Starting phenix.real_space_refine on Wed Jun 25 05:03:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tjr_41309/06_2025/8tjr_41309.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tjr_41309/06_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_41309/06_2025/8tjr_41309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tjr_41309/06_2025/8tjr_41309.map" model { file = "/net/cci-nas-00/data/ceres_data/8tjr_41309/06_2025/8tjr_41309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tjr_41309/06_2025/8tjr_41309.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.031 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.20, per 1000 atoms: 0.61 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: 4.78 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.33 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: 5.66 Time building geometry restraints manager: 5.59 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 514 or resid 601 throu \ gh 613)) selection = (chain 'C' and (resid 32 through 140 or resid 150 through 514 or resid 601 throu \ gh 613)) } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 519 through 664 or resid 701 through 703)) selection = (chain 'F' and (resid 519 through 664 or resid 701 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: 4.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.020 Extract box with map and model: 0.820 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 42.940 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.900 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (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 TRP 0.032 0.001 TRP C 488 HIS 0.003 0.001 HIS B 225 PHE 0.010 0.001 PHE B 53 TYR 0.011 0.001 TYR D 586 ARG 0.014 0.000 ARG F 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00685 ( 48) link_NAG-ASN : angle 3.72551 ( 144) 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_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) hydrogen bonds : bond 0.24437 ( 477) hydrogen bonds : angle 8.70015 ( 1344) SS BOND : bond 0.00501 ( 40) SS BOND : angle 1.80034 ( 80) covalent geometry : bond 0.00524 (18639) covalent geometry : angle 0.76630 (25293) *********************** 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 : 1.868 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: 0.6502 (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: 0.7608 (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: 0.7840 (tt0) REVERT: E 655 LYS cc_start: 0.7533 (pttp) cc_final: 0.7095 (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: 0.7467 (mm-30) REVERT: C 241 LYS cc_start: 0.7971 (tppt) cc_final: 0.7770 (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: 0.6879 (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: 0.7337 (tp40) outliers start: 2 outliers final: 0 residues processed: 306 average time/residue: 0.3392 time to fit residues: 156.2523 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 : 1.861 ------------------------------------------------------------------------------- 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 183 optimal weight: 0.8980 chunk 164 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.142930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.102718 restraints weight = 24267.338| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.16 r_work: 0.3034 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18748 Z= 0.161 Angle : 0.682 14.407 25580 Z= 0.328 Chirality : 0.048 0.517 3056 Planarity : 0.004 0.083 3132 Dihedral : 11.615 108.697 3967 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.50 % Allowed : 7.37 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.17), residues: 2154 helix: -1.83 (0.26), residues: 376 sheet: -0.02 (0.21), residues: 650 loop : -1.57 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 571 HIS 0.003 0.001 HIS C 383 PHE 0.012 0.002 PHE B 385 TYR 0.010 0.001 TYR H 103 ARG 0.005 0.000 ARG F 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00515 ( 48) link_NAG-ASN : angle 2.97943 ( 144) link_ALPHA1-6 : bond 0.00576 ( 3) link_ALPHA1-6 : angle 1.84078 ( 9) link_BETA1-4 : bond 0.00390 ( 12) link_BETA1-4 : angle 1.57360 ( 36) link_ALPHA1-2 : bond 0.01252 ( 3) link_ALPHA1-2 : angle 3.38913 ( 9) link_ALPHA1-3 : bond 0.01013 ( 3) link_ALPHA1-3 : angle 2.23926 ( 9) hydrogen bonds : bond 0.04719 ( 477) hydrogen bonds : angle 5.73907 ( 1344) SS BOND : bond 0.00502 ( 40) SS BOND : angle 1.67274 ( 80) covalent geometry : bond 0.00374 (18639) covalent geometry : angle 0.63286 (25293) *********************** 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 261 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 232 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8292 (tt0) cc_final: 0.7938 (tt0) REVERT: A 151 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7451 (mmt-90) REVERT: D 542 ARG cc_start: 0.8566 (mtp85) cc_final: 0.8290 (mtt90) REVERT: D 611 ASN cc_start: 0.4755 (t0) cc_final: 0.4406 (t0) REVERT: D 655 LYS cc_start: 0.8385 (ttmt) cc_final: 0.8035 (ttpt) REVERT: E 620 SER cc_start: 0.9117 (m) cc_final: 0.8649 (p) REVERT: E 625 ASN cc_start: 0.8758 (m-40) cc_final: 0.8497 (m110) REVERT: E 636 SER cc_start: 0.8105 (t) cc_final: 0.7666 (p) REVERT: E 655 LYS cc_start: 0.7680 (pttp) cc_final: 0.7111 (tttt) REVERT: C 241 LYS cc_start: 0.8155 (tppt) cc_final: 0.7901 (mtmm) REVERT: C 341 ASN cc_start: 0.7865 (p0) cc_final: 0.7491 (p0) REVERT: C 367 ILE cc_start: 0.7794 (mm) cc_final: 0.7592 (mm) REVERT: C 484 MET cc_start: 0.8683 (tpp) cc_final: 0.8323 (tpp) REVERT: C 513 ARG cc_start: 0.7819 (mtt180) cc_final: 0.7327 (mmt90) outliers start: 29 outliers final: 13 residues processed: 244 average time/residue: 0.3380 time to fit residues: 123.2568 Evaluate side-chains 223 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 209 time to evaluate : 2.072 ------------------------------------------------------------------------------- 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 A residue 151 ARG Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain B residue 211 THR 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 F residue 546 SER Chi-restraints excluded: chain F residue 581 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 6 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 61 ASN B 67 ASN E 656 ASN L 98 GLN C 271 ASN F 658 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.095594 restraints weight = 24536.909| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.12 r_work: 0.2933 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 18748 Z= 0.233 Angle : 0.765 14.853 25580 Z= 0.370 Chirality : 0.051 0.515 3056 Planarity : 0.005 0.074 3132 Dihedral : 10.194 104.949 3966 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.01 % Allowed : 9.86 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.17), residues: 2154 helix: -1.76 (0.26), residues: 385 sheet: -0.29 (0.20), residues: 691 loop : -1.68 (0.17), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 614 HIS 0.006 0.001 HIS B 383 PHE 0.019 0.002 PHE K 76 TYR 0.013 0.002 TYR F 638 ARG 0.007 0.001 ARG F 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00512 ( 48) link_NAG-ASN : angle 3.15728 ( 144) link_ALPHA1-6 : bond 0.01151 ( 3) link_ALPHA1-6 : angle 1.76530 ( 9) link_BETA1-4 : bond 0.00572 ( 12) link_BETA1-4 : angle 1.58292 ( 36) link_ALPHA1-2 : bond 0.01482 ( 3) link_ALPHA1-2 : angle 3.42941 ( 9) link_ALPHA1-3 : bond 0.01112 ( 3) link_ALPHA1-3 : angle 1.19612 ( 9) hydrogen bonds : bond 0.05790 ( 477) hydrogen bonds : angle 5.45337 ( 1344) SS BOND : bond 0.00437 ( 40) SS BOND : angle 1.97907 ( 80) covalent geometry : bond 0.00574 (18639) covalent geometry : angle 0.71693 (25293) *********************** 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 291 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 233 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 7 THR cc_start: 0.2619 (OUTLIER) cc_final: 0.2419 (m) REVERT: K 27 GLN cc_start: 0.8529 (tt0) cc_final: 0.7897 (mt0) REVERT: A 114 GLN cc_start: 0.8222 (tt0) cc_final: 0.7951 (tt0) REVERT: A 151 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8156 (tpp80) REVERT: A 509 ARG cc_start: 0.7559 (mtm-85) cc_final: 0.7338 (mtm180) REVERT: D 611 ASN cc_start: 0.5392 (t0) cc_final: 0.5178 (t0) REVERT: D 621 GLU cc_start: 0.8256 (pt0) cc_final: 0.7368 (pm20) REVERT: D 625 ASN cc_start: 0.7823 (t0) cc_final: 0.7369 (t0) REVERT: D 653 GLN cc_start: 0.8248 (tt0) cc_final: 0.7903 (tt0) REVERT: D 655 LYS cc_start: 0.8416 (ttmt) cc_final: 0.8200 (ttpt) REVERT: B 280 MET cc_start: 0.8339 (mmt) cc_final: 0.7933 (mmt) REVERT: E 543 ASN cc_start: 0.8752 (t0) cc_final: 0.8537 (t0) REVERT: E 620 SER cc_start: 0.9106 (m) cc_final: 0.8691 (p) REVERT: E 655 LYS cc_start: 0.7917 (pttp) cc_final: 0.7165 (tttt) REVERT: H 6 GLU cc_start: 0.8054 (mp0) cc_final: 0.7827 (mt-10) REVERT: C 178 ARG cc_start: 0.8767 (tmm-80) cc_final: 0.8471 (tmm-80) REVERT: C 241 LYS cc_start: 0.8205 (tppt) cc_final: 0.7915 (mtmm) REVERT: C 281 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8836 (mp) REVERT: C 367 ILE cc_start: 0.7842 (mm) cc_final: 0.7641 (mm) REVERT: C 503 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9020 (tt) REVERT: F 543 ASN cc_start: 0.8718 (m-40) cc_final: 0.8403 (m-40) REVERT: F 659 ASP cc_start: 0.7293 (t70) cc_final: 0.6631 (t0) outliers start: 58 outliers final: 35 residues processed: 271 average time/residue: 0.3252 time to fit residues: 131.0483 Evaluate side-chains 249 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 50 LEU 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 7 THR 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 75 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 211 THR 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 304 ASN Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 656 ASN Chi-restraints excluded: chain H residue 27 PHE 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 207 THR Chi-restraints excluded: chain C residue 281 ILE 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 433 ILE Chi-restraints excluded: chain C residue 503 LEU 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 641 ILE Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain F residue 658 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 14 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 L 54 HIS C 137 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.134049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.094529 restraints weight = 24682.371| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.10 r_work: 0.2915 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 18748 Z= 0.243 Angle : 0.756 14.442 25580 Z= 0.363 Chirality : 0.050 0.509 3056 Planarity : 0.004 0.072 3132 Dihedral : 9.496 102.221 3966 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.06 % Allowed : 11.36 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.17), residues: 2154 helix: -1.65 (0.27), residues: 382 sheet: -0.24 (0.20), residues: 681 loop : -1.80 (0.17), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 69 HIS 0.004 0.001 HIS A 383 PHE 0.015 0.002 PHE B 392 TYR 0.010 0.002 TYR J 82 ARG 0.008 0.000 ARG F 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 48) link_NAG-ASN : angle 3.15805 ( 144) link_ALPHA1-6 : bond 0.00694 ( 3) link_ALPHA1-6 : angle 1.57783 ( 9) link_BETA1-4 : bond 0.00406 ( 12) link_BETA1-4 : angle 1.50942 ( 36) link_ALPHA1-2 : bond 0.01851 ( 3) link_ALPHA1-2 : angle 3.95269 ( 9) link_ALPHA1-3 : bond 0.00950 ( 3) link_ALPHA1-3 : angle 1.66869 ( 9) hydrogen bonds : bond 0.05142 ( 477) hydrogen bonds : angle 5.25532 ( 1344) SS BOND : bond 0.00395 ( 40) SS BOND : angle 2.40128 ( 80) covalent geometry : bond 0.00598 (18639) covalent geometry : angle 0.70220 (25293) *********************** 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 273 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 214 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 100 ASP cc_start: 0.7391 (t0) cc_final: 0.7164 (t0) REVERT: K 27 GLN cc_start: 0.8508 (tt0) cc_final: 0.7826 (mt0) REVERT: A 114 GLN cc_start: 0.8205 (tt0) cc_final: 0.7945 (tt0) REVERT: D 611 ASN cc_start: 0.5544 (t0) cc_final: 0.5316 (t0) REVERT: D 621 GLU cc_start: 0.8293 (pt0) cc_final: 0.7373 (pm20) REVERT: D 625 ASN cc_start: 0.7852 (t0) cc_final: 0.7349 (t0) REVERT: B 57 ASP cc_start: 0.7752 (t0) cc_final: 0.7316 (t0) REVERT: B 280 MET cc_start: 0.8379 (mmt) cc_final: 0.8018 (mmt) REVERT: B 510 CYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6548 (t) REVERT: E 543 ASN cc_start: 0.8798 (t0) cc_final: 0.8535 (t0) REVERT: E 620 SER cc_start: 0.9104 (m) cc_final: 0.8802 (p) REVERT: E 656 ASN cc_start: 0.8793 (t0) cc_final: 0.8526 (t0) REVERT: H 6 GLU cc_start: 0.8113 (mp0) cc_final: 0.7836 (mt-10) REVERT: H 97 TYR cc_start: 0.8913 (m-80) cc_final: 0.8686 (m-80) REVERT: L 84 GLU cc_start: 0.7715 (mp0) cc_final: 0.7373 (mp0) REVERT: C 178 ARG cc_start: 0.8817 (tmm-80) cc_final: 0.8444 (ttp80) REVERT: C 241 LYS cc_start: 0.8246 (tppt) cc_final: 0.7926 (mtmm) REVERT: F 543 ASN cc_start: 0.8675 (m-40) cc_final: 0.8317 (m-40) outliers start: 59 outliers final: 40 residues processed: 250 average time/residue: 0.3273 time to fit residues: 121.6346 Evaluate side-chains 244 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 203 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 SER 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 J residue 108 VAL Chi-restraints excluded: chain K residue 21 MET 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 332 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 75 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 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 612 SER Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain F residue 655 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 203 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 650 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.137087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.096802 restraints weight = 24819.134| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.19 r_work: 0.2933 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3356 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= 0.146 Angle : 0.673 14.036 25580 Z= 0.320 Chirality : 0.047 0.500 3056 Planarity : 0.004 0.064 3132 Dihedral : 8.649 100.759 3966 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.44 % Allowed : 13.13 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.18), residues: 2154 helix: -1.33 (0.28), residues: 371 sheet: -0.20 (0.21), residues: 674 loop : -1.71 (0.17), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 571 HIS 0.003 0.001 HIS B 383 PHE 0.011 0.001 PHE C 53 TYR 0.008 0.001 TYR F 638 ARG 0.009 0.000 ARG F 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 48) link_NAG-ASN : angle 3.04817 ( 144) link_ALPHA1-6 : bond 0.00460 ( 3) link_ALPHA1-6 : angle 1.52606 ( 9) link_BETA1-4 : bond 0.00337 ( 12) link_BETA1-4 : angle 1.40582 ( 36) link_ALPHA1-2 : bond 0.02164 ( 3) link_ALPHA1-2 : angle 4.37856 ( 9) link_ALPHA1-3 : bond 0.00937 ( 3) link_ALPHA1-3 : angle 1.51371 ( 9) hydrogen bonds : bond 0.04199 ( 477) hydrogen bonds : angle 4.93985 ( 1344) SS BOND : bond 0.00338 ( 40) SS BOND : angle 2.06231 ( 80) covalent geometry : bond 0.00346 (18639) covalent geometry : angle 0.61664 (25293) *********************** 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 258 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 100 ASP cc_start: 0.7305 (t0) cc_final: 0.7080 (t0) REVERT: K 7 THR cc_start: 0.2167 (OUTLIER) cc_final: 0.1936 (m) REVERT: K 27 GLN cc_start: 0.8427 (tt0) cc_final: 0.7909 (mt0) REVERT: A 114 GLN cc_start: 0.8152 (tt0) cc_final: 0.7896 (tt0) REVERT: D 611 ASN cc_start: 0.5447 (t0) cc_final: 0.5110 (t0) REVERT: D 621 GLU cc_start: 0.8276 (pt0) cc_final: 0.7333 (pm20) REVERT: D 625 ASN cc_start: 0.7924 (t0) cc_final: 0.7409 (t0) REVERT: B 57 ASP cc_start: 0.7825 (t0) cc_final: 0.7413 (t0) REVERT: B 280 MET cc_start: 0.8355 (mmt) cc_final: 0.8031 (mmt) REVERT: E 620 SER cc_start: 0.9094 (m) cc_final: 0.8731 (p) REVERT: E 656 ASN cc_start: 0.8811 (t0) cc_final: 0.8502 (t0) REVERT: H 6 GLU cc_start: 0.8036 (mp0) cc_final: 0.7834 (mt-10) REVERT: L 84 GLU cc_start: 0.7772 (mp0) cc_final: 0.7396 (mp0) REVERT: C 178 ARG cc_start: 0.8811 (tmm-80) cc_final: 0.8371 (ttp80) REVERT: C 241 LYS cc_start: 0.8176 (tppt) cc_final: 0.7839 (mtmm) REVERT: F 543 ASN cc_start: 0.8663 (m-40) cc_final: 0.8302 (m-40) outliers start: 47 outliers final: 32 residues processed: 243 average time/residue: 0.3245 time to fit residues: 117.2592 Evaluate side-chains 240 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 J residue 108 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 21 MET 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 A residue 358 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 112 VAL 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 508 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 116 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 187 optimal weight: 0.4980 chunk 189 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.135723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.095499 restraints weight = 24742.897| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.18 r_work: 0.2928 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18748 Z= 0.187 Angle : 0.700 14.038 25580 Z= 0.334 Chirality : 0.048 0.496 3056 Planarity : 0.004 0.061 3132 Dihedral : 8.315 98.819 3966 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.04 % Favored : 93.92 % Rotamer: Outliers : 3.17 % Allowed : 12.92 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.18), residues: 2154 helix: -1.28 (0.28), residues: 373 sheet: -0.19 (0.21), residues: 670 loop : -1.75 (0.17), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 571 HIS 0.004 0.001 HIS L 54 PHE 0.018 0.002 PHE C 53 TYR 0.009 0.001 TYR E 586 ARG 0.011 0.000 ARG F 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 48) link_NAG-ASN : angle 3.06517 ( 144) link_ALPHA1-6 : bond 0.00345 ( 3) link_ALPHA1-6 : angle 1.55875 ( 9) link_BETA1-4 : bond 0.00372 ( 12) link_BETA1-4 : angle 1.46387 ( 36) link_ALPHA1-2 : bond 0.02277 ( 3) link_ALPHA1-2 : angle 4.58124 ( 9) link_ALPHA1-3 : bond 0.00959 ( 3) link_ALPHA1-3 : angle 1.52550 ( 9) hydrogen bonds : bond 0.04438 ( 477) hydrogen bonds : angle 4.91754 ( 1344) SS BOND : bond 0.00360 ( 40) SS BOND : angle 2.12970 ( 80) covalent geometry : bond 0.00455 (18639) covalent geometry : angle 0.64456 (25293) *********************** 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 270 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 209 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 7 THR cc_start: 0.2250 (OUTLIER) cc_final: 0.2011 (m) REVERT: K 27 GLN cc_start: 0.8467 (tt0) cc_final: 0.7802 (mt0) REVERT: K 94 MET cc_start: 0.5689 (OUTLIER) cc_final: 0.5383 (mtt) REVERT: A 114 GLN cc_start: 0.8154 (tt0) cc_final: 0.7897 (tt0) REVERT: D 611 ASN cc_start: 0.5472 (t0) cc_final: 0.5148 (t0) REVERT: D 621 GLU cc_start: 0.8254 (pt0) cc_final: 0.7302 (pm20) REVERT: D 625 ASN cc_start: 0.7992 (t0) cc_final: 0.7459 (t0) REVERT: B 57 ASP cc_start: 0.7872 (t0) cc_final: 0.7467 (t0) REVERT: B 280 MET cc_start: 0.8334 (mmt) cc_final: 0.8041 (mmt) REVERT: E 620 SER cc_start: 0.9109 (m) cc_final: 0.8810 (p) REVERT: E 656 ASN cc_start: 0.8862 (t0) cc_final: 0.8655 (t0) REVERT: L 84 GLU cc_start: 0.7874 (mp0) cc_final: 0.7508 (mp0) REVERT: C 102 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: C 178 ARG cc_start: 0.8826 (tmm-80) cc_final: 0.8553 (ttp-110) REVERT: C 241 LYS cc_start: 0.8192 (tppt) cc_final: 0.7852 (mtmm) REVERT: C 351 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7769 (mp) REVERT: F 543 ASN cc_start: 0.8668 (m-40) cc_final: 0.8300 (m-40) outliers start: 61 outliers final: 45 residues processed: 251 average time/residue: 0.3369 time to fit residues: 125.7955 Evaluate side-chains 254 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 205 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 60 THR 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 7 THR Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 94 MET Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 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 358 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain L residue 75 ASP 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 301 VAL Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 433 ILE 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 612 SER 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 154 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 214 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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** D 650 GLN C 271 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.133144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.093610 restraints weight = 24708.610| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.08 r_work: 0.2901 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 18748 Z= 0.229 Angle : 0.748 14.049 25580 Z= 0.357 Chirality : 0.049 0.499 3056 Planarity : 0.004 0.058 3132 Dihedral : 8.139 96.133 3966 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.55 % Favored : 93.41 % Rotamer: Outliers : 3.32 % Allowed : 13.28 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.18), residues: 2154 helix: -1.30 (0.28), residues: 373 sheet: -0.28 (0.20), residues: 681 loop : -1.79 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 488 HIS 0.005 0.001 HIS L 54 PHE 0.018 0.002 PHE C 53 TYR 0.010 0.001 TYR E 586 ARG 0.011 0.000 ARG F 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 48) link_NAG-ASN : angle 3.16674 ( 144) link_ALPHA1-6 : bond 0.00326 ( 3) link_ALPHA1-6 : angle 1.57589 ( 9) link_BETA1-4 : bond 0.00375 ( 12) link_BETA1-4 : angle 1.55665 ( 36) link_ALPHA1-2 : bond 0.02326 ( 3) link_ALPHA1-2 : angle 4.79377 ( 9) link_ALPHA1-3 : bond 0.00932 ( 3) link_ALPHA1-3 : angle 1.47903 ( 9) hydrogen bonds : bond 0.04859 ( 477) hydrogen bonds : angle 5.00706 ( 1344) SS BOND : bond 0.00382 ( 40) SS BOND : angle 2.26429 ( 80) covalent geometry : bond 0.00563 (18639) covalent geometry : angle 0.69188 (25293) *********************** 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 273 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 209 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 7 THR cc_start: 0.2376 (OUTLIER) cc_final: 0.2131 (m) REVERT: K 27 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7845 (mt0) REVERT: A 114 GLN cc_start: 0.8220 (tt0) cc_final: 0.7961 (tt0) REVERT: A 151 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8314 (tpp80) REVERT: D 621 GLU cc_start: 0.8272 (pt0) cc_final: 0.7301 (pm20) REVERT: D 625 ASN cc_start: 0.7995 (t0) cc_final: 0.7433 (t0) REVERT: B 57 ASP cc_start: 0.7889 (t0) cc_final: 0.7464 (t0) REVERT: B 280 MET cc_start: 0.8364 (mmt) cc_final: 0.8106 (mmt) REVERT: E 620 SER cc_start: 0.9110 (m) cc_final: 0.8830 (p) REVERT: E 655 LYS cc_start: 0.7801 (pttp) cc_final: 0.7104 (tttt) REVERT: L 84 GLU cc_start: 0.7874 (mp0) cc_final: 0.7527 (mp0) REVERT: C 33 ASN cc_start: 0.7488 (m-40) cc_final: 0.7155 (m-40) REVERT: C 102 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: C 178 ARG cc_start: 0.8859 (tmm-80) cc_final: 0.8586 (ttp-110) REVERT: C 241 LYS cc_start: 0.8170 (tppt) cc_final: 0.7836 (mtmm) REVERT: C 351 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7781 (mp) outliers start: 64 outliers final: 53 residues processed: 254 average time/residue: 0.3233 time to fit residues: 122.3246 Evaluate side-chains 266 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 208 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 94 MET Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 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 358 LEU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain L residue 75 ASP 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 271 ASN Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 433 ILE 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 612 SER Chi-restraints excluded: chain F residue 641 ILE 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 167 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 chunk 190 optimal weight: 3.9990 chunk 136 optimal weight: 0.2980 chunk 165 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 210 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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** D 543 ASN D 650 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.093993 restraints weight = 24639.845| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.10 r_work: 0.2909 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18748 Z= 0.192 Angle : 0.716 13.926 25580 Z= 0.341 Chirality : 0.048 0.496 3056 Planarity : 0.004 0.058 3132 Dihedral : 7.874 94.707 3966 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.13 % Favored : 93.83 % Rotamer: Outliers : 3.32 % Allowed : 14.01 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.18), residues: 2154 helix: -1.27 (0.28), residues: 375 sheet: -0.31 (0.20), residues: 689 loop : -1.79 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 488 HIS 0.004 0.001 HIS L 54 PHE 0.016 0.002 PHE C 53 TYR 0.009 0.001 TYR E 586 ARG 0.011 0.000 ARG F 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 48) link_NAG-ASN : angle 3.16972 ( 144) link_ALPHA1-6 : bond 0.00322 ( 3) link_ALPHA1-6 : angle 1.57530 ( 9) link_BETA1-4 : bond 0.00341 ( 12) link_BETA1-4 : angle 1.51283 ( 36) link_ALPHA1-2 : bond 0.02345 ( 3) link_ALPHA1-2 : angle 5.12216 ( 9) link_ALPHA1-3 : bond 0.00893 ( 3) link_ALPHA1-3 : angle 1.47570 ( 9) hydrogen bonds : bond 0.04532 ( 477) hydrogen bonds : angle 4.92896 ( 1344) SS BOND : bond 0.00359 ( 40) SS BOND : angle 2.15722 ( 80) covalent geometry : bond 0.00467 (18639) covalent geometry : angle 0.65792 (25293) *********************** 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 268 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 204 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 7 THR cc_start: 0.2196 (OUTLIER) cc_final: 0.1947 (m) REVERT: K 27 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7827 (mt0) REVERT: A 114 GLN cc_start: 0.8181 (tt0) cc_final: 0.7922 (tt0) REVERT: A 151 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8324 (tpp80) REVERT: A 161 MET cc_start: 0.8739 (tpp) cc_final: 0.8538 (mmm) REVERT: D 621 GLU cc_start: 0.8282 (pt0) cc_final: 0.7299 (pm20) REVERT: D 625 ASN cc_start: 0.8044 (t0) cc_final: 0.7482 (t0) REVERT: B 57 ASP cc_start: 0.7902 (t0) cc_final: 0.7483 (t0) REVERT: B 280 MET cc_start: 0.8362 (mmt) cc_final: 0.8155 (mmt) REVERT: E 620 SER cc_start: 0.9106 (m) cc_final: 0.8828 (p) REVERT: E 655 LYS cc_start: 0.7769 (pttp) cc_final: 0.7055 (tttt) REVERT: L 84 GLU cc_start: 0.7886 (mp0) cc_final: 0.7506 (mp0) REVERT: C 33 ASN cc_start: 0.7461 (m-40) cc_final: 0.7161 (m-40) REVERT: C 102 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: C 178 ARG cc_start: 0.8840 (tmm-80) cc_final: 0.8570 (ttp-110) REVERT: C 241 LYS cc_start: 0.8173 (tppt) cc_final: 0.7822 (mtmm) REVERT: C 351 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7760 (mp) outliers start: 64 outliers final: 49 residues processed: 249 average time/residue: 0.3577 time to fit residues: 133.7971 Evaluate side-chains 259 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 205 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 SER 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 7 THR Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 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 358 LEU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 76 ASP 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 301 VAL Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 351 LEU 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 612 SER Chi-restraints excluded: chain F residue 641 ILE 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 116 optimal weight: 0.9990 chunk 198 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 126 optimal weight: 0.0270 overall best weight: 1.9644 ------------------------------------------------------------------------------- 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** D 650 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.133341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.093684 restraints weight = 24865.538| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.11 r_work: 0.2904 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18748 Z= 0.195 Angle : 0.718 13.887 25580 Z= 0.342 Chirality : 0.048 0.493 3056 Planarity : 0.004 0.056 3132 Dihedral : 7.734 93.015 3966 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.27 % Favored : 93.69 % Rotamer: Outliers : 3.27 % Allowed : 14.27 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.17), residues: 2154 helix: -1.20 (0.28), residues: 371 sheet: -0.32 (0.20), residues: 680 loop : -1.81 (0.17), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 488 HIS 0.004 0.001 HIS L 54 PHE 0.016 0.002 PHE C 53 TYR 0.009 0.001 TYR E 586 ARG 0.011 0.000 ARG F 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 48) link_NAG-ASN : angle 3.17038 ( 144) link_ALPHA1-6 : bond 0.00306 ( 3) link_ALPHA1-6 : angle 1.57437 ( 9) link_BETA1-4 : bond 0.00343 ( 12) link_BETA1-4 : angle 1.50071 ( 36) link_ALPHA1-2 : bond 0.02285 ( 3) link_ALPHA1-2 : angle 5.12522 ( 9) link_ALPHA1-3 : bond 0.00919 ( 3) link_ALPHA1-3 : angle 1.41316 ( 9) hydrogen bonds : bond 0.04510 ( 477) hydrogen bonds : angle 4.91145 ( 1344) SS BOND : bond 0.00376 ( 40) SS BOND : angle 2.17735 ( 80) covalent geometry : bond 0.00477 (18639) covalent geometry : angle 0.65930 (25293) *********************** 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 265 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 202 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 27 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7822 (mt0) REVERT: A 114 GLN cc_start: 0.8193 (tt0) cc_final: 0.7931 (tt0) REVERT: A 151 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8326 (tpp80) REVERT: D 621 GLU cc_start: 0.8284 (pt0) cc_final: 0.7313 (pm20) REVERT: D 625 ASN cc_start: 0.8040 (t0) cc_final: 0.7466 (t0) REVERT: B 57 ASP cc_start: 0.7951 (t0) cc_final: 0.7557 (t0) REVERT: B 280 MET cc_start: 0.8371 (mmt) cc_final: 0.8166 (mmt) REVERT: E 620 SER cc_start: 0.9104 (m) cc_final: 0.8836 (p) REVERT: E 655 LYS cc_start: 0.7766 (pttp) cc_final: 0.7071 (tttt) REVERT: L 84 GLU cc_start: 0.7918 (mp0) cc_final: 0.7527 (mp0) REVERT: C 33 ASN cc_start: 0.7506 (m-40) cc_final: 0.7208 (m-40) REVERT: C 102 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: C 178 ARG cc_start: 0.8841 (tmm-80) cc_final: 0.8574 (ttp-110) REVERT: C 241 LYS cc_start: 0.8162 (tppt) cc_final: 0.7535 (pttt) REVERT: C 296 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8594 (tt0) REVERT: C 351 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7776 (mp) outliers start: 63 outliers final: 50 residues processed: 247 average time/residue: 0.3615 time to fit residues: 132.5120 Evaluate side-chains 257 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 202 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 SER 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 27 GLN Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 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 358 LEU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 76 ASP 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 296 GLN Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 351 LEU 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 612 SER 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 56 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 54 optimal weight: 0.0970 chunk 126 optimal weight: 0.0470 chunk 158 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 overall best weight: 1.4280 ------------------------------------------------------------------------------- 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** D 543 ASN D 650 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.134348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.094794 restraints weight = 24646.571| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.09 r_work: 0.2920 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3917 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= 0.156 Angle : 0.691 13.753 25580 Z= 0.328 Chirality : 0.047 0.490 3056 Planarity : 0.004 0.057 3132 Dihedral : 7.534 91.189 3966 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.99 % Favored : 93.96 % Rotamer: Outliers : 2.80 % Allowed : 14.74 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.17), residues: 2154 helix: -1.12 (0.28), residues: 371 sheet: -0.20 (0.20), residues: 670 loop : -1.80 (0.17), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 488 HIS 0.003 0.001 HIS A 383 PHE 0.015 0.001 PHE C 53 TYR 0.008 0.001 TYR E 586 ARG 0.011 0.000 ARG F 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 48) link_NAG-ASN : angle 3.13756 ( 144) link_ALPHA1-6 : bond 0.00325 ( 3) link_ALPHA1-6 : angle 1.55664 ( 9) link_BETA1-4 : bond 0.00318 ( 12) link_BETA1-4 : angle 1.45014 ( 36) link_ALPHA1-2 : bond 0.02208 ( 3) link_ALPHA1-2 : angle 5.08049 ( 9) link_ALPHA1-3 : bond 0.00902 ( 3) link_ALPHA1-3 : angle 1.33374 ( 9) hydrogen bonds : bond 0.04126 ( 477) hydrogen bonds : angle 4.82227 ( 1344) SS BOND : bond 0.00345 ( 40) SS BOND : angle 2.06433 ( 80) covalent geometry : bond 0.00375 (18639) covalent geometry : angle 0.63210 (25293) ********************** 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 258 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 204 time to evaluate : 2.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8171 (tp30) cc_final: 0.7854 (tp30) REVERT: A 114 GLN cc_start: 0.8163 (tt0) cc_final: 0.7900 (tt0) REVERT: A 151 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8281 (tpp80) REVERT: D 621 GLU cc_start: 0.8270 (pt0) cc_final: 0.7304 (pm20) REVERT: D 625 ASN cc_start: 0.8041 (t0) cc_final: 0.7477 (t0) REVERT: B 57 ASP cc_start: 0.8009 (t0) cc_final: 0.7632 (t0) REVERT: B 280 MET cc_start: 0.8360 (mmt) cc_final: 0.8141 (mmt) REVERT: E 615 SER cc_start: 0.9081 (OUTLIER) cc_final: 0.8877 (t) REVERT: E 620 SER cc_start: 0.9104 (m) cc_final: 0.8830 (p) REVERT: L 84 GLU cc_start: 0.7953 (mp0) cc_final: 0.7541 (mp0) REVERT: C 33 ASN cc_start: 0.7503 (m-40) cc_final: 0.7218 (m-40) REVERT: C 102 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: C 178 ARG cc_start: 0.8827 (tmm-80) cc_final: 0.8565 (ttp-110) REVERT: C 241 LYS cc_start: 0.8166 (tppt) cc_final: 0.7580 (pttt) REVERT: C 351 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7778 (mp) outliers start: 54 outliers final: 47 residues processed: 245 average time/residue: 0.3190 time to fit residues: 115.3727 Evaluate side-chains 252 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 201 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 SER 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 94 MET Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 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 358 LEU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 85 MET 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 301 VAL Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 351 LEU 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 612 SER 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 4 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 214 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 189 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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** D 650 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.135488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.096218 restraints weight = 24485.446| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.07 r_work: 0.2940 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18748 Z= 0.124 Angle : 0.658 13.534 25580 Z= 0.311 Chirality : 0.046 0.484 3056 Planarity : 0.004 0.056 3132 Dihedral : 7.256 88.980 3966 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.71 % Favored : 94.24 % Rotamer: Outliers : 2.49 % Allowed : 15.15 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.17), residues: 2154 helix: -1.01 (0.29), residues: 370 sheet: -0.21 (0.21), residues: 644 loop : -1.73 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 488 HIS 0.002 0.001 HIS B 383 PHE 0.013 0.001 PHE C 53 TYR 0.007 0.001 TYR E 586 ARG 0.011 0.000 ARG F 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 48) link_NAG-ASN : angle 3.07156 ( 144) link_ALPHA1-6 : bond 0.00324 ( 3) link_ALPHA1-6 : angle 1.52848 ( 9) link_BETA1-4 : bond 0.00321 ( 12) link_BETA1-4 : angle 1.40768 ( 36) link_ALPHA1-2 : bond 0.02196 ( 3) link_ALPHA1-2 : angle 5.00212 ( 9) link_ALPHA1-3 : bond 0.00911 ( 3) link_ALPHA1-3 : angle 1.27165 ( 9) hydrogen bonds : bond 0.03666 ( 477) hydrogen bonds : angle 4.68410 ( 1344) SS BOND : bond 0.00358 ( 40) SS BOND : angle 1.92041 ( 80) covalent geometry : bond 0.00292 (18639) covalent geometry : angle 0.59914 (25293) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8193.23 seconds wall clock time: 143 minutes 22.20 seconds (8602.20 seconds total)