERT: D 625 ASN cc_start: 0.7861 (t0) cc_final: 0.7357 (t0) REVERT: B 280 MET cc_start: 0.8357 (mmt) cc_final: 0.7924 (mmt) REVERT: E 620 SER cc_start: 0.9118 (m) cc_final: 0.8783 (p) REVERT: E 632 ASP cc_start: 0.8839 (t0) cc_final: 0.8371 (t0) REVERT: E 655 LYS cc_start: 0.7760 (pttp) cc_final: 0.7112 (tttt) REVERT: C 178 ARG cc_start: 0.8761 (tmm-80) cc_final: 0.8370 (ttp80) REVERT: C 241 LYS cc_start: 0.8163 (tppt) cc_final: 0.7862 (mtmm) outliers start: 43 outliers final: 28 residues processed: 257 average time/residue: 0.1332 time to fit residues: 50.4613 Evaluate side-chains 235 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain F residue 658 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 4 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 12 optimal weight: 0.0770 chunk 210 optimal weight: 0.0870 chunk 59 optimal weight: 0.3980 chunk 61 optimal weight: 3.9990 chunk 199 optimal weight: 7.9990 chunk 114 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 543 ASN D 650 GLN B 67 ASN F 540 GLN F 658 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.140365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.100637 restraints weight = 24359.224| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.12 r_work: 0.3005 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18748 Z= 0.102 Angle : 0.610 13.269 25580 Z= 0.288 Chirality : 0.045 0.481 3056 Planarity : 0.004 0.060 3132 Dihedral : 7.804 100.123 3966 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.92 % Allowed : 12.04 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.18), residues: 2154 helix: -1.02 (0.28), residues: 366 sheet: -0.06 (0.21), residues: 675 loop : -1.48 (0.17), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 513 TYR 0.008 0.001 TYR F 638 PHE 0.009 0.001 PHE H 27 TRP 0.010 0.001 TRP F 571 HIS 0.002 0.000 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00226 (18639) covalent geometry : angle 0.55776 (25293) SS BOND : bond 0.00308 ( 40) SS BOND : angle 1.61213 ( 80) hydrogen bonds : bond 0.03516 ( 477) hydrogen bonds : angle 4.67910 ( 1344) link_ALPHA1-2 : bond 0.02292 ( 3) link_ALPHA1-2 : angle 4.56291 ( 9) link_ALPHA1-3 : bond 0.00889 ( 3) link_ALPHA1-3 : angle 1.62133 ( 9) link_ALPHA1-6 : bond 0.00343 ( 3) link_ALPHA1-6 : angle 1.55452 ( 9) link_BETA1-4 : bond 0.00354 ( 12) link_BETA1-4 : angle 1.38906 ( 36) link_NAG-ASN : bond 0.00487 ( 48) link_NAG-ASN : angle 2.82833 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 204 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 100 ASP cc_start: 0.6960 (t0) cc_final: 0.6727 (t0) REVERT: K 27 GLN cc_start: 0.8433 (tt0) cc_final: 0.7821 (mt0) REVERT: K 94 MET cc_start: 0.5669 (mtm) cc_final: 0.5412 (mtt) REVERT: A 114 GLN cc_start: 0.8136 (tt0) cc_final: 0.7883 (tt0) REVERT: D 588 ARG cc_start: 0.7791 (ttm170) cc_final: 0.7527 (mtm180) REVERT: D 621 GLU cc_start: 0.8260 (pt0) cc_final: 0.7532 (pm20) REVERT: B 280 MET cc_start: 0.8370 (mmt) cc_final: 0.7953 (mmt) REVERT: E 620 SER cc_start: 0.9100 (m) cc_final: 0.8716 (p) REVERT: E 636 SER cc_start: 0.8383 (t) cc_final: 0.7966 (p) REVERT: E 655 LYS cc_start: 0.7769 (pttp) cc_final: 0.7108 (tttt) REVERT: C 178 ARG cc_start: 0.8713 (tmm-80) cc_final: 0.8380 (ttp80) REVERT: C 241 LYS cc_start: 0.8132 (tppt) cc_final: 0.7828 (mtmm) REVERT: C 341 ASN cc_start: 0.7784 (p0) cc_final: 0.7469 (p0) REVERT: F 542 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7114 (mmt90) outliers start: 37 outliers final: 22 residues processed: 226 average time/residue: 0.1273 time to fit residues: 42.4475 Evaluate side-chains 219 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain F residue 542 ARG Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 655 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 6 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 213 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 54 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.098419 restraints weight = 24450.123| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.11 r_work: 0.2973 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18748 Z= 0.139 Angle : 0.643 13.111 25580 Z= 0.303 Chirality : 0.046 0.467 3056 Planarity : 0.004 0.061 3132 Dihedral : 7.468 97.976 3966 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.52 % Favored : 94.43 % Rotamer: Outliers : 1.87 % Allowed : 12.56 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.18), residues: 2154 helix: -0.96 (0.29), residues: 368 sheet: -0.03 (0.21), residues: 657 loop : -1.47 (0.17), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 513 TYR 0.007 0.001 TYR E 586 PHE 0.014 0.001 PHE C 53 TRP 0.012 0.001 TRP F 571 HIS 0.003 0.001 HIS C 383 Details of bonding type rmsd covalent geometry : bond 0.00332 (18639) covalent geometry : angle 0.58938 (25293) SS BOND : bond 0.00306 ( 40) SS BOND : angle 1.77093 ( 80) hydrogen bonds : bond 0.03890 ( 477) hydrogen bonds : angle 4.63452 ( 1344) link_ALPHA1-2 : bond 0.02290 ( 3) link_ALPHA1-2 : angle 4.89967 ( 9) link_ALPHA1-3 : bond 0.00933 ( 3) link_ALPHA1-3 : angle 1.49050 ( 9) link_ALPHA1-6 : bond 0.00319 ( 3) link_ALPHA1-6 : angle 1.55571 ( 9) link_BETA1-4 : bond 0.00466 ( 12) link_BETA1-4 : angle 1.73654 ( 36) link_NAG-ASN : bond 0.00458 ( 48) link_NAG-ASN : angle 2.84907 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 100 ASP cc_start: 0.7035 (t0) cc_final: 0.6789 (t0) REVERT: K 27 GLN cc_start: 0.8472 (tt0) cc_final: 0.7855 (mt0) REVERT: K 94 MET cc_start: 0.5693 (mtm) cc_final: 0.5362 (mmt) REVERT: A 114 GLN cc_start: 0.8172 (tt0) cc_final: 0.7920 (tt0) REVERT: D 611 ASN cc_start: 0.5185 (t0) cc_final: 0.4846 (t0) REVERT: D 621 GLU cc_start: 0.8313 (pt0) cc_final: 0.7478 (pm20) REVERT: D 625 ASN cc_start: 0.7848 (t0) cc_final: 0.7326 (t0) REVERT: B 57 ASP cc_start: 0.7812 (t0) cc_final: 0.7351 (t0) REVERT: B 280 MET cc_start: 0.8371 (mmt) cc_final: 0.8000 (mmt) REVERT: E 620 SER cc_start: 0.9091 (m) cc_final: 0.8714 (p) REVERT: E 655 LYS cc_start: 0.7746 (pttp) cc_final: 0.7067 (tttt) REVERT: C 178 ARG cc_start: 0.8753 (tmm-80) cc_final: 0.8428 (ttp80) REVERT: C 241 LYS cc_start: 0.8116 (tppt) cc_final: 0.7798 (mtmm) outliers start: 36 outliers final: 28 residues processed: 224 average time/residue: 0.1292 time to fit residues: 43.1041 Evaluate side-chains 224 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 655 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 104 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 100 optimal weight: 0.0980 chunk 194 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 167 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN D 543 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.139113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.099329 restraints weight = 24581.199| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.12 r_work: 0.2987 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18748 Z= 0.118 Angle : 0.613 13.007 25580 Z= 0.290 Chirality : 0.045 0.468 3056 Planarity : 0.004 0.058 3132 Dihedral : 7.145 95.291 3966 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.78 % Favored : 95.17 % Rotamer: Outliers : 1.97 % Allowed : 12.71 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.18), residues: 2154 helix: -0.86 (0.29), residues: 366 sheet: -0.04 (0.21), residues: 661 loop : -1.42 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 542 TYR 0.007 0.001 TYR F 638 PHE 0.016 0.001 PHE J 27 TRP 0.011 0.001 TRP F 571 HIS 0.003 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00276 (18639) covalent geometry : angle 0.55968 (25293) SS BOND : bond 0.00301 ( 40) SS BOND : angle 1.56490 ( 80) hydrogen bonds : bond 0.03469 ( 477) hydrogen bonds : angle 4.51854 ( 1344) link_ALPHA1-2 : bond 0.02359 ( 3) link_ALPHA1-2 : angle 5.02268 ( 9) link_ALPHA1-3 : bond 0.00921 ( 3) link_ALPHA1-3 : angle 1.40722 ( 9) link_ALPHA1-6 : bond 0.00332 ( 3) link_ALPHA1-6 : angle 1.54148 ( 9) link_BETA1-4 : bond 0.00313 ( 12) link_BETA1-4 : angle 1.51913 ( 36) link_NAG-ASN : bond 0.00466 ( 48) link_NAG-ASN : angle 2.83043 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 100 ASP cc_start: 0.6954 (t0) cc_final: 0.6686 (t0) REVERT: K 27 GLN cc_start: 0.8418 (tt0) cc_final: 0.7868 (mt0) REVERT: K 94 MET cc_start: 0.5737 (mtm) cc_final: 0.5326 (mmt) REVERT: A 114 GLN cc_start: 0.8169 (tt0) cc_final: 0.7915 (tt0) REVERT: D 588 ARG cc_start: 0.7827 (ttm170) cc_final: 0.7571 (mtm110) REVERT: D 611 ASN cc_start: 0.5115 (t0) cc_final: 0.4783 (t0) REVERT: D 621 GLU cc_start: 0.8287 (pt0) cc_final: 0.7569 (pm20) REVERT: B 57 ASP cc_start: 0.7878 (t0) cc_final: 0.7424 (t0) REVERT: B 280 MET cc_start: 0.8401 (mmt) cc_final: 0.8045 (mmt) REVERT: E 620 SER cc_start: 0.9072 (m) cc_final: 0.8698 (p) REVERT: E 655 LYS cc_start: 0.7700 (pttp) cc_final: 0.7045 (tttt) REVERT: C 178 ARG cc_start: 0.8747 (tmm-80) cc_final: 0.8419 (ttp80) REVERT: C 241 LYS cc_start: 0.8119 (tppt) cc_final: 0.7785 (mtmm) REVERT: C 276 GLU cc_start: 0.7848 (mp0) cc_final: 0.7636 (mp0) REVERT: F 542 ARG cc_start: 0.7747 (mmt90) cc_final: 0.7539 (mmt90) outliers start: 38 outliers final: 28 residues processed: 226 average time/residue: 0.1478 time to fit residues: 49.1960 Evaluate side-chains 227 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 655 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 76 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 127 optimal weight: 0.0020 chunk 100 optimal weight: 0.0970 chunk 26 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 543 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN F 607 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.137063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.097323 restraints weight = 24591.259| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.12 r_work: 0.2955 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18748 Z= 0.151 Angle : 0.647 12.901 25580 Z= 0.307 Chirality : 0.046 0.455 3056 Planarity : 0.004 0.056 3132 Dihedral : 7.141 92.068 3966 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.85 % Favored : 94.10 % Rotamer: Outliers : 2.23 % Allowed : 12.97 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.18), residues: 2154 helix: -0.82 (0.29), residues: 365 sheet: -0.05 (0.21), residues: 653 loop : -1.47 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 542 TYR 0.010 0.001 TYR J 82 PHE 0.014 0.001 PHE C 53 TRP 0.016 0.001 TRP A 488 HIS 0.003 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00364 (18639) covalent geometry : angle 0.59378 (25293) SS BOND : bond 0.00347 ( 40) SS BOND : angle 1.83909 ( 80) hydrogen bonds : bond 0.03936 ( 477) hydrogen bonds : angle 4.58141 ( 1344) link_ALPHA1-2 : bond 0.02257 ( 3) link_ALPHA1-2 : angle 4.88464 ( 9) link_ALPHA1-3 : bond 0.00822 ( 3) link_ALPHA1-3 : angle 1.27080 ( 9) link_ALPHA1-6 : bond 0.00314 ( 3) link_ALPHA1-6 : angle 1.55762 ( 9) link_BETA1-4 : bond 0.00355 ( 12) link_BETA1-4 : angle 1.49971 ( 36) link_NAG-ASN : bond 0.00442 ( 48) link_NAG-ASN : angle 2.88801 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 82 TYR cc_start: 0.7468 (m-80) cc_final: 0.7096 (m-80) REVERT: J 100 ASP cc_start: 0.7006 (t0) cc_final: 0.6751 (t0) REVERT: K 27 GLN cc_start: 0.8512 (tt0) cc_final: 0.7747 (mt0) REVERT: K 94 MET cc_start: 0.5725 (mtm) cc_final: 0.5372 (mmt) REVERT: A 114 GLN cc_start: 0.8173 (tt0) cc_final: 0.7924 (tt0) REVERT: D 588 ARG cc_start: 0.7888 (ttm170) cc_final: 0.7628 (mtm110) REVERT: D 611 ASN cc_start: 0.5266 (t0) cc_final: 0.4931 (t0) REVERT: D 621 GLU cc_start: 0.8332 (pt0) cc_final: 0.7472 (pm20) REVERT: D 625 ASN cc_start: 0.7945 (t0) cc_final: 0.7379 (t0) REVERT: B 57 ASP cc_start: 0.7889 (t0) cc_final: 0.7450 (t0) REVERT: B 280 MET cc_start: 0.8363 (mmt) cc_final: 0.8062 (mmt) REVERT: E 620 SER cc_start: 0.9078 (m) cc_final: 0.8720 (p) REVERT: E 655 LYS cc_start: 0.7774 (pttp) cc_final: 0.7120 (tttt) REVERT: L 84 GLU cc_start: 0.7850 (mp0) cc_final: 0.7448 (mp0) REVERT: C 102 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: C 178 ARG cc_start: 0.8796 (tmm-80) cc_final: 0.8475 (ttp80) REVERT: C 241 LYS cc_start: 0.8147 (tppt) cc_final: 0.7769 (mtmm) REVERT: F 542 ARG cc_start: 0.7798 (mmt90) cc_final: 0.7253 (mtt-85) outliers start: 43 outliers final: 32 residues processed: 231 average time/residue: 0.1398 time to fit residues: 47.7028 Evaluate side-chains 235 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 655 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 130 optimal weight: 0.4980 chunk 158 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 543 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.137243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.097641 restraints weight = 24489.615| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.11 r_work: 0.2960 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 18748 Z= 0.140 Angle : 0.643 12.984 25580 Z= 0.305 Chirality : 0.046 0.462 3056 Planarity : 0.004 0.055 3132 Dihedral : 7.085 89.445 3966 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.20 % Favored : 94.75 % Rotamer: Outliers : 1.97 % Allowed : 13.23 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.18), residues: 2154 helix: -0.77 (0.29), residues: 365 sheet: 0.06 (0.21), residues: 639 loop : -1.49 (0.17), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 542 TYR 0.012 0.001 TYR J 82 PHE 0.014 0.001 PHE C 53 TRP 0.012 0.001 TRP A 488 HIS 0.003 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00338 (18639) covalent geometry : angle 0.58798 (25293) SS BOND : bond 0.00322 ( 40) SS BOND : angle 1.94435 ( 80) hydrogen bonds : bond 0.03739 ( 477) hydrogen bonds : angle 4.54294 ( 1344) link_ALPHA1-2 : bond 0.02210 ( 3) link_ALPHA1-2 : angle 4.80823 ( 9) link_ALPHA1-3 : bond 0.00923 ( 3) link_ALPHA1-3 : angle 1.27144 ( 9) link_ALPHA1-6 : bond 0.00330 ( 3) link_ALPHA1-6 : angle 1.54364 ( 9) link_BETA1-4 : bond 0.00324 ( 12) link_BETA1-4 : angle 1.45204 ( 36) link_NAG-ASN : bond 0.00447 ( 48) link_NAG-ASN : angle 2.89898 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 82 TYR cc_start: 0.7368 (m-80) cc_final: 0.7089 (m-80) REVERT: J 100 ASP cc_start: 0.6988 (t0) cc_final: 0.6744 (t0) REVERT: K 27 GLN cc_start: 0.8474 (tt0) cc_final: 0.7835 (mt0) REVERT: K 94 MET cc_start: 0.5814 (mtm) cc_final: 0.5387 (mmt) REVERT: A 114 GLN cc_start: 0.8158 (tt0) cc_final: 0.7901 (tt0) REVERT: D 588 ARG cc_start: 0.7859 (ttm170) cc_final: 0.7604 (mtm110) REVERT: D 611 ASN cc_start: 0.5242 (t0) cc_final: 0.4910 (t0) REVERT: D 621 GLU cc_start: 0.8330 (pt0) cc_final: 0.7483 (pm20) REVERT: D 625 ASN cc_start: 0.7933 (t0) cc_final: 0.7341 (t0) REVERT: B 57 ASP cc_start: 0.7915 (t0) cc_final: 0.7471 (t0) REVERT: B 280 MET cc_start: 0.8364 (mmt) cc_final: 0.8063 (mmt) REVERT: E 620 SER cc_start: 0.9066 (m) cc_final: 0.8710 (p) REVERT: E 655 LYS cc_start: 0.7720 (pttp) cc_final: 0.7103 (tttt) REVERT: L 84 GLU cc_start: 0.7865 (mp0) cc_final: 0.7458 (mp0) REVERT: C 102 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: C 178 ARG cc_start: 0.8801 (tmm-80) cc_final: 0.8477 (ttp80) REVERT: C 241 LYS cc_start: 0.8154 (tppt) cc_final: 0.7761 (mtmm) REVERT: F 542 ARG cc_start: 0.7824 (mmt90) cc_final: 0.7267 (mtt-85) REVERT: F 625 ASN cc_start: 0.8767 (m-40) cc_final: 0.8492 (m-40) outliers start: 38 outliers final: 33 residues processed: 228 average time/residue: 0.1328 time to fit residues: 44.6880 Evaluate side-chains 231 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 655 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 160 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 138 optimal weight: 0.0030 chunk 155 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 214 optimal weight: 0.0370 chunk 178 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.8072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.099171 restraints weight = 24459.074| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.11 r_work: 0.2972 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18748 Z= 0.112 Angle : 0.611 12.823 25580 Z= 0.289 Chirality : 0.044 0.443 3056 Planarity : 0.004 0.055 3132 Dihedral : 6.766 84.312 3966 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.15 % Favored : 94.80 % Rotamer: Outliers : 1.97 % Allowed : 13.49 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.18), residues: 2154 helix: -0.66 (0.30), residues: 366 sheet: 0.11 (0.21), residues: 652 loop : -1.40 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 513 TYR 0.011 0.001 TYR J 82 PHE 0.012 0.001 PHE C 53 TRP 0.013 0.001 TRP A 488 HIS 0.002 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00263 (18639) covalent geometry : angle 0.55817 (25293) SS BOND : bond 0.00294 ( 40) SS BOND : angle 1.67631 ( 80) hydrogen bonds : bond 0.03254 ( 477) hydrogen bonds : angle 4.39667 ( 1344) link_ALPHA1-2 : bond 0.02135 ( 3) link_ALPHA1-2 : angle 4.71146 ( 9) link_ALPHA1-3 : bond 0.00876 ( 3) link_ALPHA1-3 : angle 1.18308 ( 9) link_ALPHA1-6 : bond 0.00337 ( 3) link_ALPHA1-6 : angle 1.53611 ( 9) link_BETA1-4 : bond 0.00318 ( 12) link_BETA1-4 : angle 1.39216 ( 36) link_NAG-ASN : bond 0.00456 ( 48) link_NAG-ASN : angle 2.82932 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 100 ASP cc_start: 0.6983 (t0) cc_final: 0.6749 (t0) REVERT: K 27 GLN cc_start: 0.8476 (tt0) cc_final: 0.7834 (mt0) REVERT: K 94 MET cc_start: 0.5858 (mtm) cc_final: 0.5411 (mmt) REVERT: A 114 GLN cc_start: 0.8141 (tt0) cc_final: 0.7881 (tt0) REVERT: D 588 ARG cc_start: 0.7866 (ttm170) cc_final: 0.7609 (mtm110) REVERT: D 611 ASN cc_start: 0.5203 (t0) cc_final: 0.4884 (t0) REVERT: D 621 GLU cc_start: 0.8336 (pt0) cc_final: 0.7512 (pm20) REVERT: D 625 ASN cc_start: 0.7941 (t0) cc_final: 0.7375 (t0) REVERT: D 633 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8227 (ttmm) REVERT: B 57 ASP cc_start: 0.7967 (t0) cc_final: 0.7521 (t0) REVERT: B 280 MET cc_start: 0.8382 (mmt) cc_final: 0.8103 (mmt) REVERT: E 620 SER cc_start: 0.9068 (m) cc_final: 0.8716 (p) REVERT: L 84 GLU cc_start: 0.7944 (mp0) cc_final: 0.7528 (mp0) REVERT: C 102 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: C 178 ARG cc_start: 0.8788 (tmm-80) cc_final: 0.8470 (ttp80) REVERT: C 241 LYS cc_start: 0.8149 (tppt) cc_final: 0.7797 (mtmm) REVERT: F 542 ARG cc_start: 0.7780 (mmt90) cc_final: 0.7250 (mtt-85) REVERT: F 625 ASN cc_start: 0.8738 (m-40) cc_final: 0.8443 (m-40) outliers start: 38 outliers final: 33 residues processed: 229 average time/residue: 0.1460 time to fit residues: 49.5268 Evaluate side-chains 238 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 607 ASN Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 655 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 166 optimal weight: 0.9990 chunk 156 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 73 optimal weight: 0.0870 chunk 63 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.138816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.099142 restraints weight = 24587.294| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.12 r_work: 0.2983 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18748 Z= 0.111 Angle : 0.612 12.903 25580 Z= 0.289 Chirality : 0.045 0.444 3056 Planarity : 0.004 0.054 3132 Dihedral : 6.682 82.091 3966 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.94 % Rotamer: Outliers : 2.02 % Allowed : 13.54 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.18), residues: 2154 helix: -0.64 (0.30), residues: 366 sheet: 0.11 (0.21), residues: 652 loop : -1.37 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 513 TYR 0.006 0.001 TYR F 638 PHE 0.014 0.001 PHE C 53 TRP 0.015 0.001 TRP E 571 HIS 0.002 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00261 (18639) covalent geometry : angle 0.55927 (25293) SS BOND : bond 0.00299 ( 40) SS BOND : angle 1.70389 ( 80) hydrogen bonds : bond 0.03251 ( 477) hydrogen bonds : angle 4.38641 ( 1344) link_ALPHA1-2 : bond 0.02094 ( 3) link_ALPHA1-2 : angle 4.65249 ( 9) link_ALPHA1-3 : bond 0.00878 ( 3) link_ALPHA1-3 : angle 1.18490 ( 9) link_ALPHA1-6 : bond 0.00328 ( 3) link_ALPHA1-6 : angle 1.53346 ( 9) link_BETA1-4 : bond 0.00334 ( 12) link_BETA1-4 : angle 1.38510 ( 36) link_NAG-ASN : bond 0.00443 ( 48) link_NAG-ASN : angle 2.82567 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3505.08 seconds wall clock time: 60 minutes 55.52 seconds (3655.52 seconds total)